pax_global_header 0000666 0000000 0000000 00000000064 13547635037 0014527 g ustar 00root root 0000000 0000000 52 comment=e87964c7aa38ce2e809b802e2ff03ec6aa379be6
mirtop-0.4.23/ 0000775 0000000 0000000 00000000000 13547635037 0013127 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/.gitignore 0000664 0000000 0000000 00000002247 13547635037 0015124 0 ustar 00root root 0000000 0000000 # data
*res*
*test_out_mirs_fasta*
test/test_automated_output
*test_out*
*bam
# instalation
mirtop/version.py
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
*.swp
*.swo
*.Rhistory
*.DS_Store
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*,cover
.hypothesis/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# IPython Notebook
.ipynb_checkpoints
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# dotenv
.env
# virtualenv
venv/
ENV/
# Spyder project settings
.spyderproject
# Rope project settings
.ropeproject
mirtop-0.4.23/.travis.yml 0000664 0000000 0000000 00000003253 13547635037 0015243 0 ustar 00root root 0000000 0000000 sudo: required
dist: trusty
language: python
python:
- "3.6"
- "2.7"
notifications:
email:
recipients:
- lorena.pantano@gmail.com
on_failure: always
before_install:
- echo $TRAVIS_PYTHON_VERSION
- miniconda="Miniconda3-latest-Linux-x86_64.sh"
- if [[ $TRAVIS_PYTHON_VERSION == "2.7" ]] ; then miniconda="Miniconda2-latest-Linux-x86_64.sh"; fi
- wget -O miniconda.sh http://repo.continuum.io/miniconda/${miniconda}
- bash miniconda.sh -b -p ~/install
install:
- export PATH=~/install/bin/:$PATH
- conda install --yes ncurses -c conda-forge
- conda install --yes -c conda-forge -c bioconda bedtools samtools razers3 pip nose pysam pandas pyyaml pybedtools biopython setuptools codecov -q
script:
- python setup.py develop
- nosetests --with-coverage
after_success:
- codecov
deploy:
provider: pypi
user: lpantano
password:
secure: 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
skip_existing: true
on:
all_branches: true
condition: $TRAVIS_BRANCH =~ ^master|dev$
distributions: sdist bdist_wheel
repo: miRTop/mirtop
mirtop-0.4.23/CODE_OF_CONDUCT.md 0000664 0000000 0000000 00000001623 13547635037 0015730 0 ustar 00root root 0000000 0000000 * miRTop is dedicated to providing a harassment-free enviroment for everyone, regardless of gender, sexual orientation, disability, physical appearance, body size, race, religion, or choice of text editor. We do not tolerate harassment of participants in any form.
* All communication should be appropriate for a professional audience including people of many different backgrounds. Sexual language and imagery is not appropriate for any event.
* Be kind to others. Do not insult or put down other attendees.
* Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate.
* Members violating these rules may be asked to leave the community at the sole discretion of the organizers.
Thank you for helping make this a welcoming, friendly event for all.
Following advice from: https://github.com/mozillascience/working-open-workshop/blob/gh-pages/CODE_OF_CONDUCT.md
mirtop-0.4.23/HISTORY.md 0000664 0000000 0000000 00000007436 13547635037 0014624 0 ustar 00root root 0000000 0000000 - 0.4.23
* fix empty stats file [#61](https://github.com/miRTop/mirtop/issues/61) by @leontienvdbent
- 0.4.22
* fix when reads map halfway on to the edge
* fix edge case where limit==variant_size
- 0.4.21
* Missing trimming events since 0.4.19
- 0.4.20
* Support export isomiR rawData output
* Support genomic coordinates as output in the gff
* Make TOOLS mandatory in header
* Implement method to create gff line
* Improve docs
- 0.4.19
* Add --version option
* Fix bug that ignore sequences starting at 0 in bam files
- 0.4.18
* Cast map object to list to avoid errors in py3.
* Support Manatee output.
* Support chunk reading for genomic BAM files.
* Support chunk reading for seqbuster files.
* Support chunk reading for BAM files.
* Normalize functions to support different databases.
* Support miRgeneDB.
* Export to VCF. Thanks to Roderic Espin.
* Support isomiRs that go beyond 5p end
* Support genomic coordinates.
* Fix missing reads when using --keep-read in the final mirtop.gff file.
* Allow longer truncation and addition events.
* Accept seqbuster input without frequency column.
* Allow keep name of the sequence.
* Accept indels in snv category.
* Additions are only last nucleotides that are mismatches.
* Adapt mintplate license.
* Revert sign in iso_5p, replace snp by snv.
* Skip lines that contain malformed UID.
* Add FASTA as an exporter from GFF.
* Fix BAM parsing to new GFF rules.
* Add the possibility to work with spikeins to detect random variability.
* Fixing UID attribute for tools that don't use our cypher system
* Add class to parse GFF line as a first move toward isolation
* Add JSON log for stats command.
- 0.3.17
* Normalize the read of the tool outputs.
* Add docs with autodoc plugin.
* Validator by @Vbarrera.
* Improve examples commands and test coverage.
* Only counts sequences with Filter == Pass during stats.
* Counts cmd add nucleotide information when --add-extra option is on.
* Fix error in stats that open the file in addition mode.
* Importer for sRNAbench just convert lines from input to GFF format.
* Skip lines with non-valid UID or miRNAs not in reference at counts cmd.
* Fix separators in counts cmd.
* Make --sps optional.
* Add synthetic data with known isomiRs to data set.
* Allow extra columns when converting to counts TSV file.
* Allow extra attributes for isomir-sea as well.
* Allow extra attributes to show the nts
that change in each isomiR type.
* Fix Expression attrb when join gff files.Thanks @AlisR.
* Print help when no files are giving to any subcommand.
* Fix bug for duplicated isomiRs tags. Thanks @AlisR.
* Fix bug in order of merged gff file. Thanks @AlisR.
* Add module to read GFF/GTF line in body.py
* Add version line to stats output
* Improve PROST! importer
* Fix output for isomiRs package
- 0.2.*
* Make GTF default output
* Add function to get SNPs from Variant attribute
* Improve PROST with last version output
* Add isomiR-SEA compatibility
* Fix sRNAbench exact match to NA in GFF
* Change stats to use only 1 level isomiR classification
* Add GFF to count matrix
* Add read_attributes function
* Improve isomiR reading from srnabench tool
* Add PROST to supported tools
- 0.1.7
* Remove deletion from addition isomiRs
* Support for srnabench output
* Fix bug mixing up source column
* Support Seqbuster output
* Functin to guess database used from GTF file through --mirna parameter
* Adapt output format to https://github.com/miRTop/incubator/blob/master/format/definition.md
- 0.1.5
* add function to check correct annotation
* add test data for SAM parsing
* add script to simulate isomiRs
* parse indels from bam file
- 0.1.4
* fix index BAM file command line
* add function to accept indels and test unit
* change header from subs -> mism to be compatible with isomiRs
mirtop-0.4.23/LICENSE 0000664 0000000 0000000 00000002060 13547635037 0014132 0 ustar 00root root 0000000 0000000 The MIT License (MIT)
Copyright (c) 2014 Lorena
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. mirtop-0.4.23/MANIFEST.in 0000664 0000000 0000000 00000000131 13547635037 0014660 0 ustar 00root root 0000000 0000000 include README.md
include LICENSE
include artwork/logo.png
recursive-include mirtop *.py
mirtop-0.4.23/README.md 0000664 0000000 0000000 00000006650 13547635037 0014415 0 ustar 00root root 0000000 0000000 # mirtop 
[](https://travis-ci.org/miRTop/mirtop#)
[](http://www.repostatus.org/#active)
[](https://www.biorxiv.org/content/10.1101/505222v1)
Command line tool to annotate with a standard naming miRNAs e isomiRs.
This tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/mirGFF3
Chat
----
[Ask question, ideas](https://gitter.im/mirtop/Lobby#)
[Contributors to code](https://gitter.im/mirtop/devel)
Cite
----
http://mirtop.github.io
Contributing
------------
Everybody is welcome to contribute, fork the `devel` branch and start working!
If you are interesting in miRNA or small RNA analysis, you can jump into the incubator issue pages to propose/ask or say hi:
https://github.com/miRTop/incubator/issues
About
-----
Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928
Read more: http://mirtop.github.io
Installation
------------
### Bioconda
`conda install mirtop -c bioconda`
### PIP
`pip install mirtop`
### develop version
Thes best solution is to install conda to get an independent enviroment.
```
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
export PATH=$PATH:~/mirtop_env
conda install -c bioconda pysam pybedtools pandas biopython samtools
git clone http://github.com/miRTop/mirtop
cd mirtop
python setup.py develop
```
Quick start
-----------
Read complete commands at: https://mirtop.readthedocs.org
```
git clone mirtop
cd mirtop/data
mirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam
```
Output
------
The `mirtop gff` generates the GFF3 adapted format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/mirGFF3).
Contributors
------------
* [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)
* [Shruthi Bhat Bandyadka](https://github.com/sbb25) (Partners Personalized Medicine, Cambridge MA, USA)
* [Iñaki Martínez de Ilarduya](http://www.germanstrias.org/technology-services/high-performance-computing/contact/)(HPC core, IGTP, Badalona, Spain)
* Rafael Alis
* [Victor Barrera](https://github.com/vbarrera) (Bioinformatic Core, Harvard Chan School, Boston, USA)
* [Steffen Möller](https://github.com/smoe) (University of Rostock)
* [Kieran O'Neill](https://github.com/oneillkza)
* [Roderic Espin](Universitat Oberta de Barcelona)
Citizens
--------
Here we cite any person who has contribute somehow to the project different than through code development and/or
bioinformatic concepts.
Gianvito Urgese,
Jan Oppelt(CEITEC Masaryk University, Brno, Czech Republic),
Thomas Desvignes,
Bastian,
Kieran O'Neill (BC Cancer),
Charles Reid (University of California Davis),
Radhika Khetani (Harvard Chan School of Public Health),
Shannan Ho Sui (Harvard Chan School of Public Health),
Simonas Juzenas(CAU),
Rafael Alis (Catholic University of Valencia),
Aida Arcas (Instituto de Neurociencias (CSIC-UMH)),
Yufei Lin (Harvard University),
Victor Barrera(Harvard Chan School of Public Health),
Marc Halushka (Johns Hopkins University)
mirtop-0.4.23/artwork/ 0000775 0000000 0000000 00000000000 13547635037 0014620 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/artwork/logo.png 0000664 0000000 0000000 00000040077 13547635037 0016276 0 ustar 00root root 0000000 0000000 PNG
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@PG ID:razers3 VN:3.3 PN:razers3 CL:-dr 0 -i 80 -rr 90 -f -o /n/scratch2/hsph_bioinformatic_core/lp113/mirtop/example-merged/work/bcbiotx/tmp83ZqWA/SRR5756178.bam /n/app/bcbio/dev/genomes/Hsapiens/hg19/srnaseq/hairpin.fa /n/scratch2/hsph_bioinformatic_core/lp113/mirtop/example-merged/work/trimmed/SRR5756178/SRR5756178.clean.trimming.fastq
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@SQ SN:hsa-mir-802 LN:94
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@SQ SN:hsa-mir-1178 LN:91
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@SQ SN:hsa-mir-1200 LN:76
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@SQ SN:hsa-mir-663b LN:115
@SQ SN:hsa-mir-1204 LN:67
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@SQ SN:hsa-mir-1289-1 LN:144
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@SQ SN:hsa-mir-1294 LN:142
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@SQ SN:hsa-mir-1302-1 LN:143
@SQ SN:hsa-mir-1302-2 LN:138
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@SQ SN:hsa-mir-1302-4 LN:150
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@SQ SN:hsa-mir-1302-6 LN:90
@SQ SN:hsa-mir-1302-7 LN:72
@SQ SN:hsa-mir-1302-8 LN:128
@SQ SN:hsa-mir-1303 LN:86
@SQ SN:hsa-mir-1304 LN:91
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@SQ SN:hsa-mir-548f-2 LN:98
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@SQ SN:hsa-mir-548f-4 LN:105
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@SQ SN:hsa-mir-1247 LN:136
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@SQ SN:hsa-mir-1250 LN:113
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@SQ SN:hsa-mir-1256 LN:119
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@SQ SN:hsa-mir-1265 LN:86
@SQ SN:hsa-mir-548o LN:114
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@SQ SN:hsa-mir-1272 LN:129
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@SQ SN:hsa-mir-548h-2 LN:88
@SQ SN:hsa-mir-548h-3 LN:118
@SQ SN:hsa-mir-548h-4 LN:111
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@SQ SN:hsa-mir-548i-1 LN:149
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@SQ SN:hsa-mir-548i-4 LN:77
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@SQ SN:hsa-mir-1282 LN:101
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@SQ SN:hsa-mir-1284 LN:120
@SQ SN:hsa-mir-1288 LN:75
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@SQ SN:hsa-mir-1972-1 LN:77
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@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-3174 LN:87
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@SQ SN:hsa-mir-3180-3 LN:94
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@SQ SN:hsa-mir-1302-10 LN:138
@SQ SN:hsa-mir-1302-11 LN:138
@SQ SN:hsa-mir-4283-2 LN:80
@SQ SN:hsa-mir-4315-2 LN:73
@SQ SN:hsa-mir-3605 LN:100
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@SQ SN:hsa-mir-3614 LN:86
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@SQ SN:hsa-mir-3616 LN:92
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@SQ SN:hsa-mir-3618 LN:88
@SQ SN:hsa-mir-3619 LN:83
@SQ SN:hsa-mir-23c LN:100
@SQ SN:hsa-mir-3620 LN:79
@SQ SN:hsa-mir-3621 LN:85
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@SQ SN:hsa-mir-3648-1 LN:180
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@SQ SN:hsa-mir-3651 LN:90
@SQ SN:hsa-mir-3652 LN:131
@SQ SN:hsa-mir-3653 LN:110
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@SQ SN:hsa-mir-1273e LN:102
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@SQ SN:hsa-mir-3688-1 LN:93
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@SQ SN:hsa-mir-3180-4 LN:153
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@SQ SN:hsa-mir-3907 LN:151
@SQ SN:hsa-mir-3689b LN:148
@SQ SN:hsa-mir-3908 LN:126
@SQ SN:hsa-mir-3909 LN:119
@SQ SN:hsa-mir-3910-1 LN:111
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@SQ SN:hsa-mir-3912 LN:105
@SQ SN:hsa-mir-3913-1 LN:102
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@SQ SN:hsa-mir-3914-2 LN:95
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@SQ SN:hsa-mir-3919 LN:89
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@SQ SN:hsa-mir-548y LN:110
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@SQ SN:hsa-mir-3945 LN:98
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@SQ SN:hsa-mir-550b-1 LN:97
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@SQ SN:hsa-mir-548aa-1 LN:97
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@SQ SN:hsa-mir-548o-2 LN:70
@SQ SN:hsa-mir-1254-2 LN:63
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@SQ SN:hsa-mir-378d-1 LN:54
@SQ SN:hsa-mir-378e LN:79
@SQ SN:hsa-mir-548h-5 LN:60
@SQ SN:hsa-mir-548ab LN:84
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@SQ SN:hsa-mir-378g LN:41
@SQ SN:hsa-mir-548ac LN:88
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@SQ SN:hsa-mir-4430 LN:49
@SQ SN:hsa-mir-548ad LN:82
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@SQ SN:hsa-mir-548ae-1 LN:70
@SQ SN:hsa-mir-548ae-2 LN:67
@SQ SN:hsa-mir-4438 LN:93
@SQ SN:hsa-mir-4439 LN:80
@SQ SN:hsa-mir-4440 LN:98
@SQ SN:hsa-mir-4441 LN:100
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@SQ SN:hsa-mir-4444-1 LN:74
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@SQ SN:hsa-mir-4447 LN:91
@SQ SN:hsa-mir-4448 LN:86
@SQ SN:hsa-mir-4449 LN:66
@SQ SN:hsa-mir-548ag-1 LN:66
@SQ SN:hsa-mir-548ag-2 LN:64
@SQ SN:hsa-mir-4450 LN:65
@SQ SN:hsa-mir-548ah LN:76
@SQ SN:hsa-mir-4451 LN:66
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@SQ SN:hsa-mir-4453 LN:89
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@SQ SN:hsa-mir-4458 LN:75
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@SQ SN:hsa-mir-4460 LN:86
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@SQ SN:hsa-mir-378h LN:83
@SQ SN:hsa-mir-3135b LN:68
@SQ SN:hsa-mir-4462 LN:58
@SQ SN:hsa-mir-4463 LN:67
@SQ SN:hsa-mir-4464 LN:92
@SQ SN:hsa-mir-548ai LN:88
@SQ SN:hsa-mir-548aj-1 LN:72
@SQ SN:hsa-mir-548aj-2 LN:92
@SQ SN:hsa-mir-4465 LN:70
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@SQ SN:hsa-mir-4473 LN:91
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@SQ SN:hsa-mir-4477a LN:81
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@SQ SN:hsa-mir-4478 LN:86
@SQ SN:hsa-mir-3689c LN:72
@SQ SN:hsa-mir-548x-2 LN:100
@SQ SN:hsa-mir-3689d-1 LN:74
@SQ SN:hsa-mir-3689d-2 LN:80
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@SQ SN:hsa-mir-548al LN:97
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@SQ SN:hsa-mir-4497 LN:89
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@SQ SN:hsa-mir-4504 LN:92
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@SQ SN:hsa-mir-4508 LN:70
@SQ SN:hsa-mir-4509-1 LN:94
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@SQ SN:hsa-mir-4509-3 LN:94
@SQ SN:hsa-mir-4510 LN:68
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@SQ SN:hsa-mir-4536-1 LN:88
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@SQ SN:hsa-mir-3960 LN:91
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@SQ SN:hsa-mir-3976 LN:139
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@SQ SN:hsa-mir-219b LN:88
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@SQ SN:hsa-mir-4674 LN:87
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@SQ SN:hsa-mir-4679-2 LN:77
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@SQ SN:hsa-mir-4689 LN:70
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@SQ SN:hsa-mir-4696 LN:70
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@SQ SN:hsa-mir-4701 LN:63
@SQ SN:hsa-mir-3198-2 LN:80
@SQ SN:hsa-mir-4703 LN:79
@SQ SN:hsa-mir-4704 LN:75
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@SQ SN:hsa-mir-4706 LN:82
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@SQ SN:hsa-mir-4708 LN:67
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@SQ SN:hsa-mir-203b LN:86
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@SQ SN:hsa-mir-4712 LN:82
@SQ SN:hsa-mir-4713 LN:75
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@SQ SN:hsa-mir-4723 LN:81
@SQ SN:hsa-mir-451b LN:68
@SQ SN:hsa-mir-4724 LN:89
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@SQ SN:hsa-mir-548ap LN:96
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@SQ SN:hsa-mir-5009 LN:100
@SQ SN:hsa-mir-5010 LN:120
@SQ SN:hsa-mir-5011 LN:103
@SQ SN:hsa-mir-5047 LN:100
@SQ SN:hsa-mir-5087 LN:76
@SQ SN:hsa-mir-5088 LN:79
@SQ SN:hsa-mir-5089 LN:84
@SQ SN:hsa-mir-5090 LN:85
@SQ SN:hsa-mir-5091 LN:93
@SQ SN:hsa-mir-5092 LN:88
@SQ SN:hsa-mir-5093 LN:100
@SQ SN:hsa-mir-5094 LN:85
@SQ SN:hsa-mir-5095 LN:88
@SQ SN:hsa-mir-1273f LN:99
@SQ SN:hsa-mir-1273g LN:100
@SQ SN:hsa-mir-5096 LN:70
@SQ SN:hsa-mir-5186 LN:120
@SQ SN:hsa-mir-5187 LN:76
@SQ SN:hsa-mir-5188 LN:113
@SQ SN:hsa-mir-5189 LN:114
@SQ SN:hsa-mir-5190 LN:80
@SQ SN:hsa-mir-5191 LN:120
@SQ SN:hsa-mir-5192 LN:92
@SQ SN:hsa-mir-5193 LN:109
@SQ SN:hsa-mir-5194 LN:120
@SQ SN:hsa-mir-5195 LN:115
@SQ SN:hsa-mir-5196 LN:115
@SQ SN:hsa-mir-5197 LN:112
@SQ SN:hsa-mir-4436b-2 LN:91
@SQ SN:hsa-mir-4444-2 LN:74
@SQ SN:hsa-mir-3670-2 LN:65
@SQ SN:hsa-mir-3680-2 LN:87
@SQ SN:hsa-mir-4524b LN:115
@SQ SN:hsa-mir-5571 LN:113
@SQ SN:hsa-mir-5100 LN:119
@SQ SN:hsa-mir-5572 LN:137
@SQ SN:hsa-mir-548aq LN:58
@SQ SN:hsa-mir-548ar LN:57
@SQ SN:hsa-mir-548as LN:58
@SQ SN:hsa-mir-5579 LN:58
@SQ SN:hsa-mir-664b LN:61
@SQ SN:hsa-mir-5580 LN:58
@SQ SN:hsa-mir-5581 LN:60
@SQ SN:hsa-mir-548at LN:58
@SQ SN:hsa-mir-5582 LN:68
@SQ SN:hsa-mir-5583-1 LN:59
@SQ SN:hsa-mir-5583-2 LN:59
@SQ SN:hsa-mir-5584 LN:60
@SQ SN:hsa-mir-5585 LN:59
@SQ SN:hsa-mir-5586 LN:59
@SQ SN:hsa-mir-5587 LN:53
@SQ SN:hsa-mir-548au LN:54
@SQ SN:hsa-mir-1295b LN:60
@SQ SN:hsa-mir-5588 LN:63
@SQ SN:hsa-mir-5589 LN:60
@SQ SN:hsa-mir-4536-2 LN:88
@SQ SN:hsa-mir-5590 LN:54
@SQ SN:hsa-mir-5591 LN:65
@SQ SN:hsa-mir-548av LN:62
@SQ SN:hsa-mir-5680 LN:84
@SQ SN:hsa-mir-5681a LN:75
@SQ SN:hsa-mir-5682 LN:76
@SQ SN:hsa-mir-548aw LN:65
@SQ SN:hsa-mir-5683 LN:76
@SQ SN:hsa-mir-5684 LN:65
@SQ SN:hsa-mir-548ax LN:73
@SQ SN:hsa-mir-5685 LN:79
@SQ SN:hsa-mir-5692c-1 LN:91
@SQ SN:hsa-mir-5692c-2 LN:77
@SQ SN:hsa-mir-5687 LN:77
@SQ SN:hsa-mir-5688 LN:83
@SQ SN:hsa-mir-5681b LN:60
@SQ SN:hsa-mir-5689 LN:78
@SQ SN:hsa-mir-5690 LN:73
@SQ SN:hsa-mir-5691 LN:68
@SQ SN:hsa-mir-5692a-1 LN:69
@SQ SN:hsa-mir-5692a-2 LN:59
@SQ SN:hsa-mir-4666b LN:81
@SQ SN:hsa-mir-5693 LN:73
@SQ SN:hsa-mir-5694 LN:76
@SQ SN:hsa-mir-5695 LN:85
@SQ SN:hsa-mir-5696 LN:85
@SQ SN:hsa-mir-5697 LN:78
@SQ SN:hsa-mir-5698 LN:72
@SQ SN:hsa-mir-5699 LN:90
@SQ SN:hsa-mir-5700 LN:71
@SQ SN:hsa-mir-5701-1 LN:82
@SQ SN:hsa-mir-5702 LN:84
@SQ SN:hsa-mir-5703 LN:56
@SQ SN:hsa-mir-5692b LN:87
@SQ SN:hsa-mir-5704 LN:77
@SQ SN:hsa-mir-5705 LN:89
@SQ SN:hsa-mir-5706 LN:80
@SQ SN:hsa-mir-5707 LN:81
@SQ SN:hsa-mir-5708 LN:85
@SQ SN:hsa-mir-5739 LN:80
@SQ SN:hsa-mir-5701-2 LN:82
@SQ SN:hsa-mir-5787 LN:55
@SQ SN:hsa-mir-1199 LN:119
@SQ SN:hsa-mir-6068 LN:60
@SQ SN:hsa-mir-6069 LN:79
@SQ SN:hsa-mir-6070 LN:103
@SQ SN:hsa-mir-6071 LN:78
@SQ SN:hsa-mir-6072 LN:71
@SQ SN:hsa-mir-6073 LN:89
@SQ SN:hsa-mir-6074 LN:107
@SQ SN:hsa-mir-6075 LN:95
@SQ SN:hsa-mir-6076 LN:113
@SQ SN:hsa-mir-6077 LN:82
@SQ SN:hsa-mir-6078 LN:100
@SQ SN:hsa-mir-6079 LN:62
@SQ SN:hsa-mir-6080 LN:66
@SQ SN:hsa-mir-6081 LN:97
@SQ SN:hsa-mir-6082 LN:109
@SQ SN:hsa-mir-6083 LN:106
@SQ SN:hsa-mir-6084 LN:110
@SQ SN:hsa-mir-6085 LN:110
@SQ SN:hsa-mir-6086 LN:55
@SQ SN:hsa-mir-6087 LN:49
@SQ SN:hsa-mir-6088 LN:51
@SQ SN:hsa-mir-6089-1 LN:64
@SQ SN:hsa-mir-6090 LN:60
@SQ SN:hsa-mir-6124 LN:85
@SQ SN:hsa-mir-6125 LN:96
@SQ SN:hsa-mir-6126 LN:89
@SQ SN:hsa-mir-6127 LN:109
@SQ SN:hsa-mir-6128 LN:109
@SQ SN:hsa-mir-378j LN:109
@SQ SN:hsa-mir-6129 LN:109
@SQ SN:hsa-mir-6130 LN:109
@SQ SN:hsa-mir-6131 LN:109
@SQ SN:hsa-mir-6132 LN:109
@SQ SN:hsa-mir-6133 LN:108
@SQ SN:hsa-mir-6134 LN:109
@SQ SN:hsa-mir-6165 LN:84
@SQ SN:hsa-mir-6499 LN:62
@SQ SN:hsa-mir-548ay LN:107
@SQ SN:hsa-mir-6500 LN:86
@SQ SN:hsa-mir-548az LN:95
@SQ SN:hsa-mir-6501 LN:67
@SQ SN:hsa-mir-6502 LN:76
@SQ SN:hsa-mir-6503 LN:86
@SQ SN:hsa-mir-6504 LN:61
@SQ SN:hsa-mir-6505 LN:71
@SQ SN:hsa-mir-6506 LN:66
@SQ SN:hsa-mir-6507 LN:70
@SQ SN:hsa-mir-6508 LN:60
@SQ SN:hsa-mir-6509 LN:85
@SQ SN:hsa-mir-6510 LN:54
@SQ SN:hsa-mir-6511a-1 LN:67
@SQ SN:hsa-mir-6512 LN:77
@SQ SN:hsa-mir-6513 LN:64
@SQ SN:hsa-mir-6514 LN:70
@SQ SN:hsa-mir-6515 LN:57
@SQ SN:hsa-mir-6715a LN:79
@SQ SN:hsa-mir-6715b LN:77
@SQ SN:hsa-mir-6716 LN:80
@SQ SN:hsa-mir-6717 LN:73
@SQ SN:hsa-mir-6511b-1 LN:85
@SQ SN:hsa-mir-6718 LN:80
@SQ SN:hsa-mir-6719 LN:87
@SQ SN:hsa-mir-6720 LN:98
@SQ SN:hsa-mir-6721 LN:87
@SQ SN:hsa-mir-6722 LN:78
@SQ SN:hsa-mir-6723 LN:89
@SQ SN:hsa-mir-6724-1 LN:92
@SQ SN:hsa-mir-892c LN:77
@SQ SN:hsa-mir-6726 LN:61
@SQ SN:hsa-mir-6727 LN:65
@SQ SN:hsa-mir-6728 LN:89
@SQ SN:hsa-mir-6729 LN:65
@SQ SN:hsa-mir-6730 LN:67
@SQ SN:hsa-mir-6731 LN:72
@SQ SN:hsa-mir-6732 LN:60
@SQ SN:hsa-mir-6733 LN:61
@SQ SN:hsa-mir-6734 LN:68
@SQ SN:hsa-mir-6735 LN:73
@SQ SN:hsa-mir-6736 LN:59
@SQ SN:hsa-mir-6737 LN:70
@SQ SN:hsa-mir-6738 LN:64
@SQ SN:hsa-mir-6739 LN:75
@SQ SN:hsa-mir-6740 LN:113
@SQ SN:hsa-mir-6741 LN:63
@SQ SN:hsa-mir-6742 LN:62
@SQ SN:hsa-mir-6743 LN:71
@SQ SN:hsa-mir-6744 LN:66
@SQ SN:hsa-mir-6745 LN:127
@SQ SN:hsa-mir-6746 LN:63
@SQ SN:hsa-mir-6747 LN:61
@SQ SN:hsa-mir-6748 LN:71
@SQ SN:hsa-mir-6749 LN:69
@SQ SN:hsa-mir-6750 LN:75
@SQ SN:hsa-mir-6751 LN:63
@SQ SN:hsa-mir-6752 LN:71
@SQ SN:hsa-mir-6753 LN:164
@SQ SN:hsa-mir-6754 LN:66
@SQ SN:hsa-mir-6755 LN:66
@SQ SN:hsa-mir-6756 LN:63
@SQ SN:hsa-mir-6757 LN:69
@SQ SN:hsa-mir-6758 LN:63
@SQ SN:hsa-mir-6759 LN:65
@SQ SN:hsa-mir-6760 LN:68
@SQ SN:hsa-mir-6761 LN:72
@SQ SN:hsa-mir-6762 LN:86
@SQ SN:hsa-mir-6763 LN:65
@SQ SN:hsa-mir-6764 LN:61
@SQ SN:hsa-mir-6765 LN:87
@SQ SN:hsa-mir-6766 LN:72
@SQ SN:hsa-mir-6767 LN:66
@SQ SN:hsa-mir-6768 LN:72
@SQ SN:hsa-mir-6769a LN:73
@SQ SN:hsa-mir-6770-1 LN:60
@SQ SN:hsa-mir-6771 LN:60
@SQ SN:hsa-mir-6772 LN:64
@SQ SN:hsa-mir-6773 LN:74
@SQ SN:hsa-mir-6774 LN:70
@SQ SN:hsa-mir-6775 LN:69
@SQ SN:hsa-mir-6776 LN:59
@SQ SN:hsa-mir-6777 LN:66
@SQ SN:hsa-mir-6778 LN:73
@SQ SN:hsa-mir-6779 LN:64
@SQ SN:hsa-mir-6780a LN:68
@SQ SN:hsa-mir-6781 LN:64
@SQ SN:hsa-mir-6782 LN:69
@SQ SN:hsa-mir-6783 LN:64
@SQ SN:hsa-mir-6784 LN:67
@SQ SN:hsa-mir-6785 LN:81
@SQ SN:hsa-mir-6786 LN:113
@SQ SN:hsa-mir-6787 LN:61
@SQ SN:hsa-mir-6788 LN:66
@SQ SN:hsa-mir-6789 LN:98
@SQ SN:hsa-mir-6790 LN:63
@SQ SN:hsa-mir-6791 LN:67
@SQ SN:hsa-mir-6792 LN:67
@SQ SN:hsa-mir-6793 LN:63
@SQ SN:hsa-mir-6794 LN:68
@SQ SN:hsa-mir-6795 LN:68
@SQ SN:hsa-mir-6796 LN:62
@SQ SN:hsa-mir-6797 LN:72
@SQ SN:hsa-mir-6798 LN:67
@SQ SN:hsa-mir-6799 LN:69
@SQ SN:hsa-mir-6800 LN:82
@SQ SN:hsa-mir-6801 LN:79
@SQ SN:hsa-mir-6802 LN:65
@SQ SN:hsa-mir-6803 LN:65
@SQ SN:hsa-mir-6804 LN:68
@SQ SN:hsa-mir-6805 LN:62
@SQ SN:hsa-mir-6806 LN:64
@SQ SN:hsa-mir-6807 LN:92
@SQ SN:hsa-mir-6808 LN:59
@SQ SN:hsa-mir-6809 LN:116
@SQ SN:hsa-mir-6810 LN:70
@SQ SN:hsa-mir-6811 LN:58
@SQ SN:hsa-mir-6812 LN:64
@SQ SN:hsa-mir-6813 LN:56
@SQ SN:hsa-mir-6814 LN:70
@SQ SN:hsa-mir-6815 LN:61
@SQ SN:hsa-mir-6816 LN:66
@SQ SN:hsa-mir-6817 LN:66
@SQ SN:hsa-mir-6818 LN:65
@SQ SN:hsa-mir-6819 LN:61
@SQ SN:hsa-mir-6820 LN:62
@SQ SN:hsa-mir-6821 LN:74
@SQ SN:hsa-mir-6822 LN:61
@SQ SN:hsa-mir-6823 LN:61
@SQ SN:hsa-mir-6824 LN:63
@SQ SN:hsa-mir-6825 LN:66
@SQ SN:hsa-mir-6826 LN:98
@SQ SN:hsa-mir-6827 LN:59
@SQ SN:hsa-mir-6828 LN:60
@SQ SN:hsa-mir-6829 LN:67
@SQ SN:hsa-mir-6830 LN:70
@SQ SN:hsa-mir-6831 LN:81
@SQ SN:hsa-mir-6832 LN:72
@SQ SN:hsa-mir-6833 LN:61
@SQ SN:hsa-mir-6834 LN:81
@SQ SN:hsa-mir-6835 LN:64
@SQ SN:hsa-mir-6780b LN:79
@SQ SN:hsa-mir-6836 LN:63
@SQ SN:hsa-mir-6837 LN:64
@SQ SN:hsa-mir-6838 LN:56
@SQ SN:hsa-mir-6839 LN:113
@SQ SN:hsa-mir-6840 LN:71
@SQ SN:hsa-mir-6841 LN:72
@SQ SN:hsa-mir-6842 LN:65
@SQ SN:hsa-mir-6843 LN:151
@SQ SN:hsa-mir-6844 LN:62
@SQ SN:hsa-mir-6845 LN:61
@SQ SN:hsa-mir-6846 LN:60
@SQ SN:hsa-mir-6847 LN:69
@SQ SN:hsa-mir-6848 LN:70
@SQ SN:hsa-mir-6849 LN:69
@SQ SN:hsa-mir-6850 LN:61
@SQ SN:hsa-mir-6851 LN:67
@SQ SN:hsa-mir-6852 LN:66
@SQ SN:hsa-mir-6853 LN:74
@SQ SN:hsa-mir-6854 LN:69
@SQ SN:hsa-mir-6855 LN:67
@SQ SN:hsa-mir-6856 LN:67
@SQ SN:hsa-mir-6857 LN:93
@SQ SN:hsa-mir-6858 LN:67
@SQ SN:hsa-mir-6859-1 LN:68
@SQ SN:hsa-mir-6769b LN:62
@SQ SN:hsa-mir-6860 LN:66
@SQ SN:hsa-mir-6861 LN:64
@SQ SN:hsa-mir-6862-1 LN:70
@SQ SN:hsa-mir-6863 LN:90
@SQ SN:hsa-mir-6864 LN:70
@SQ SN:hsa-mir-6865 LN:65
@SQ SN:hsa-mir-6866 LN:69
@SQ SN:hsa-mir-6867 LN:67
@SQ SN:hsa-mir-6868 LN:58
@SQ SN:hsa-mir-6869 LN:62
@SQ SN:hsa-mir-6870 LN:60
@SQ SN:hsa-mir-6871 LN:56
@SQ SN:hsa-mir-6872 LN:62
@SQ SN:hsa-mir-6873 LN:63
@SQ SN:hsa-mir-6874 LN:71
@SQ SN:hsa-mir-6875 LN:72
@SQ SN:hsa-mir-6876 LN:73
@SQ SN:hsa-mir-6877 LN:64
@SQ SN:hsa-mir-6878 LN:66
@SQ SN:hsa-mir-6879 LN:66
@SQ SN:hsa-mir-6880 LN:62
@SQ SN:hsa-mir-6881 LN:76
@SQ SN:hsa-mir-6882 LN:66
@SQ SN:hsa-mir-6883 LN:78
@SQ SN:hsa-mir-6884 LN:78
@SQ SN:hsa-mir-6885 LN:66
@SQ SN:hsa-mir-6886 LN:61
@SQ SN:hsa-mir-6887 LN:65
@SQ SN:hsa-mir-6888 LN:67
@SQ SN:hsa-mir-6889 LN:59
@SQ SN:hsa-mir-6890 LN:61
@SQ SN:hsa-mir-6891 LN:93
@SQ SN:hsa-mir-6892 LN:115
@SQ SN:hsa-mir-6893 LN:69
@SQ SN:hsa-mir-6894 LN:57
@SQ SN:hsa-mir-6895 LN:78
@SQ SN:hsa-mir-7106 LN:65
@SQ SN:hsa-mir-7107 LN:80
@SQ SN:hsa-mir-7108 LN:87
@SQ SN:hsa-mir-7109 LN:65
@SQ SN:hsa-mir-7110 LN:86
@SQ SN:hsa-mir-7111 LN:72
@SQ SN:hsa-mir-7112 LN:65
@SQ SN:hsa-mir-7113 LN:59
@SQ SN:hsa-mir-7114 LN:61
@SQ SN:hsa-mir-6511b-2 LN:71
@SQ SN:hsa-mir-3690-2 LN:75
@SQ SN:hsa-mir-6089-2 LN:64
@SQ SN:hsa-mir-6511a-2 LN:67
@SQ SN:hsa-mir-6511a-3 LN:67
@SQ SN:hsa-mir-6511a-4 LN:67
@SQ SN:hsa-mir-7150 LN:94
@SQ SN:hsa-mir-7151 LN:60
@SQ SN:hsa-mir-7152 LN:54
@SQ SN:hsa-mir-7153 LN:57
@SQ SN:hsa-mir-7154 LN:73
@SQ SN:hsa-mir-7155 LN:56
@SQ SN:hsa-mir-7156 LN:60
@SQ SN:hsa-mir-7157 LN:60
@SQ SN:hsa-mir-7158 LN:71
@SQ SN:hsa-mir-7161 LN:84
@SQ SN:hsa-mir-7159 LN:66
@SQ SN:hsa-mir-7160 LN:52
@SQ SN:hsa-mir-486-2 LN:64
@SQ SN:hsa-mir-7162 LN:69
@SQ SN:hsa-mir-7515 LN:67
@SQ SN:hsa-mir-7641-1 LN:61
@SQ SN:hsa-mir-7641-2 LN:53
@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_27096_x8 0 hsa-let-7f-1 63 255 22M1D * 0 0 CTATACAATCTATTGCCTTCCT BABFFFFDGHHHGIIIIIIIII NM:i:1 MD:Z:21C^T
seq_5365_x5 0 hsa-let-7f-1 63 255 21M * 0 0 CTATACAATCTATTGCCTTCT BBBFFEEEHHHHHJIJJJIIJ NM:i:1 MD:Z:20C
mirtop-0.4.23/data/aligments/let7-1D.sam 0000664 0000000 0000000 00000140523 13547635037 0017647 0 ustar 00root root 0000000 0000000 @SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
@SQ SN:hsa-let-7b LN:83
@SQ SN:hsa-let-7c LN:84
@SQ SN:hsa-let-7d LN:87
@SQ SN:hsa-let-7e LN:79
@SQ SN:hsa-let-7f-1 LN:87
@SQ SN:hsa-let-7f-2 LN:83
@SQ SN:hsa-mir-15a LN:83
@SQ SN:hsa-mir-16-1 LN:89
@SQ SN:hsa-mir-17 LN:84
@SQ SN:hsa-mir-18a LN:71
@SQ SN:hsa-mir-19a LN:82
@SQ SN:hsa-mir-19b-1 LN:87
@SQ SN:hsa-mir-19b-2 LN:96
@SQ SN:hsa-mir-20a LN:71
@SQ SN:hsa-mir-21 LN:72
@SQ SN:hsa-mir-22 LN:85
@SQ SN:hsa-mir-23a LN:73
@SQ SN:hsa-mir-24-1 LN:68
@SQ SN:hsa-mir-24-2 LN:73
@SQ SN:hsa-mir-25 LN:84
@SQ SN:hsa-mir-26a-1 LN:77
@SQ SN:hsa-mir-26b LN:77
@SQ SN:hsa-mir-27a LN:78
@SQ SN:hsa-mir-28 LN:86
@SQ SN:hsa-mir-29a LN:64
@SQ SN:hsa-mir-30a LN:71
@SQ SN:hsa-mir-31 LN:71
@SQ SN:hsa-mir-32 LN:70
@SQ SN:hsa-mir-33a LN:69
@SQ SN:hsa-mir-92a-1 LN:78
@SQ SN:hsa-mir-92a-2 LN:75
@SQ SN:hsa-mir-93 LN:80
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@SQ SN:hsa-mir-96 LN:78
@SQ SN:hsa-mir-98 LN:119
@SQ SN:hsa-mir-99a LN:81
@SQ SN:hsa-mir-100 LN:80
@SQ SN:hsa-mir-101-1 LN:75
@SQ SN:hsa-mir-29b-1 LN:81
@SQ SN:hsa-mir-29b-2 LN:81
@SQ SN:hsa-mir-103a-2 LN:78
@SQ SN:hsa-mir-103a-1 LN:78
@SQ SN:hsa-mir-105-1 LN:81
@SQ SN:hsa-mir-105-2 LN:81
@SQ SN:hsa-mir-106a LN:81
@SQ SN:hsa-mir-107 LN:81
@SQ SN:hsa-mir-16-2 LN:81
@SQ SN:hsa-mir-192 LN:110
@SQ SN:hsa-mir-196a-1 LN:70
@SQ SN:hsa-mir-197 LN:75
@SQ SN:hsa-mir-198 LN:62
@SQ SN:hsa-mir-199a-1 LN:71
@SQ SN:hsa-mir-208a LN:71
@SQ SN:hsa-mir-129-1 LN:72
@SQ SN:hsa-mir-148a LN:68
@SQ SN:hsa-mir-30c-2 LN:72
@SQ SN:hsa-mir-30d LN:70
@SQ SN:hsa-mir-139 LN:68
@SQ SN:hsa-mir-147a LN:72
@SQ SN:hsa-mir-7-1 LN:110
@SQ SN:hsa-mir-7-2 LN:110
@SQ SN:hsa-mir-7-3 LN:110
@SQ SN:hsa-mir-10a LN:110
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@SQ SN:hsa-mir-34a LN:110
@SQ SN:hsa-mir-181a-2 LN:110
@SQ SN:hsa-mir-181b-1 LN:110
@SQ SN:hsa-mir-181c LN:110
@SQ SN:hsa-mir-182 LN:110
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@SQ SN:hsa-mir-187 LN:109
@SQ SN:hsa-mir-196a-2 LN:110
@SQ SN:hsa-mir-199a-2 LN:110
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@SQ SN:hsa-mir-203a LN:110
@SQ SN:hsa-mir-204 LN:110
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@SQ SN:hsa-mir-181a-1 LN:110
@SQ SN:hsa-mir-214 LN:110
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@SQ SN:hsa-mir-217 LN:110
@SQ SN:hsa-mir-218-1 LN:110
@SQ SN:hsa-mir-218-2 LN:110
@SQ SN:hsa-mir-219a-1 LN:110
@SQ SN:hsa-mir-221 LN:110
@SQ SN:hsa-mir-222 LN:110
@SQ SN:hsa-mir-223 LN:110
@SQ SN:hsa-mir-224 LN:81
@SQ SN:hsa-mir-200b LN:95
@SQ SN:hsa-let-7g LN:84
@SQ SN:hsa-let-7i LN:84
@SQ SN:hsa-mir-1-2 LN:85
@SQ SN:hsa-mir-15b LN:98
@SQ SN:hsa-mir-23b LN:97
@SQ SN:hsa-mir-27b LN:97
@SQ SN:hsa-mir-30b LN:88
@SQ SN:hsa-mir-122 LN:85
@SQ SN:hsa-mir-124-1 LN:85
@SQ SN:hsa-mir-124-2 LN:109
@SQ SN:hsa-mir-124-3 LN:87
@SQ SN:hsa-mir-125b-1 LN:88
@SQ SN:hsa-mir-128-1 LN:82
@SQ SN:hsa-mir-130a LN:89
@SQ SN:hsa-mir-132 LN:101
@SQ SN:hsa-mir-133a-1 LN:88
@SQ SN:hsa-mir-133a-2 LN:102
@SQ SN:hsa-mir-135a-1 LN:90
@SQ SN:hsa-mir-135a-2 LN:100
@SQ SN:hsa-mir-137 LN:102
@SQ SN:hsa-mir-138-2 LN:84
@SQ SN:hsa-mir-140 LN:100
@SQ SN:hsa-mir-141 LN:95
@SQ SN:hsa-mir-142 LN:87
@SQ SN:hsa-mir-143 LN:106
@SQ SN:hsa-mir-144 LN:86
@SQ SN:hsa-mir-145 LN:88
@SQ SN:hsa-mir-152 LN:87
@SQ SN:hsa-mir-153-1 LN:90
@SQ SN:hsa-mir-153-2 LN:87
@SQ SN:hsa-mir-191 LN:92
@SQ SN:hsa-mir-9-1 LN:89
@SQ SN:hsa-mir-9-2 LN:87
@SQ SN:hsa-mir-9-3 LN:90
@SQ SN:hsa-mir-125a LN:86
@SQ SN:hsa-mir-125b-2 LN:89
@SQ SN:hsa-mir-126 LN:85
@SQ SN:hsa-mir-127 LN:97
@SQ SN:hsa-mir-129-2 LN:90
@SQ SN:hsa-mir-134 LN:73
@SQ SN:hsa-mir-136 LN:82
@SQ SN:hsa-mir-138-1 LN:99
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@SQ SN:hsa-mir-149 LN:89
@SQ SN:hsa-mir-150 LN:84
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@SQ SN:hsa-mir-185 LN:82
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@SQ SN:hsa-mir-193a LN:88
@SQ SN:hsa-mir-194-1 LN:85
@SQ SN:hsa-mir-195 LN:87
@SQ SN:hsa-mir-206 LN:86
@SQ SN:hsa-mir-320a LN:82
@SQ SN:hsa-mir-200c LN:68
@SQ SN:hsa-mir-1-1 LN:71
@SQ SN:hsa-mir-155 LN:65
@SQ SN:hsa-mir-181b-2 LN:89
@SQ SN:hsa-mir-128-2 LN:84
@SQ SN:hsa-mir-194-2 LN:85
@SQ SN:hsa-mir-106b LN:82
@SQ SN:hsa-mir-29c LN:88
@SQ SN:hsa-mir-30c-1 LN:89
@SQ SN:hsa-mir-200a LN:90
@SQ SN:hsa-mir-302a LN:69
@SQ SN:hsa-mir-101-2 LN:79
@SQ SN:hsa-mir-219a-2 LN:97
@SQ SN:hsa-mir-34b LN:84
@SQ SN:hsa-mir-34c LN:77
@SQ SN:hsa-mir-299 LN:63
@SQ SN:hsa-mir-301a LN:86
@SQ SN:hsa-mir-99b LN:70
@SQ SN:hsa-mir-296 LN:80
@SQ SN:hsa-mir-130b LN:82
@SQ SN:hsa-mir-30e LN:92
@SQ SN:hsa-mir-26a-2 LN:84
@SQ SN:hsa-mir-361 LN:72
@SQ SN:hsa-mir-362 LN:65
@SQ SN:hsa-mir-363 LN:75
@SQ SN:hsa-mir-365a LN:87
@SQ SN:hsa-mir-365b LN:111
@SQ SN:hsa-mir-302b LN:73
@SQ SN:hsa-mir-302c LN:68
@SQ SN:hsa-mir-302d LN:68
@SQ SN:hsa-mir-367 LN:68
@SQ SN:hsa-mir-376c LN:66
@SQ SN:hsa-mir-369 LN:70
@SQ SN:hsa-mir-370 LN:75
@SQ SN:hsa-mir-371a LN:67
@SQ SN:hsa-mir-372 LN:67
@SQ SN:hsa-mir-373 LN:69
@SQ SN:hsa-mir-374a LN:72
@SQ SN:hsa-mir-375 LN:64
@SQ SN:hsa-mir-376a-1 LN:68
@SQ SN:hsa-mir-377 LN:69
@SQ SN:hsa-mir-378a LN:66
@SQ SN:hsa-mir-379 LN:67
@SQ SN:hsa-mir-380 LN:61
@SQ SN:hsa-mir-381 LN:75
@SQ SN:hsa-mir-382 LN:76
@SQ SN:hsa-mir-383 LN:73
@SQ SN:hsa-mir-340 LN:95
@SQ SN:hsa-mir-330 LN:94
@SQ SN:hsa-mir-328 LN:75
@SQ SN:hsa-mir-342 LN:99
@SQ SN:hsa-mir-337 LN:93
@SQ SN:hsa-mir-323a LN:86
@SQ SN:hsa-mir-326 LN:95
@SQ SN:hsa-mir-151a LN:90
@SQ SN:hsa-mir-135b LN:97
@SQ SN:hsa-mir-148b LN:99
@SQ SN:hsa-mir-331 LN:94
@SQ SN:hsa-mir-324 LN:83
@SQ SN:hsa-mir-338 LN:67
@SQ SN:hsa-mir-339 LN:94
@SQ SN:hsa-mir-335 LN:94
@SQ SN:hsa-mir-133b LN:119
@SQ SN:hsa-mir-325 LN:98
@SQ SN:hsa-mir-345 LN:98
@SQ SN:hsa-mir-346 LN:95
@SQ SN:hsa-mir-384 LN:88
@SQ SN:hsa-mir-196b LN:84
@SQ SN:hsa-mir-422a LN:90
@SQ SN:hsa-mir-423 LN:94
@SQ SN:hsa-mir-424 LN:98
@SQ SN:hsa-mir-425 LN:87
@SQ SN:hsa-mir-18b LN:71
@SQ SN:hsa-mir-20b LN:69
@SQ SN:hsa-mir-448 LN:111
@SQ SN:hsa-mir-429 LN:83
@SQ SN:hsa-mir-449a LN:91
@SQ SN:hsa-mir-450a-1 LN:91
@SQ SN:hsa-mir-431 LN:114
@SQ SN:hsa-mir-433 LN:93
@SQ SN:hsa-mir-329-1 LN:80
@SQ SN:hsa-mir-329-2 LN:84
@SQ SN:hsa-mir-451a LN:72
@SQ SN:hsa-mir-452 LN:85
@SQ SN:hsa-mir-409 LN:79
@SQ SN:hsa-mir-412 LN:91
@SQ SN:hsa-mir-410 LN:80
@SQ SN:hsa-mir-376b LN:100
@SQ SN:hsa-mir-483 LN:76
@SQ SN:hsa-mir-484 LN:79
@SQ SN:hsa-mir-485 LN:73
@SQ SN:hsa-mir-486-1 LN:68
@SQ SN:hsa-mir-487a LN:80
@SQ SN:hsa-mir-488 LN:83
@SQ SN:hsa-mir-489 LN:84
@SQ SN:hsa-mir-490 LN:128
@SQ SN:hsa-mir-491 LN:84
@SQ SN:hsa-mir-511 LN:87
@SQ SN:hsa-mir-146b LN:73
@SQ SN:hsa-mir-202 LN:110
@SQ SN:hsa-mir-492 LN:116
@SQ SN:hsa-mir-493 LN:89
@SQ SN:hsa-mir-432 LN:94
@SQ SN:hsa-mir-494 LN:81
@SQ SN:hsa-mir-495 LN:82
@SQ SN:hsa-mir-496 LN:102
@SQ SN:hsa-mir-193b LN:83
@SQ SN:hsa-mir-497 LN:112
@SQ SN:hsa-mir-181d LN:137
@SQ SN:hsa-mir-512-1 LN:84
@SQ SN:hsa-mir-512-2 LN:98
@SQ SN:hsa-mir-498 LN:124
@SQ SN:hsa-mir-520e LN:87
@SQ SN:hsa-mir-515-1 LN:83
@SQ SN:hsa-mir-519e LN:84
@SQ SN:hsa-mir-520f LN:87
@SQ SN:hsa-mir-515-2 LN:83
@SQ SN:hsa-mir-519c LN:87
@SQ SN:hsa-mir-520a LN:85
@SQ SN:hsa-mir-526b LN:83
@SQ SN:hsa-mir-519b LN:81
@SQ SN:hsa-mir-525 LN:85
@SQ SN:hsa-mir-523 LN:87
@SQ SN:hsa-mir-518f LN:87
@SQ SN:hsa-mir-520b LN:61
@SQ SN:hsa-mir-518b LN:83
@SQ SN:hsa-mir-526a-1 LN:85
@SQ SN:hsa-mir-520c LN:87
@SQ SN:hsa-mir-518c LN:101
@SQ SN:hsa-mir-524 LN:87
@SQ SN:hsa-mir-517a LN:87
@SQ SN:hsa-mir-519d LN:88
@SQ SN:hsa-mir-521-2 LN:87
@SQ SN:hsa-mir-520d LN:87
@SQ SN:hsa-mir-517b LN:67
@SQ SN:hsa-mir-520g LN:90
@SQ SN:hsa-mir-516b-2 LN:85
@SQ SN:hsa-mir-526a-2 LN:65
@SQ SN:hsa-mir-518e LN:88
@SQ SN:hsa-mir-518a-1 LN:85
@SQ SN:hsa-mir-518d LN:87
@SQ SN:hsa-mir-516b-1 LN:90
@SQ SN:hsa-mir-518a-2 LN:87
@SQ SN:hsa-mir-517c LN:95
@SQ SN:hsa-mir-520h LN:88
@SQ SN:hsa-mir-521-1 LN:87
@SQ SN:hsa-mir-522 LN:87
@SQ SN:hsa-mir-519a-1 LN:85
@SQ SN:hsa-mir-527 LN:85
@SQ SN:hsa-mir-516a-1 LN:90
@SQ SN:hsa-mir-516a-2 LN:90
@SQ SN:hsa-mir-519a-2 LN:87
@SQ SN:hsa-mir-499a LN:122
@SQ SN:hsa-mir-500a LN:84
@SQ SN:hsa-mir-501 LN:84
@SQ SN:hsa-mir-502 LN:86
@SQ SN:hsa-mir-450a-2 LN:100
@SQ SN:hsa-mir-503 LN:71
@SQ SN:hsa-mir-504 LN:83
@SQ SN:hsa-mir-505 LN:84
@SQ SN:hsa-mir-513a-1 LN:129
@SQ SN:hsa-mir-513a-2 LN:127
@SQ SN:hsa-mir-506 LN:124
@SQ SN:hsa-mir-507 LN:94
@SQ SN:hsa-mir-508 LN:115
@SQ SN:hsa-mir-509-1 LN:94
@SQ SN:hsa-mir-510 LN:74
@SQ SN:hsa-mir-514a-1 LN:98
@SQ SN:hsa-mir-514a-2 LN:88
@SQ SN:hsa-mir-514a-3 LN:88
@SQ SN:hsa-mir-532 LN:91
@SQ SN:hsa-mir-455 LN:96
@SQ SN:hsa-mir-539 LN:78
@SQ SN:hsa-mir-544a LN:91
@SQ SN:hsa-mir-545 LN:106
@SQ SN:hsa-mir-376a-2 LN:80
@SQ SN:hsa-mir-487b LN:84
@SQ SN:hsa-mir-551a LN:96
@SQ SN:hsa-mir-552 LN:96
@SQ SN:hsa-mir-553 LN:68
@SQ SN:hsa-mir-554 LN:96
@SQ SN:hsa-mir-92b LN:96
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@SQ SN:hsa-mir-557 LN:98
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@SQ SN:hsa-mir-563 LN:79
@SQ SN:hsa-mir-564 LN:94
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@SQ SN:hsa-mir-567 LN:98
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@SQ SN:hsa-mir-569 LN:96
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@SQ SN:hsa-mir-573 LN:99
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@SQ SN:hsa-mir-576 LN:98
@SQ SN:hsa-mir-577 LN:96
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@SQ SN:hsa-mir-583 LN:75
@SQ SN:hsa-mir-584 LN:97
@SQ SN:hsa-mir-585 LN:94
@SQ SN:hsa-mir-548a-1 LN:97
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@SQ SN:hsa-mir-588 LN:83
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@SQ SN:hsa-mir-589 LN:99
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@SQ SN:hsa-mir-591 LN:95
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@SQ SN:hsa-mir-593 LN:100
@SQ SN:hsa-mir-595 LN:96
@SQ SN:hsa-mir-596 LN:77
@SQ SN:hsa-mir-597 LN:97
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@SQ SN:hsa-mir-599 LN:95
@SQ SN:hsa-mir-548a-3 LN:97
@SQ SN:hsa-mir-600 LN:98
@SQ SN:hsa-mir-601 LN:79
@SQ SN:hsa-mir-602 LN:98
@SQ SN:hsa-mir-603 LN:97
@SQ SN:hsa-mir-604 LN:94
@SQ SN:hsa-mir-605 LN:83
@SQ SN:hsa-mir-606 LN:96
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@SQ SN:hsa-mir-608 LN:100
@SQ SN:hsa-mir-609 LN:95
@SQ SN:hsa-mir-610 LN:96
@SQ SN:hsa-mir-611 LN:67
@SQ SN:hsa-mir-612 LN:100
@SQ SN:hsa-mir-613 LN:95
@SQ SN:hsa-mir-614 LN:90
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@SQ SN:hsa-mir-617 LN:97
@SQ SN:hsa-mir-618 LN:98
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@SQ SN:hsa-mir-620 LN:95
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@SQ SN:hsa-mir-623 LN:98
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@SQ SN:hsa-mir-625 LN:85
@SQ SN:hsa-mir-626 LN:94
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@SQ SN:hsa-mir-628 LN:95
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@SQ SN:hsa-mir-631 LN:75
@SQ SN:hsa-mir-33b LN:96
@SQ SN:hsa-mir-632 LN:94
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@SQ SN:hsa-mir-640 LN:96
@SQ SN:hsa-mir-641 LN:99
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@SQ SN:hsa-mir-644a LN:94
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@SQ SN:hsa-mir-647 LN:96
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@SQ SN:hsa-mir-651 LN:97
@SQ SN:hsa-mir-652 LN:98
@SQ SN:hsa-mir-548d-1 LN:97
@SQ SN:hsa-mir-661 LN:89
@SQ SN:hsa-mir-662 LN:95
@SQ SN:hsa-mir-548d-2 LN:97
@SQ SN:hsa-mir-663a LN:93
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@SQ SN:hsa-mir-653 LN:96
@SQ SN:hsa-mir-411 LN:96
@SQ SN:hsa-mir-654 LN:81
@SQ SN:hsa-mir-655 LN:97
@SQ SN:hsa-mir-656 LN:78
@SQ SN:hsa-mir-549a LN:96
@SQ SN:hsa-mir-657 LN:98
@SQ SN:hsa-mir-658 LN:100
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@SQ SN:hsa-mir-421 LN:85
@SQ SN:hsa-mir-542 LN:97
@SQ SN:hsa-mir-758 LN:88
@SQ SN:hsa-mir-1264 LN:69
@SQ SN:hsa-mir-671 LN:118
@SQ SN:hsa-mir-668 LN:66
@SQ SN:hsa-mir-550a-3 LN:95
@SQ SN:hsa-mir-767 LN:109
@SQ SN:hsa-mir-1224 LN:85
@SQ SN:hsa-mir-151b LN:96
@SQ SN:hsa-mir-320b-1 LN:79
@SQ SN:hsa-mir-320c-1 LN:88
@SQ SN:hsa-mir-1296 LN:92
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@SQ SN:hsa-mir-1323 LN:73
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@SQ SN:hsa-mir-1301 LN:82
@SQ SN:hsa-mir-454 LN:115
@SQ SN:hsa-mir-1185-2 LN:86
@SQ SN:hsa-mir-449c LN:92
@SQ SN:hsa-mir-1283-1 LN:87
@SQ SN:hsa-mir-769 LN:118
@SQ SN:hsa-mir-766 LN:111
@SQ SN:hsa-mir-320b-2 LN:138
@SQ SN:hsa-mir-378d-2 LN:98
@SQ SN:hsa-mir-1185-1 LN:86
@SQ SN:hsa-mir-762 LN:83
@SQ SN:hsa-mir-802 LN:94
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@SQ SN:hsa-mir-1298 LN:112
@SQ SN:hsa-mir-2113 LN:91
@SQ SN:hsa-mir-761 LN:59
@SQ SN:hsa-mir-764 LN:85
@SQ SN:hsa-mir-759 LN:91
@SQ SN:hsa-mir-765 LN:114
@SQ SN:hsa-mir-770 LN:98
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@SQ SN:hsa-mir-298 LN:88
@SQ SN:hsa-mir-891a LN:79
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@SQ SN:hsa-mir-892a LN:75
@SQ SN:hsa-mir-509-2 LN:91
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@SQ SN:hsa-mir-541 LN:84
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@SQ SN:hsa-mir-708 LN:88
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@SQ SN:hsa-mir-744 LN:98
@SQ SN:hsa-mir-885 LN:74
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@SQ SN:hsa-mir-665 LN:72
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@SQ SN:hsa-mir-297 LN:66
@SQ SN:hsa-mir-1178 LN:91
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@SQ SN:hsa-mir-1180 LN:69
@SQ SN:hsa-mir-1181 LN:81
@SQ SN:hsa-mir-1182 LN:97
@SQ SN:hsa-mir-1183 LN:89
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@SQ SN:hsa-mir-663b LN:115
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@SQ SN:hsa-mir-1289-1 LN:144
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@SQ SN:hsa-mir-1302-4 LN:150
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@SQ SN:hsa-mir-1302-8 LN:128
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@SQ SN:hsa-mir-548f-2 LN:98
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@SQ SN:hsa-mir-548o LN:114
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@SQ SN:hsa-mir-1272 LN:129
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@SQ SN:hsa-mir-548h-2 LN:88
@SQ SN:hsa-mir-548h-3 LN:118
@SQ SN:hsa-mir-548h-4 LN:111
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@SQ SN:hsa-mir-548i-1 LN:149
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@SQ SN:hsa-mir-1284 LN:120
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@SQ SN:hsa-mir-103b-1 LN:62
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@SQ SN:hsa-mir-1825 LN:53
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@SQ SN:hsa-mir-1911 LN:80
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@SQ SN:hsa-mir-1972-1 LN:77
@SQ SN:hsa-mir-1973 LN:44
@SQ SN:hsa-mir-1976 LN:52
@SQ SN:hsa-mir-2052 LN:55
@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-2276 LN:89
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@SQ SN:hsa-mir-2278 LN:96
@SQ SN:hsa-mir-2681 LN:105
@SQ SN:hsa-mir-2682 LN:110
@SQ SN:hsa-mir-711 LN:76
@SQ SN:hsa-mir-718 LN:70
@SQ SN:hsa-mir-2861 LN:90
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@SQ SN:hsa-mir-3116-1 LN:74
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@SQ SN:hsa-mir-3117 LN:78
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@SQ SN:hsa-mir-3119-1 LN:85
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@SQ SN:hsa-mir-3124 LN:67
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@SQ SN:hsa-mir-3131 LN:63
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@SQ SN:hsa-mir-3137 LN:75
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@SQ SN:hsa-mir-3156-1 LN:75
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@SQ SN:hsa-mir-3160-1 LN:85
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@SQ SN:hsa-mir-3180-3 LN:94
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@SQ SN:hsa-mir-500b LN:79
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@SQ SN:hsa-mir-1184-2 LN:99
@SQ SN:hsa-mir-1184-3 LN:99
@SQ SN:hsa-mir-1233-2 LN:82
@SQ SN:hsa-mir-1244-2 LN:85
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@SQ SN:hsa-mir-1972-2 LN:77
@SQ SN:hsa-mir-1302-9 LN:138
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@SQ SN:hsa-mir-4283-2 LN:80
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@SQ SN:hsa-mir-3648-1 LN:180
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@SQ SN:hsa-mir-548aa-2 LN:97
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@SQ SN:hsa-mir-1254-2 LN:63
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@SQ SN:hsa-mir-548al LN:97
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@SQ SN:hsa-mir-4509-1 LN:94
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@SQ SN:hsa-mir-378i LN:76
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@SQ SN:hsa-mir-4536-1 LN:88
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@SQ SN:hsa-mir-3960 LN:91
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@SQ SN:hsa-mir-3976 LN:139
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@SQ SN:hsa-mir-4638 LN:68
@SQ SN:hsa-mir-4639 LN:69
@SQ SN:hsa-mir-4640 LN:90
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@SQ SN:hsa-mir-4999 LN:91
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@SQ SN:hsa-mir-5004 LN:107
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@SQ SN:hsa-mir-5010 LN:120
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@SQ SN:hsa-mir-6090 LN:60
@SQ SN:hsa-mir-6124 LN:85
@SQ SN:hsa-mir-6125 LN:96
@SQ SN:hsa-mir-6126 LN:89
@SQ SN:hsa-mir-6127 LN:109
@SQ SN:hsa-mir-6128 LN:109
@SQ SN:hsa-mir-378j LN:109
@SQ SN:hsa-mir-6129 LN:109
@SQ SN:hsa-mir-6130 LN:109
@SQ SN:hsa-mir-6131 LN:109
@SQ SN:hsa-mir-6132 LN:109
@SQ SN:hsa-mir-6133 LN:108
@SQ SN:hsa-mir-6134 LN:109
@SQ SN:hsa-mir-6165 LN:84
@SQ SN:hsa-mir-6499 LN:62
@SQ SN:hsa-mir-548ay LN:107
@SQ SN:hsa-mir-6500 LN:86
@SQ SN:hsa-mir-548az LN:95
@SQ SN:hsa-mir-6501 LN:67
@SQ SN:hsa-mir-6502 LN:76
@SQ SN:hsa-mir-6503 LN:86
@SQ SN:hsa-mir-6504 LN:61
@SQ SN:hsa-mir-6505 LN:71
@SQ SN:hsa-mir-6506 LN:66
@SQ SN:hsa-mir-6507 LN:70
@SQ SN:hsa-mir-6508 LN:60
@SQ SN:hsa-mir-6509 LN:85
@SQ SN:hsa-mir-6510 LN:54
@SQ SN:hsa-mir-6511a-1 LN:67
@SQ SN:hsa-mir-6512 LN:77
@SQ SN:hsa-mir-6513 LN:64
@SQ SN:hsa-mir-6514 LN:70
@SQ SN:hsa-mir-6515 LN:57
@SQ SN:hsa-mir-6715a LN:79
@SQ SN:hsa-mir-6715b LN:77
@SQ SN:hsa-mir-6716 LN:80
@SQ SN:hsa-mir-6717 LN:73
@SQ SN:hsa-mir-6511b-1 LN:85
@SQ SN:hsa-mir-6718 LN:80
@SQ SN:hsa-mir-6719 LN:87
@SQ SN:hsa-mir-6720 LN:98
@SQ SN:hsa-mir-6721 LN:87
@SQ SN:hsa-mir-6722 LN:78
@SQ SN:hsa-mir-6723 LN:89
@SQ SN:hsa-mir-6724-1 LN:92
@SQ SN:hsa-mir-892c LN:77
@SQ SN:hsa-mir-6726 LN:61
@SQ SN:hsa-mir-6727 LN:65
@SQ SN:hsa-mir-6728 LN:89
@SQ SN:hsa-mir-6729 LN:65
@SQ SN:hsa-mir-6730 LN:67
@SQ SN:hsa-mir-6731 LN:72
@SQ SN:hsa-mir-6732 LN:60
@SQ SN:hsa-mir-6733 LN:61
@SQ SN:hsa-mir-6734 LN:68
@SQ SN:hsa-mir-6735 LN:73
@SQ SN:hsa-mir-6736 LN:59
@SQ SN:hsa-mir-6737 LN:70
@SQ SN:hsa-mir-6738 LN:64
@SQ SN:hsa-mir-6739 LN:75
@SQ SN:hsa-mir-6740 LN:113
@SQ SN:hsa-mir-6741 LN:63
@SQ SN:hsa-mir-6742 LN:62
@SQ SN:hsa-mir-6743 LN:71
@SQ SN:hsa-mir-6744 LN:66
@SQ SN:hsa-mir-6745 LN:127
@SQ SN:hsa-mir-6746 LN:63
@SQ SN:hsa-mir-6747 LN:61
@SQ SN:hsa-mir-6748 LN:71
@SQ SN:hsa-mir-6749 LN:69
@SQ SN:hsa-mir-6750 LN:75
@SQ SN:hsa-mir-6751 LN:63
@SQ SN:hsa-mir-6752 LN:71
@SQ SN:hsa-mir-6753 LN:164
@SQ SN:hsa-mir-6754 LN:66
@SQ SN:hsa-mir-6755 LN:66
@SQ SN:hsa-mir-6756 LN:63
@SQ SN:hsa-mir-6757 LN:69
@SQ SN:hsa-mir-6758 LN:63
@SQ SN:hsa-mir-6759 LN:65
@SQ SN:hsa-mir-6760 LN:68
@SQ SN:hsa-mir-6761 LN:72
@SQ SN:hsa-mir-6762 LN:86
@SQ SN:hsa-mir-6763 LN:65
@SQ SN:hsa-mir-6764 LN:61
@SQ SN:hsa-mir-6765 LN:87
@SQ SN:hsa-mir-6766 LN:72
@SQ SN:hsa-mir-6767 LN:66
@SQ SN:hsa-mir-6768 LN:72
@SQ SN:hsa-mir-6769a LN:73
@SQ SN:hsa-mir-6770-1 LN:60
@SQ SN:hsa-mir-6771 LN:60
@SQ SN:hsa-mir-6772 LN:64
@SQ SN:hsa-mir-6773 LN:74
@SQ SN:hsa-mir-6774 LN:70
@SQ SN:hsa-mir-6775 LN:69
@SQ SN:hsa-mir-6776 LN:59
@SQ SN:hsa-mir-6777 LN:66
@SQ SN:hsa-mir-6778 LN:73
@SQ SN:hsa-mir-6779 LN:64
@SQ SN:hsa-mir-6780a LN:68
@SQ SN:hsa-mir-6781 LN:64
@SQ SN:hsa-mir-6782 LN:69
@SQ SN:hsa-mir-6783 LN:64
@SQ SN:hsa-mir-6784 LN:67
@SQ SN:hsa-mir-6785 LN:81
@SQ SN:hsa-mir-6786 LN:113
@SQ SN:hsa-mir-6787 LN:61
@SQ SN:hsa-mir-6788 LN:66
@SQ SN:hsa-mir-6789 LN:98
@SQ SN:hsa-mir-6790 LN:63
@SQ SN:hsa-mir-6791 LN:67
@SQ SN:hsa-mir-6792 LN:67
@SQ SN:hsa-mir-6793 LN:63
@SQ SN:hsa-mir-6794 LN:68
@SQ SN:hsa-mir-6795 LN:68
@SQ SN:hsa-mir-6796 LN:62
@SQ SN:hsa-mir-6797 LN:72
@SQ SN:hsa-mir-6798 LN:67
@SQ SN:hsa-mir-6799 LN:69
@SQ SN:hsa-mir-6800 LN:82
@SQ SN:hsa-mir-6801 LN:79
@SQ SN:hsa-mir-6802 LN:65
@SQ SN:hsa-mir-6803 LN:65
@SQ SN:hsa-mir-6804 LN:68
@SQ SN:hsa-mir-6805 LN:62
@SQ SN:hsa-mir-6806 LN:64
@SQ SN:hsa-mir-6807 LN:92
@SQ SN:hsa-mir-6808 LN:59
@SQ SN:hsa-mir-6809 LN:116
@SQ SN:hsa-mir-6810 LN:70
@SQ SN:hsa-mir-6811 LN:58
@SQ SN:hsa-mir-6812 LN:64
@SQ SN:hsa-mir-6813 LN:56
@SQ SN:hsa-mir-6814 LN:70
@SQ SN:hsa-mir-6815 LN:61
@SQ SN:hsa-mir-6816 LN:66
@SQ SN:hsa-mir-6817 LN:66
@SQ SN:hsa-mir-6818 LN:65
@SQ SN:hsa-mir-6819 LN:61
@SQ SN:hsa-mir-6820 LN:62
@SQ SN:hsa-mir-6821 LN:74
@SQ SN:hsa-mir-6822 LN:61
@SQ SN:hsa-mir-6823 LN:61
@SQ SN:hsa-mir-6824 LN:63
@SQ SN:hsa-mir-6825 LN:66
@SQ SN:hsa-mir-6826 LN:98
@SQ SN:hsa-mir-6827 LN:59
@SQ SN:hsa-mir-6828 LN:60
@SQ SN:hsa-mir-6829 LN:67
@SQ SN:hsa-mir-6830 LN:70
@SQ SN:hsa-mir-6831 LN:81
@SQ SN:hsa-mir-6832 LN:72
@SQ SN:hsa-mir-6833 LN:61
@SQ SN:hsa-mir-6834 LN:81
@SQ SN:hsa-mir-6835 LN:64
@SQ SN:hsa-mir-6780b LN:79
@SQ SN:hsa-mir-6836 LN:63
@SQ SN:hsa-mir-6837 LN:64
@SQ SN:hsa-mir-6838 LN:56
@SQ SN:hsa-mir-6839 LN:113
@SQ SN:hsa-mir-6840 LN:71
@SQ SN:hsa-mir-6841 LN:72
@SQ SN:hsa-mir-6842 LN:65
@SQ SN:hsa-mir-6843 LN:151
@SQ SN:hsa-mir-6844 LN:62
@SQ SN:hsa-mir-6845 LN:61
@SQ SN:hsa-mir-6846 LN:60
@SQ SN:hsa-mir-6847 LN:69
@SQ SN:hsa-mir-6848 LN:70
@SQ SN:hsa-mir-6849 LN:69
@SQ SN:hsa-mir-6850 LN:61
@SQ SN:hsa-mir-6851 LN:67
@SQ SN:hsa-mir-6852 LN:66
@SQ SN:hsa-mir-6853 LN:74
@SQ SN:hsa-mir-6854 LN:69
@SQ SN:hsa-mir-6855 LN:67
@SQ SN:hsa-mir-6856 LN:67
@SQ SN:hsa-mir-6857 LN:93
@SQ SN:hsa-mir-6858 LN:67
@SQ SN:hsa-mir-6859-1 LN:68
@SQ SN:hsa-mir-6769b LN:62
@SQ SN:hsa-mir-6860 LN:66
@SQ SN:hsa-mir-6861 LN:64
@SQ SN:hsa-mir-6862-1 LN:70
@SQ SN:hsa-mir-6863 LN:90
@SQ SN:hsa-mir-6864 LN:70
@SQ SN:hsa-mir-6865 LN:65
@SQ SN:hsa-mir-6866 LN:69
@SQ SN:hsa-mir-6867 LN:67
@SQ SN:hsa-mir-6868 LN:58
@SQ SN:hsa-mir-6869 LN:62
@SQ SN:hsa-mir-6870 LN:60
@SQ SN:hsa-mir-6871 LN:56
@SQ SN:hsa-mir-6872 LN:62
@SQ SN:hsa-mir-6873 LN:63
@SQ SN:hsa-mir-6874 LN:71
@SQ SN:hsa-mir-6875 LN:72
@SQ SN:hsa-mir-6876 LN:73
@SQ SN:hsa-mir-6877 LN:64
@SQ SN:hsa-mir-6878 LN:66
@SQ SN:hsa-mir-6879 LN:66
@SQ SN:hsa-mir-6880 LN:62
@SQ SN:hsa-mir-6881 LN:76
@SQ SN:hsa-mir-6882 LN:66
@SQ SN:hsa-mir-6883 LN:78
@SQ SN:hsa-mir-6884 LN:78
@SQ SN:hsa-mir-6885 LN:66
@SQ SN:hsa-mir-6886 LN:61
@SQ SN:hsa-mir-6887 LN:65
@SQ SN:hsa-mir-6888 LN:67
@SQ SN:hsa-mir-6889 LN:59
@SQ SN:hsa-mir-6890 LN:61
@SQ SN:hsa-mir-6891 LN:93
@SQ SN:hsa-mir-6892 LN:115
@SQ SN:hsa-mir-6893 LN:69
@SQ SN:hsa-mir-6894 LN:57
@SQ SN:hsa-mir-6895 LN:78
@SQ SN:hsa-mir-7106 LN:65
@SQ SN:hsa-mir-7107 LN:80
@SQ SN:hsa-mir-7108 LN:87
@SQ SN:hsa-mir-7109 LN:65
@SQ SN:hsa-mir-7110 LN:86
@SQ SN:hsa-mir-7111 LN:72
@SQ SN:hsa-mir-7112 LN:65
@SQ SN:hsa-mir-7113 LN:59
@SQ SN:hsa-mir-7114 LN:61
@SQ SN:hsa-mir-6511b-2 LN:71
@SQ SN:hsa-mir-3690-2 LN:75
@SQ SN:hsa-mir-6089-2 LN:64
@SQ SN:hsa-mir-6511a-2 LN:67
@SQ SN:hsa-mir-6511a-3 LN:67
@SQ SN:hsa-mir-6511a-4 LN:67
@SQ SN:hsa-mir-7150 LN:94
@SQ SN:hsa-mir-7151 LN:60
@SQ SN:hsa-mir-7152 LN:54
@SQ SN:hsa-mir-7153 LN:57
@SQ SN:hsa-mir-7154 LN:73
@SQ SN:hsa-mir-7155 LN:56
@SQ SN:hsa-mir-7156 LN:60
@SQ SN:hsa-mir-7157 LN:60
@SQ SN:hsa-mir-7158 LN:71
@SQ SN:hsa-mir-7161 LN:84
@SQ SN:hsa-mir-7159 LN:66
@SQ SN:hsa-mir-7160 LN:52
@SQ SN:hsa-mir-486-2 LN:64
@SQ SN:hsa-mir-7162 LN:69
@SQ SN:hsa-mir-7515 LN:67
@SQ SN:hsa-mir-7641-1 LN:61
@SQ SN:hsa-mir-7641-2 LN:53
@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_1d_x2 0 hsa-let-7a-1 6 255 1D17M * 0 0 AGAGGTAGTAGGTTGTA AGAGGTAGTAGGTTGTA NM:i:2 MD:Z:^A0T16 mirtop-0.4.23/data/aligments/let7-last1D.sam 0000664 0000000 0000000 00000140654 13547635037 0020540 0 ustar 00root root 0000000 0000000 @SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
@SQ SN:hsa-let-7b LN:83
@SQ SN:hsa-let-7c LN:84
@SQ SN:hsa-let-7d LN:87
@SQ SN:hsa-let-7e LN:79
@SQ SN:hsa-let-7f-1 LN:87
@SQ SN:hsa-let-7f-2 LN:83
@SQ SN:hsa-mir-15a LN:83
@SQ SN:hsa-mir-16-1 LN:89
@SQ SN:hsa-mir-17 LN:84
@SQ SN:hsa-mir-18a LN:71
@SQ SN:hsa-mir-19a LN:82
@SQ SN:hsa-mir-19b-1 LN:87
@SQ SN:hsa-mir-19b-2 LN:96
@SQ SN:hsa-mir-20a LN:71
@SQ SN:hsa-mir-21 LN:72
@SQ SN:hsa-mir-22 LN:85
@SQ SN:hsa-mir-23a LN:73
@SQ SN:hsa-mir-24-1 LN:68
@SQ SN:hsa-mir-24-2 LN:73
@SQ SN:hsa-mir-25 LN:84
@SQ SN:hsa-mir-26a-1 LN:77
@SQ SN:hsa-mir-26b LN:77
@SQ SN:hsa-mir-27a LN:78
@SQ SN:hsa-mir-28 LN:86
@SQ SN:hsa-mir-29a LN:64
@SQ SN:hsa-mir-30a LN:71
@SQ SN:hsa-mir-31 LN:71
@SQ SN:hsa-mir-32 LN:70
@SQ SN:hsa-mir-33a LN:69
@SQ SN:hsa-mir-92a-1 LN:78
@SQ SN:hsa-mir-92a-2 LN:75
@SQ SN:hsa-mir-93 LN:80
@SQ SN:hsa-mir-95 LN:81
@SQ SN:hsa-mir-96 LN:78
@SQ SN:hsa-mir-98 LN:119
@SQ SN:hsa-mir-99a LN:81
@SQ SN:hsa-mir-100 LN:80
@SQ SN:hsa-mir-101-1 LN:75
@SQ SN:hsa-mir-29b-1 LN:81
@SQ SN:hsa-mir-29b-2 LN:81
@SQ SN:hsa-mir-103a-2 LN:78
@SQ SN:hsa-mir-103a-1 LN:78
@SQ SN:hsa-mir-105-1 LN:81
@SQ SN:hsa-mir-105-2 LN:81
@SQ SN:hsa-mir-106a LN:81
@SQ SN:hsa-mir-107 LN:81
@SQ SN:hsa-mir-16-2 LN:81
@SQ SN:hsa-mir-192 LN:110
@SQ SN:hsa-mir-196a-1 LN:70
@SQ SN:hsa-mir-197 LN:75
@SQ SN:hsa-mir-198 LN:62
@SQ SN:hsa-mir-199a-1 LN:71
@SQ SN:hsa-mir-208a LN:71
@SQ SN:hsa-mir-129-1 LN:72
@SQ SN:hsa-mir-148a LN:68
@SQ SN:hsa-mir-30c-2 LN:72
@SQ SN:hsa-mir-30d LN:70
@SQ SN:hsa-mir-139 LN:68
@SQ SN:hsa-mir-147a LN:72
@SQ SN:hsa-mir-7-1 LN:110
@SQ SN:hsa-mir-7-2 LN:110
@SQ SN:hsa-mir-7-3 LN:110
@SQ SN:hsa-mir-10a LN:110
@SQ SN:hsa-mir-10b LN:110
@SQ SN:hsa-mir-34a LN:110
@SQ SN:hsa-mir-181a-2 LN:110
@SQ SN:hsa-mir-181b-1 LN:110
@SQ SN:hsa-mir-181c LN:110
@SQ SN:hsa-mir-182 LN:110
@SQ SN:hsa-mir-183 LN:110
@SQ SN:hsa-mir-187 LN:109
@SQ SN:hsa-mir-196a-2 LN:110
@SQ SN:hsa-mir-199a-2 LN:110
@SQ SN:hsa-mir-199b LN:110
@SQ SN:hsa-mir-203a LN:110
@SQ SN:hsa-mir-204 LN:110
@SQ SN:hsa-mir-205 LN:110
@SQ SN:hsa-mir-210 LN:110
@SQ SN:hsa-mir-211 LN:110
@SQ SN:hsa-mir-212 LN:110
@SQ SN:hsa-mir-181a-1 LN:110
@SQ SN:hsa-mir-214 LN:110
@SQ SN:hsa-mir-215 LN:110
@SQ SN:hsa-mir-216a LN:110
@SQ SN:hsa-mir-217 LN:110
@SQ SN:hsa-mir-218-1 LN:110
@SQ SN:hsa-mir-218-2 LN:110
@SQ SN:hsa-mir-219a-1 LN:110
@SQ SN:hsa-mir-221 LN:110
@SQ SN:hsa-mir-222 LN:110
@SQ SN:hsa-mir-223 LN:110
@SQ SN:hsa-mir-224 LN:81
@SQ SN:hsa-mir-200b LN:95
@SQ SN:hsa-let-7g LN:84
@SQ SN:hsa-let-7i LN:84
@SQ SN:hsa-mir-1-2 LN:85
@SQ SN:hsa-mir-15b LN:98
@SQ SN:hsa-mir-23b LN:97
@SQ SN:hsa-mir-27b LN:97
@SQ SN:hsa-mir-30b LN:88
@SQ SN:hsa-mir-122 LN:85
@SQ SN:hsa-mir-124-1 LN:85
@SQ SN:hsa-mir-124-2 LN:109
@SQ SN:hsa-mir-124-3 LN:87
@SQ SN:hsa-mir-125b-1 LN:88
@SQ SN:hsa-mir-128-1 LN:82
@SQ SN:hsa-mir-130a LN:89
@SQ SN:hsa-mir-132 LN:101
@SQ SN:hsa-mir-133a-1 LN:88
@SQ SN:hsa-mir-133a-2 LN:102
@SQ SN:hsa-mir-135a-1 LN:90
@SQ SN:hsa-mir-135a-2 LN:100
@SQ SN:hsa-mir-137 LN:102
@SQ SN:hsa-mir-138-2 LN:84
@SQ SN:hsa-mir-140 LN:100
@SQ SN:hsa-mir-141 LN:95
@SQ SN:hsa-mir-142 LN:87
@SQ SN:hsa-mir-143 LN:106
@SQ SN:hsa-mir-144 LN:86
@SQ SN:hsa-mir-145 LN:88
@SQ SN:hsa-mir-152 LN:87
@SQ SN:hsa-mir-153-1 LN:90
@SQ SN:hsa-mir-153-2 LN:87
@SQ SN:hsa-mir-191 LN:92
@SQ SN:hsa-mir-9-1 LN:89
@SQ SN:hsa-mir-9-2 LN:87
@SQ SN:hsa-mir-9-3 LN:90
@SQ SN:hsa-mir-125a LN:86
@SQ SN:hsa-mir-125b-2 LN:89
@SQ SN:hsa-mir-126 LN:85
@SQ SN:hsa-mir-127 LN:97
@SQ SN:hsa-mir-129-2 LN:90
@SQ SN:hsa-mir-134 LN:73
@SQ SN:hsa-mir-136 LN:82
@SQ SN:hsa-mir-138-1 LN:99
@SQ SN:hsa-mir-146a LN:99
@SQ SN:hsa-mir-149 LN:89
@SQ SN:hsa-mir-150 LN:84
@SQ SN:hsa-mir-154 LN:84
@SQ SN:hsa-mir-184 LN:84
@SQ SN:hsa-mir-185 LN:82
@SQ SN:hsa-mir-186 LN:86
@SQ SN:hsa-mir-188 LN:86
@SQ SN:hsa-mir-190a LN:85
@SQ SN:hsa-mir-193a LN:88
@SQ SN:hsa-mir-194-1 LN:85
@SQ SN:hsa-mir-195 LN:87
@SQ SN:hsa-mir-206 LN:86
@SQ SN:hsa-mir-320a LN:82
@SQ SN:hsa-mir-200c LN:68
@SQ SN:hsa-mir-1-1 LN:71
@SQ SN:hsa-mir-155 LN:65
@SQ SN:hsa-mir-181b-2 LN:89
@SQ SN:hsa-mir-128-2 LN:84
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@SQ SN:hsa-mir-367 LN:68
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@SQ SN:hsa-mir-377 LN:69
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@SQ SN:hsa-mir-448 LN:111
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@SQ SN:hsa-mir-431 LN:114
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@SQ SN:hsa-mir-409 LN:79
@SQ SN:hsa-mir-412 LN:91
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@SQ SN:hsa-mir-483 LN:76
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@SQ SN:hsa-mir-490 LN:128
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@SQ SN:hsa-mir-202 LN:110
@SQ SN:hsa-mir-492 LN:116
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@SQ SN:hsa-mir-496 LN:102
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@SQ SN:hsa-mir-497 LN:112
@SQ SN:hsa-mir-181d LN:137
@SQ SN:hsa-mir-512-1 LN:84
@SQ SN:hsa-mir-512-2 LN:98
@SQ SN:hsa-mir-498 LN:124
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@SQ SN:hsa-mir-519b LN:81
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@SQ SN:hsa-mir-523 LN:87
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@SQ SN:hsa-mir-520c LN:87
@SQ SN:hsa-mir-518c LN:101
@SQ SN:hsa-mir-524 LN:87
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@SQ SN:hsa-mir-519d LN:88
@SQ SN:hsa-mir-521-2 LN:87
@SQ SN:hsa-mir-520d LN:87
@SQ SN:hsa-mir-517b LN:67
@SQ SN:hsa-mir-520g LN:90
@SQ SN:hsa-mir-516b-2 LN:85
@SQ SN:hsa-mir-526a-2 LN:65
@SQ SN:hsa-mir-518e LN:88
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@SQ SN:hsa-mir-516b-1 LN:90
@SQ SN:hsa-mir-518a-2 LN:87
@SQ SN:hsa-mir-517c LN:95
@SQ SN:hsa-mir-520h LN:88
@SQ SN:hsa-mir-521-1 LN:87
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@SQ SN:hsa-mir-519a-1 LN:85
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@SQ SN:hsa-mir-516a-1 LN:90
@SQ SN:hsa-mir-516a-2 LN:90
@SQ SN:hsa-mir-519a-2 LN:87
@SQ SN:hsa-mir-499a LN:122
@SQ SN:hsa-mir-500a LN:84
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@SQ SN:hsa-mir-502 LN:86
@SQ SN:hsa-mir-450a-2 LN:100
@SQ SN:hsa-mir-503 LN:71
@SQ SN:hsa-mir-504 LN:83
@SQ SN:hsa-mir-505 LN:84
@SQ SN:hsa-mir-513a-1 LN:129
@SQ SN:hsa-mir-513a-2 LN:127
@SQ SN:hsa-mir-506 LN:124
@SQ SN:hsa-mir-507 LN:94
@SQ SN:hsa-mir-508 LN:115
@SQ SN:hsa-mir-509-1 LN:94
@SQ SN:hsa-mir-510 LN:74
@SQ SN:hsa-mir-514a-1 LN:98
@SQ SN:hsa-mir-514a-2 LN:88
@SQ SN:hsa-mir-514a-3 LN:88
@SQ SN:hsa-mir-532 LN:91
@SQ SN:hsa-mir-455 LN:96
@SQ SN:hsa-mir-539 LN:78
@SQ SN:hsa-mir-544a LN:91
@SQ SN:hsa-mir-545 LN:106
@SQ SN:hsa-mir-376a-2 LN:80
@SQ SN:hsa-mir-487b LN:84
@SQ SN:hsa-mir-551a LN:96
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@SQ SN:hsa-mir-553 LN:68
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@SQ SN:hsa-mir-611 LN:67
@SQ SN:hsa-mir-612 LN:100
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@SQ SN:hsa-mir-614 LN:90
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@SQ SN:hsa-mir-661 LN:89
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@SQ SN:hsa-mir-758 LN:88
@SQ SN:hsa-mir-1264 LN:69
@SQ SN:hsa-mir-671 LN:118
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@SQ SN:hsa-mir-550a-3 LN:95
@SQ SN:hsa-mir-767 LN:109
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@SQ SN:hsa-mir-320b-1 LN:79
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@SQ SN:hsa-mir-454 LN:115
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@SQ SN:hsa-mir-320b-2 LN:138
@SQ SN:hsa-mir-378d-2 LN:98
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@SQ SN:hsa-mir-762 LN:83
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@SQ SN:hsa-mir-761 LN:59
@SQ SN:hsa-mir-764 LN:85
@SQ SN:hsa-mir-759 LN:91
@SQ SN:hsa-mir-765 LN:114
@SQ SN:hsa-mir-770 LN:98
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@SQ SN:hsa-mir-298 LN:88
@SQ SN:hsa-mir-891a LN:79
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@SQ SN:hsa-mir-892a LN:75
@SQ SN:hsa-mir-509-2 LN:91
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@SQ SN:hsa-mir-297 LN:66
@SQ SN:hsa-mir-1178 LN:91
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@SQ SN:hsa-mir-1234 LN:80
@SQ SN:hsa-mir-1236 LN:102
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@SQ SN:hsa-mir-1204 LN:67
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@SQ SN:hsa-mir-1285-2 LN:88
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@SQ SN:hsa-mir-1289-1 LN:144
@SQ SN:hsa-mir-1289-2 LN:111
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@SQ SN:hsa-mir-1302-1 LN:143
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@SQ SN:hsa-mir-1469 LN:47
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@SQ SN:hsa-mir-1972-1 LN:77
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@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-2392 LN:84
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@SQ SN:hsa-mir-6807 LN:92
@SQ SN:hsa-mir-6808 LN:59
@SQ SN:hsa-mir-6809 LN:116
@SQ SN:hsa-mir-6810 LN:70
@SQ SN:hsa-mir-6811 LN:58
@SQ SN:hsa-mir-6812 LN:64
@SQ SN:hsa-mir-6813 LN:56
@SQ SN:hsa-mir-6814 LN:70
@SQ SN:hsa-mir-6815 LN:61
@SQ SN:hsa-mir-6816 LN:66
@SQ SN:hsa-mir-6817 LN:66
@SQ SN:hsa-mir-6818 LN:65
@SQ SN:hsa-mir-6819 LN:61
@SQ SN:hsa-mir-6820 LN:62
@SQ SN:hsa-mir-6821 LN:74
@SQ SN:hsa-mir-6822 LN:61
@SQ SN:hsa-mir-6823 LN:61
@SQ SN:hsa-mir-6824 LN:63
@SQ SN:hsa-mir-6825 LN:66
@SQ SN:hsa-mir-6826 LN:98
@SQ SN:hsa-mir-6827 LN:59
@SQ SN:hsa-mir-6828 LN:60
@SQ SN:hsa-mir-6829 LN:67
@SQ SN:hsa-mir-6830 LN:70
@SQ SN:hsa-mir-6831 LN:81
@SQ SN:hsa-mir-6832 LN:72
@SQ SN:hsa-mir-6833 LN:61
@SQ SN:hsa-mir-6834 LN:81
@SQ SN:hsa-mir-6835 LN:64
@SQ SN:hsa-mir-6780b LN:79
@SQ SN:hsa-mir-6836 LN:63
@SQ SN:hsa-mir-6837 LN:64
@SQ SN:hsa-mir-6838 LN:56
@SQ SN:hsa-mir-6839 LN:113
@SQ SN:hsa-mir-6840 LN:71
@SQ SN:hsa-mir-6841 LN:72
@SQ SN:hsa-mir-6842 LN:65
@SQ SN:hsa-mir-6843 LN:151
@SQ SN:hsa-mir-6844 LN:62
@SQ SN:hsa-mir-6845 LN:61
@SQ SN:hsa-mir-6846 LN:60
@SQ SN:hsa-mir-6847 LN:69
@SQ SN:hsa-mir-6848 LN:70
@SQ SN:hsa-mir-6849 LN:69
@SQ SN:hsa-mir-6850 LN:61
@SQ SN:hsa-mir-6851 LN:67
@SQ SN:hsa-mir-6852 LN:66
@SQ SN:hsa-mir-6853 LN:74
@SQ SN:hsa-mir-6854 LN:69
@SQ SN:hsa-mir-6855 LN:67
@SQ SN:hsa-mir-6856 LN:67
@SQ SN:hsa-mir-6857 LN:93
@SQ SN:hsa-mir-6858 LN:67
@SQ SN:hsa-mir-6859-1 LN:68
@SQ SN:hsa-mir-6769b LN:62
@SQ SN:hsa-mir-6860 LN:66
@SQ SN:hsa-mir-6861 LN:64
@SQ SN:hsa-mir-6862-1 LN:70
@SQ SN:hsa-mir-6863 LN:90
@SQ SN:hsa-mir-6864 LN:70
@SQ SN:hsa-mir-6865 LN:65
@SQ SN:hsa-mir-6866 LN:69
@SQ SN:hsa-mir-6867 LN:67
@SQ SN:hsa-mir-6868 LN:58
@SQ SN:hsa-mir-6869 LN:62
@SQ SN:hsa-mir-6870 LN:60
@SQ SN:hsa-mir-6871 LN:56
@SQ SN:hsa-mir-6872 LN:62
@SQ SN:hsa-mir-6873 LN:63
@SQ SN:hsa-mir-6874 LN:71
@SQ SN:hsa-mir-6875 LN:72
@SQ SN:hsa-mir-6876 LN:73
@SQ SN:hsa-mir-6877 LN:64
@SQ SN:hsa-mir-6878 LN:66
@SQ SN:hsa-mir-6879 LN:66
@SQ SN:hsa-mir-6880 LN:62
@SQ SN:hsa-mir-6881 LN:76
@SQ SN:hsa-mir-6882 LN:66
@SQ SN:hsa-mir-6883 LN:78
@SQ SN:hsa-mir-6884 LN:78
@SQ SN:hsa-mir-6885 LN:66
@SQ SN:hsa-mir-6886 LN:61
@SQ SN:hsa-mir-6887 LN:65
@SQ SN:hsa-mir-6888 LN:67
@SQ SN:hsa-mir-6889 LN:59
@SQ SN:hsa-mir-6890 LN:61
@SQ SN:hsa-mir-6891 LN:93
@SQ SN:hsa-mir-6892 LN:115
@SQ SN:hsa-mir-6893 LN:69
@SQ SN:hsa-mir-6894 LN:57
@SQ SN:hsa-mir-6895 LN:78
@SQ SN:hsa-mir-7106 LN:65
@SQ SN:hsa-mir-7107 LN:80
@SQ SN:hsa-mir-7108 LN:87
@SQ SN:hsa-mir-7109 LN:65
@SQ SN:hsa-mir-7110 LN:86
@SQ SN:hsa-mir-7111 LN:72
@SQ SN:hsa-mir-7112 LN:65
@SQ SN:hsa-mir-7113 LN:59
@SQ SN:hsa-mir-7114 LN:61
@SQ SN:hsa-mir-6511b-2 LN:71
@SQ SN:hsa-mir-3690-2 LN:75
@SQ SN:hsa-mir-6089-2 LN:64
@SQ SN:hsa-mir-6511a-2 LN:67
@SQ SN:hsa-mir-6511a-3 LN:67
@SQ SN:hsa-mir-6511a-4 LN:67
@SQ SN:hsa-mir-7150 LN:94
@SQ SN:hsa-mir-7151 LN:60
@SQ SN:hsa-mir-7152 LN:54
@SQ SN:hsa-mir-7153 LN:57
@SQ SN:hsa-mir-7154 LN:73
@SQ SN:hsa-mir-7155 LN:56
@SQ SN:hsa-mir-7156 LN:60
@SQ SN:hsa-mir-7157 LN:60
@SQ SN:hsa-mir-7158 LN:71
@SQ SN:hsa-mir-7161 LN:84
@SQ SN:hsa-mir-7159 LN:66
@SQ SN:hsa-mir-7160 LN:52
@SQ SN:hsa-mir-486-2 LN:64
@SQ SN:hsa-mir-7162 LN:69
@SQ SN:hsa-mir-7515 LN:67
@SQ SN:hsa-mir-7641-1 LN:61
@SQ SN:hsa-mir-7641-2 LN:53
@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_1GTaT_x2 0 hsa-let-7a-1 57 255 22M1D * 0 0 CGATACAATCTACTGTCTTTCT BBBBBBBBBBBBBBBBBBBBBB NM:i:2 MD:Z:1T19C^T
seq_1GTaT_x2 256 hsa-let-7a-3 52 255 22M1D * 0 0 * * NM:i:2 MD:Z:1T19C^T
mirtop-0.4.23/data/aligments/let7-last7M1I.sam 0000664 0000000 0000000 00000140544 13547635037 0020747 0 ustar 00root root 0000000 0000000 @SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
@SQ SN:hsa-let-7b LN:83
@SQ SN:hsa-let-7c LN:84
@SQ SN:hsa-let-7d LN:87
@SQ SN:hsa-let-7e LN:79
@SQ SN:hsa-let-7f-1 LN:87
@SQ SN:hsa-let-7f-2 LN:83
@SQ SN:hsa-mir-15a LN:83
@SQ SN:hsa-mir-16-1 LN:89
@SQ SN:hsa-mir-17 LN:84
@SQ SN:hsa-mir-18a LN:71
@SQ SN:hsa-mir-19a LN:82
@SQ SN:hsa-mir-19b-1 LN:87
@SQ SN:hsa-mir-19b-2 LN:96
@SQ SN:hsa-mir-20a LN:71
@SQ SN:hsa-mir-21 LN:72
@SQ SN:hsa-mir-22 LN:85
@SQ SN:hsa-mir-23a LN:73
@SQ SN:hsa-mir-24-1 LN:68
@SQ SN:hsa-mir-24-2 LN:73
@SQ SN:hsa-mir-25 LN:84
@SQ SN:hsa-mir-26a-1 LN:77
@SQ SN:hsa-mir-26b LN:77
@SQ SN:hsa-mir-27a LN:78
@SQ SN:hsa-mir-28 LN:86
@SQ SN:hsa-mir-29a LN:64
@SQ SN:hsa-mir-30a LN:71
@SQ SN:hsa-mir-31 LN:71
@SQ SN:hsa-mir-32 LN:70
@SQ SN:hsa-mir-33a LN:69
@SQ SN:hsa-mir-92a-1 LN:78
@SQ SN:hsa-mir-92a-2 LN:75
@SQ SN:hsa-mir-93 LN:80
@SQ SN:hsa-mir-95 LN:81
@SQ SN:hsa-mir-96 LN:78
@SQ SN:hsa-mir-98 LN:119
@SQ SN:hsa-mir-99a LN:81
@SQ SN:hsa-mir-100 LN:80
@SQ SN:hsa-mir-101-1 LN:75
@SQ SN:hsa-mir-29b-1 LN:81
@SQ SN:hsa-mir-29b-2 LN:81
@SQ SN:hsa-mir-103a-2 LN:78
@SQ SN:hsa-mir-103a-1 LN:78
@SQ SN:hsa-mir-105-1 LN:81
@SQ SN:hsa-mir-105-2 LN:81
@SQ SN:hsa-mir-106a LN:81
@SQ SN:hsa-mir-107 LN:81
@SQ SN:hsa-mir-16-2 LN:81
@SQ SN:hsa-mir-192 LN:110
@SQ SN:hsa-mir-196a-1 LN:70
@SQ SN:hsa-mir-197 LN:75
@SQ SN:hsa-mir-198 LN:62
@SQ SN:hsa-mir-199a-1 LN:71
@SQ SN:hsa-mir-208a LN:71
@SQ SN:hsa-mir-129-1 LN:72
@SQ SN:hsa-mir-148a LN:68
@SQ SN:hsa-mir-30c-2 LN:72
@SQ SN:hsa-mir-30d LN:70
@SQ SN:hsa-mir-139 LN:68
@SQ SN:hsa-mir-147a LN:72
@SQ SN:hsa-mir-7-1 LN:110
@SQ SN:hsa-mir-7-2 LN:110
@SQ SN:hsa-mir-7-3 LN:110
@SQ SN:hsa-mir-10a LN:110
@SQ SN:hsa-mir-10b LN:110
@SQ SN:hsa-mir-34a LN:110
@SQ SN:hsa-mir-181a-2 LN:110
@SQ SN:hsa-mir-181b-1 LN:110
@SQ SN:hsa-mir-181c LN:110
@SQ SN:hsa-mir-182 LN:110
@SQ SN:hsa-mir-183 LN:110
@SQ SN:hsa-mir-187 LN:109
@SQ SN:hsa-mir-196a-2 LN:110
@SQ SN:hsa-mir-199a-2 LN:110
@SQ SN:hsa-mir-199b LN:110
@SQ SN:hsa-mir-203a LN:110
@SQ SN:hsa-mir-204 LN:110
@SQ SN:hsa-mir-205 LN:110
@SQ SN:hsa-mir-210 LN:110
@SQ SN:hsa-mir-211 LN:110
@SQ SN:hsa-mir-212 LN:110
@SQ SN:hsa-mir-181a-1 LN:110
@SQ SN:hsa-mir-214 LN:110
@SQ SN:hsa-mir-215 LN:110
@SQ SN:hsa-mir-216a LN:110
@SQ SN:hsa-mir-217 LN:110
@SQ SN:hsa-mir-218-1 LN:110
@SQ SN:hsa-mir-218-2 LN:110
@SQ SN:hsa-mir-219a-1 LN:110
@SQ SN:hsa-mir-221 LN:110
@SQ SN:hsa-mir-222 LN:110
@SQ SN:hsa-mir-223 LN:110
@SQ SN:hsa-mir-224 LN:81
@SQ SN:hsa-mir-200b LN:95
@SQ SN:hsa-let-7g LN:84
@SQ SN:hsa-let-7i LN:84
@SQ SN:hsa-mir-1-2 LN:85
@SQ SN:hsa-mir-15b LN:98
@SQ SN:hsa-mir-23b LN:97
@SQ SN:hsa-mir-27b LN:97
@SQ SN:hsa-mir-30b LN:88
@SQ SN:hsa-mir-122 LN:85
@SQ SN:hsa-mir-124-1 LN:85
@SQ SN:hsa-mir-124-2 LN:109
@SQ SN:hsa-mir-124-3 LN:87
@SQ SN:hsa-mir-125b-1 LN:88
@SQ SN:hsa-mir-128-1 LN:82
@SQ SN:hsa-mir-130a LN:89
@SQ SN:hsa-mir-132 LN:101
@SQ SN:hsa-mir-133a-1 LN:88
@SQ SN:hsa-mir-133a-2 LN:102
@SQ SN:hsa-mir-135a-1 LN:90
@SQ SN:hsa-mir-135a-2 LN:100
@SQ SN:hsa-mir-137 LN:102
@SQ SN:hsa-mir-138-2 LN:84
@SQ SN:hsa-mir-140 LN:100
@SQ SN:hsa-mir-141 LN:95
@SQ SN:hsa-mir-142 LN:87
@SQ SN:hsa-mir-143 LN:106
@SQ SN:hsa-mir-144 LN:86
@SQ SN:hsa-mir-145 LN:88
@SQ SN:hsa-mir-152 LN:87
@SQ SN:hsa-mir-153-1 LN:90
@SQ SN:hsa-mir-153-2 LN:87
@SQ SN:hsa-mir-191 LN:92
@SQ SN:hsa-mir-9-1 LN:89
@SQ SN:hsa-mir-9-2 LN:87
@SQ SN:hsa-mir-9-3 LN:90
@SQ SN:hsa-mir-125a LN:86
@SQ SN:hsa-mir-125b-2 LN:89
@SQ SN:hsa-mir-126 LN:85
@SQ SN:hsa-mir-127 LN:97
@SQ SN:hsa-mir-129-2 LN:90
@SQ SN:hsa-mir-134 LN:73
@SQ SN:hsa-mir-136 LN:82
@SQ SN:hsa-mir-138-1 LN:99
@SQ SN:hsa-mir-146a LN:99
@SQ SN:hsa-mir-149 LN:89
@SQ SN:hsa-mir-150 LN:84
@SQ SN:hsa-mir-154 LN:84
@SQ SN:hsa-mir-184 LN:84
@SQ SN:hsa-mir-185 LN:82
@SQ SN:hsa-mir-186 LN:86
@SQ SN:hsa-mir-188 LN:86
@SQ SN:hsa-mir-190a LN:85
@SQ SN:hsa-mir-193a LN:88
@SQ SN:hsa-mir-194-1 LN:85
@SQ SN:hsa-mir-195 LN:87
@SQ SN:hsa-mir-206 LN:86
@SQ SN:hsa-mir-320a LN:82
@SQ SN:hsa-mir-200c LN:68
@SQ SN:hsa-mir-1-1 LN:71
@SQ SN:hsa-mir-155 LN:65
@SQ SN:hsa-mir-181b-2 LN:89
@SQ SN:hsa-mir-128-2 LN:84
@SQ SN:hsa-mir-194-2 LN:85
@SQ SN:hsa-mir-106b LN:82
@SQ SN:hsa-mir-29c LN:88
@SQ SN:hsa-mir-30c-1 LN:89
@SQ SN:hsa-mir-200a LN:90
@SQ SN:hsa-mir-302a LN:69
@SQ SN:hsa-mir-101-2 LN:79
@SQ SN:hsa-mir-219a-2 LN:97
@SQ SN:hsa-mir-34b LN:84
@SQ SN:hsa-mir-34c LN:77
@SQ SN:hsa-mir-299 LN:63
@SQ SN:hsa-mir-301a LN:86
@SQ SN:hsa-mir-99b LN:70
@SQ SN:hsa-mir-296 LN:80
@SQ SN:hsa-mir-130b LN:82
@SQ SN:hsa-mir-30e LN:92
@SQ SN:hsa-mir-26a-2 LN:84
@SQ SN:hsa-mir-361 LN:72
@SQ SN:hsa-mir-362 LN:65
@SQ SN:hsa-mir-363 LN:75
@SQ SN:hsa-mir-365a LN:87
@SQ SN:hsa-mir-365b LN:111
@SQ SN:hsa-mir-302b LN:73
@SQ SN:hsa-mir-302c LN:68
@SQ SN:hsa-mir-302d LN:68
@SQ SN:hsa-mir-367 LN:68
@SQ SN:hsa-mir-376c LN:66
@SQ SN:hsa-mir-369 LN:70
@SQ SN:hsa-mir-370 LN:75
@SQ SN:hsa-mir-371a LN:67
@SQ SN:hsa-mir-372 LN:67
@SQ SN:hsa-mir-373 LN:69
@SQ SN:hsa-mir-374a LN:72
@SQ SN:hsa-mir-375 LN:64
@SQ SN:hsa-mir-376a-1 LN:68
@SQ SN:hsa-mir-377 LN:69
@SQ SN:hsa-mir-378a LN:66
@SQ SN:hsa-mir-379 LN:67
@SQ SN:hsa-mir-380 LN:61
@SQ SN:hsa-mir-381 LN:75
@SQ SN:hsa-mir-382 LN:76
@SQ SN:hsa-mir-383 LN:73
@SQ SN:hsa-mir-340 LN:95
@SQ SN:hsa-mir-330 LN:94
@SQ SN:hsa-mir-328 LN:75
@SQ SN:hsa-mir-342 LN:99
@SQ SN:hsa-mir-337 LN:93
@SQ SN:hsa-mir-323a LN:86
@SQ SN:hsa-mir-326 LN:95
@SQ SN:hsa-mir-151a LN:90
@SQ SN:hsa-mir-135b LN:97
@SQ SN:hsa-mir-148b LN:99
@SQ SN:hsa-mir-331 LN:94
@SQ SN:hsa-mir-324 LN:83
@SQ SN:hsa-mir-338 LN:67
@SQ SN:hsa-mir-339 LN:94
@SQ SN:hsa-mir-335 LN:94
@SQ SN:hsa-mir-133b LN:119
@SQ SN:hsa-mir-325 LN:98
@SQ SN:hsa-mir-345 LN:98
@SQ SN:hsa-mir-346 LN:95
@SQ SN:hsa-mir-384 LN:88
@SQ SN:hsa-mir-196b LN:84
@SQ SN:hsa-mir-422a LN:90
@SQ SN:hsa-mir-423 LN:94
@SQ SN:hsa-mir-424 LN:98
@SQ SN:hsa-mir-425 LN:87
@SQ SN:hsa-mir-18b LN:71
@SQ SN:hsa-mir-20b LN:69
@SQ SN:hsa-mir-448 LN:111
@SQ SN:hsa-mir-429 LN:83
@SQ SN:hsa-mir-449a LN:91
@SQ SN:hsa-mir-450a-1 LN:91
@SQ SN:hsa-mir-431 LN:114
@SQ SN:hsa-mir-433 LN:93
@SQ SN:hsa-mir-329-1 LN:80
@SQ SN:hsa-mir-329-2 LN:84
@SQ SN:hsa-mir-451a LN:72
@SQ SN:hsa-mir-452 LN:85
@SQ SN:hsa-mir-409 LN:79
@SQ SN:hsa-mir-412 LN:91
@SQ SN:hsa-mir-410 LN:80
@SQ SN:hsa-mir-376b LN:100
@SQ SN:hsa-mir-483 LN:76
@SQ SN:hsa-mir-484 LN:79
@SQ SN:hsa-mir-485 LN:73
@SQ SN:hsa-mir-486-1 LN:68
@SQ SN:hsa-mir-487a LN:80
@SQ SN:hsa-mir-488 LN:83
@SQ SN:hsa-mir-489 LN:84
@SQ SN:hsa-mir-490 LN:128
@SQ SN:hsa-mir-491 LN:84
@SQ SN:hsa-mir-511 LN:87
@SQ SN:hsa-mir-146b LN:73
@SQ SN:hsa-mir-202 LN:110
@SQ SN:hsa-mir-492 LN:116
@SQ SN:hsa-mir-493 LN:89
@SQ SN:hsa-mir-432 LN:94
@SQ SN:hsa-mir-494 LN:81
@SQ SN:hsa-mir-495 LN:82
@SQ SN:hsa-mir-496 LN:102
@SQ SN:hsa-mir-193b LN:83
@SQ SN:hsa-mir-497 LN:112
@SQ SN:hsa-mir-181d LN:137
@SQ SN:hsa-mir-512-1 LN:84
@SQ SN:hsa-mir-512-2 LN:98
@SQ SN:hsa-mir-498 LN:124
@SQ SN:hsa-mir-520e LN:87
@SQ SN:hsa-mir-515-1 LN:83
@SQ SN:hsa-mir-519e LN:84
@SQ SN:hsa-mir-520f LN:87
@SQ SN:hsa-mir-515-2 LN:83
@SQ SN:hsa-mir-519c LN:87
@SQ SN:hsa-mir-520a LN:85
@SQ SN:hsa-mir-526b LN:83
@SQ SN:hsa-mir-519b LN:81
@SQ SN:hsa-mir-525 LN:85
@SQ SN:hsa-mir-523 LN:87
@SQ SN:hsa-mir-518f LN:87
@SQ SN:hsa-mir-520b LN:61
@SQ SN:hsa-mir-518b LN:83
@SQ SN:hsa-mir-526a-1 LN:85
@SQ SN:hsa-mir-520c LN:87
@SQ SN:hsa-mir-518c LN:101
@SQ SN:hsa-mir-524 LN:87
@SQ SN:hsa-mir-517a LN:87
@SQ SN:hsa-mir-519d LN:88
@SQ SN:hsa-mir-521-2 LN:87
@SQ SN:hsa-mir-520d LN:87
@SQ SN:hsa-mir-517b LN:67
@SQ SN:hsa-mir-520g LN:90
@SQ SN:hsa-mir-516b-2 LN:85
@SQ SN:hsa-mir-526a-2 LN:65
@SQ SN:hsa-mir-518e LN:88
@SQ SN:hsa-mir-518a-1 LN:85
@SQ SN:hsa-mir-518d LN:87
@SQ SN:hsa-mir-516b-1 LN:90
@SQ SN:hsa-mir-518a-2 LN:87
@SQ SN:hsa-mir-517c LN:95
@SQ SN:hsa-mir-520h LN:88
@SQ SN:hsa-mir-521-1 LN:87
@SQ SN:hsa-mir-522 LN:87
@SQ SN:hsa-mir-519a-1 LN:85
@SQ SN:hsa-mir-527 LN:85
@SQ SN:hsa-mir-516a-1 LN:90
@SQ SN:hsa-mir-516a-2 LN:90
@SQ SN:hsa-mir-519a-2 LN:87
@SQ SN:hsa-mir-499a LN:122
@SQ SN:hsa-mir-500a LN:84
@SQ SN:hsa-mir-501 LN:84
@SQ SN:hsa-mir-502 LN:86
@SQ SN:hsa-mir-450a-2 LN:100
@SQ SN:hsa-mir-503 LN:71
@SQ SN:hsa-mir-504 LN:83
@SQ SN:hsa-mir-505 LN:84
@SQ SN:hsa-mir-513a-1 LN:129
@SQ SN:hsa-mir-513a-2 LN:127
@SQ SN:hsa-mir-506 LN:124
@SQ SN:hsa-mir-507 LN:94
@SQ SN:hsa-mir-508 LN:115
@SQ SN:hsa-mir-509-1 LN:94
@SQ SN:hsa-mir-510 LN:74
@SQ SN:hsa-mir-514a-1 LN:98
@SQ SN:hsa-mir-514a-2 LN:88
@SQ SN:hsa-mir-514a-3 LN:88
@SQ SN:hsa-mir-532 LN:91
@SQ SN:hsa-mir-455 LN:96
@SQ SN:hsa-mir-539 LN:78
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@SQ SN:hsa-mir-545 LN:106
@SQ SN:hsa-mir-376a-2 LN:80
@SQ SN:hsa-mir-487b LN:84
@SQ SN:hsa-mir-551a LN:96
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@SQ SN:hsa-mir-553 LN:68
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@SQ SN:hsa-mir-593 LN:100
@SQ SN:hsa-mir-595 LN:96
@SQ SN:hsa-mir-596 LN:77
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@SQ SN:hsa-mir-611 LN:67
@SQ SN:hsa-mir-612 LN:100
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@SQ SN:hsa-mir-614 LN:90
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@SQ SN:hsa-mir-628 LN:95
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@SQ SN:hsa-mir-631 LN:75
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@SQ SN:hsa-mir-661 LN:89
@SQ SN:hsa-mir-662 LN:95
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@SQ SN:hsa-mir-653 LN:96
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@SQ SN:hsa-mir-654 LN:81
@SQ SN:hsa-mir-655 LN:97
@SQ SN:hsa-mir-656 LN:78
@SQ SN:hsa-mir-549a LN:96
@SQ SN:hsa-mir-657 LN:98
@SQ SN:hsa-mir-658 LN:100
@SQ SN:hsa-mir-659 LN:97
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@SQ SN:hsa-mir-421 LN:85
@SQ SN:hsa-mir-542 LN:97
@SQ SN:hsa-mir-758 LN:88
@SQ SN:hsa-mir-1264 LN:69
@SQ SN:hsa-mir-671 LN:118
@SQ SN:hsa-mir-668 LN:66
@SQ SN:hsa-mir-550a-3 LN:95
@SQ SN:hsa-mir-767 LN:109
@SQ SN:hsa-mir-1224 LN:85
@SQ SN:hsa-mir-151b LN:96
@SQ SN:hsa-mir-320b-1 LN:79
@SQ SN:hsa-mir-320c-1 LN:88
@SQ SN:hsa-mir-1296 LN:92
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@SQ SN:hsa-mir-1323 LN:73
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@SQ SN:hsa-mir-1301 LN:82
@SQ SN:hsa-mir-454 LN:115
@SQ SN:hsa-mir-1185-2 LN:86
@SQ SN:hsa-mir-449c LN:92
@SQ SN:hsa-mir-1283-1 LN:87
@SQ SN:hsa-mir-769 LN:118
@SQ SN:hsa-mir-766 LN:111
@SQ SN:hsa-mir-320b-2 LN:138
@SQ SN:hsa-mir-378d-2 LN:98
@SQ SN:hsa-mir-1185-1 LN:86
@SQ SN:hsa-mir-762 LN:83
@SQ SN:hsa-mir-802 LN:94
@SQ SN:hsa-mir-670 LN:98
@SQ SN:hsa-mir-1298 LN:112
@SQ SN:hsa-mir-2113 LN:91
@SQ SN:hsa-mir-761 LN:59
@SQ SN:hsa-mir-764 LN:85
@SQ SN:hsa-mir-759 LN:91
@SQ SN:hsa-mir-765 LN:114
@SQ SN:hsa-mir-770 LN:98
@SQ SN:hsa-mir-675 LN:73
@SQ SN:hsa-mir-298 LN:88
@SQ SN:hsa-mir-891a LN:79
@SQ SN:hsa-mir-300 LN:83
@SQ SN:hsa-mir-892a LN:75
@SQ SN:hsa-mir-509-2 LN:91
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@SQ SN:hsa-mir-874 LN:78
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@SQ SN:hsa-mir-744 LN:98
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@SQ SN:hsa-mir-665 LN:72
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@SQ SN:hsa-mir-760 LN:80
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@SQ SN:hsa-mir-940 LN:94
@SQ SN:hsa-mir-941-1 LN:72
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@SQ SN:hsa-mir-297 LN:66
@SQ SN:hsa-mir-1178 LN:91
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@SQ SN:hsa-mir-1184-1 LN:99
@SQ SN:hsa-mir-1225 LN:90
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@SQ SN:hsa-mir-1231 LN:92
@SQ SN:hsa-mir-1233-1 LN:82
@SQ SN:hsa-mir-1234 LN:80
@SQ SN:hsa-mir-1236 LN:102
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@SQ SN:hsa-mir-1238 LN:83
@SQ SN:hsa-mir-1200 LN:76
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@SQ SN:hsa-mir-1203 LN:85
@SQ SN:hsa-mir-663b LN:115
@SQ SN:hsa-mir-1204 LN:67
@SQ SN:hsa-mir-1205 LN:63
@SQ SN:hsa-mir-1206 LN:59
@SQ SN:hsa-mir-1207 LN:87
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@SQ SN:hsa-mir-548e LN:88
@SQ SN:hsa-mir-548j LN:112
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@SQ SN:hsa-mir-1285-2 LN:88
@SQ SN:hsa-mir-1286 LN:78
@SQ SN:hsa-mir-1287 LN:90
@SQ SN:hsa-mir-1289-1 LN:144
@SQ SN:hsa-mir-1289-2 LN:111
@SQ SN:hsa-mir-1290 LN:78
@SQ SN:hsa-mir-1291 LN:87
@SQ SN:hsa-mir-548k LN:116
@SQ SN:hsa-mir-1293 LN:71
@SQ SN:hsa-mir-1294 LN:142
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@SQ SN:hsa-mir-1302-1 LN:143
@SQ SN:hsa-mir-1302-2 LN:138
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@SQ SN:hsa-mir-1302-4 LN:150
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@SQ SN:hsa-mir-1302-6 LN:90
@SQ SN:hsa-mir-1302-7 LN:72
@SQ SN:hsa-mir-1302-8 LN:128
@SQ SN:hsa-mir-1303 LN:86
@SQ SN:hsa-mir-1304 LN:91
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@SQ SN:hsa-mir-548f-2 LN:98
@SQ SN:hsa-mir-548f-3 LN:87
@SQ SN:hsa-mir-548f-4 LN:105
@SQ SN:hsa-mir-548f-5 LN:86
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@SQ SN:hsa-mir-1247 LN:136
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@SQ SN:hsa-mir-1250 LN:113
@SQ SN:hsa-mir-1251 LN:70
@SQ SN:hsa-mir-1253 LN:105
@SQ SN:hsa-mir-1254-1 LN:97
@SQ SN:hsa-mir-1255a LN:113
@SQ SN:hsa-mir-1256 LN:119
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@SQ SN:hsa-mir-548o LN:114
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@SQ SN:hsa-mir-1272 LN:129
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@SQ SN:hsa-mir-548h-2 LN:88
@SQ SN:hsa-mir-548h-3 LN:118
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@SQ SN:hsa-mir-548i-1 LN:149
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@SQ SN:hsa-mir-548i-3 LN:149
@SQ SN:hsa-mir-548i-4 LN:77
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@SQ SN:hsa-mir-1282 LN:101
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@SQ SN:hsa-mir-1284 LN:120
@SQ SN:hsa-mir-1288 LN:75
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@SQ SN:hsa-mir-664a LN:82
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@SQ SN:hsa-mir-1307 LN:149
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@SQ SN:hsa-mir-1321 LN:79
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@SQ SN:hsa-mir-1972-1 LN:77
@SQ SN:hsa-mir-1973 LN:44
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@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-3176 LN:90
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@SQ SN:hsa-mir-1302-9 LN:138
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@SQ SN:hsa-mir-4699 LN:74
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@SQ SN:hsa-mir-4701 LN:63
@SQ SN:hsa-mir-3198-2 LN:80
@SQ SN:hsa-mir-4703 LN:79
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@SQ SN:hsa-mir-5093 LN:100
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@SQ SN:hsa-mir-5193 LN:109
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@SQ SN:hsa-mir-4436b-2 LN:91
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@SQ SN:hsa-mir-3670-2 LN:65
@SQ SN:hsa-mir-3680-2 LN:87
@SQ SN:hsa-mir-4524b LN:115
@SQ SN:hsa-mir-5571 LN:113
@SQ SN:hsa-mir-5100 LN:119
@SQ SN:hsa-mir-5572 LN:137
@SQ SN:hsa-mir-548aq LN:58
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@SQ SN:hsa-mir-548ax LN:73
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@SQ SN:hsa-mir-5692c-1 LN:91
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@SQ SN:hsa-mir-5689 LN:78
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@SQ SN:hsa-mir-5691 LN:68
@SQ SN:hsa-mir-5692a-1 LN:69
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@SQ SN:hsa-mir-4666b LN:81
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@SQ SN:hsa-mir-1199 LN:119
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@SQ SN:hsa-mir-6076 LN:113
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@SQ SN:hsa-mir-6753 LN:164
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@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_7G-aA_x2 0 hsa-let-7a-1 6 255 7M1I16M * 0 0 TGAGGTAGGTAGGTTGTATAGTTA ________________________ NM:i:2 MD:Z:22T
mirtop-0.4.23/data/aligments/let7-middle1D.sam 0000664 0000000 0000000 00000140537 13547635037 0021033 0 ustar 00root root 0000000 0000000 @SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
@SQ SN:hsa-let-7b LN:83
@SQ SN:hsa-let-7c LN:84
@SQ SN:hsa-let-7d LN:87
@SQ SN:hsa-let-7e LN:79
@SQ SN:hsa-let-7f-1 LN:87
@SQ SN:hsa-let-7f-2 LN:83
@SQ SN:hsa-mir-15a LN:83
@SQ SN:hsa-mir-16-1 LN:89
@SQ SN:hsa-mir-17 LN:84
@SQ SN:hsa-mir-18a LN:71
@SQ SN:hsa-mir-19a LN:82
@SQ SN:hsa-mir-19b-1 LN:87
@SQ SN:hsa-mir-19b-2 LN:96
@SQ SN:hsa-mir-20a LN:71
@SQ SN:hsa-mir-21 LN:72
@SQ SN:hsa-mir-22 LN:85
@SQ SN:hsa-mir-23a LN:73
@SQ SN:hsa-mir-24-1 LN:68
@SQ SN:hsa-mir-24-2 LN:73
@SQ SN:hsa-mir-25 LN:84
@SQ SN:hsa-mir-26a-1 LN:77
@SQ SN:hsa-mir-26b LN:77
@SQ SN:hsa-mir-27a LN:78
@SQ SN:hsa-mir-28 LN:86
@SQ SN:hsa-mir-29a LN:64
@SQ SN:hsa-mir-30a LN:71
@SQ SN:hsa-mir-31 LN:71
@SQ SN:hsa-mir-32 LN:70
@SQ SN:hsa-mir-33a LN:69
@SQ SN:hsa-mir-92a-1 LN:78
@SQ SN:hsa-mir-92a-2 LN:75
@SQ SN:hsa-mir-93 LN:80
@SQ SN:hsa-mir-95 LN:81
@SQ SN:hsa-mir-96 LN:78
@SQ SN:hsa-mir-98 LN:119
@SQ SN:hsa-mir-99a LN:81
@SQ SN:hsa-mir-100 LN:80
@SQ SN:hsa-mir-101-1 LN:75
@SQ SN:hsa-mir-29b-1 LN:81
@SQ SN:hsa-mir-29b-2 LN:81
@SQ SN:hsa-mir-103a-2 LN:78
@SQ SN:hsa-mir-103a-1 LN:78
@SQ SN:hsa-mir-105-1 LN:81
@SQ SN:hsa-mir-105-2 LN:81
@SQ SN:hsa-mir-106a LN:81
@SQ SN:hsa-mir-107 LN:81
@SQ SN:hsa-mir-16-2 LN:81
@SQ SN:hsa-mir-192 LN:110
@SQ SN:hsa-mir-196a-1 LN:70
@SQ SN:hsa-mir-197 LN:75
@SQ SN:hsa-mir-198 LN:62
@SQ SN:hsa-mir-199a-1 LN:71
@SQ SN:hsa-mir-208a LN:71
@SQ SN:hsa-mir-129-1 LN:72
@SQ SN:hsa-mir-148a LN:68
@SQ SN:hsa-mir-30c-2 LN:72
@SQ SN:hsa-mir-30d LN:70
@SQ SN:hsa-mir-139 LN:68
@SQ SN:hsa-mir-147a LN:72
@SQ SN:hsa-mir-7-1 LN:110
@SQ SN:hsa-mir-7-2 LN:110
@SQ SN:hsa-mir-7-3 LN:110
@SQ SN:hsa-mir-10a LN:110
@SQ SN:hsa-mir-10b LN:110
@SQ SN:hsa-mir-34a LN:110
@SQ SN:hsa-mir-181a-2 LN:110
@SQ SN:hsa-mir-181b-1 LN:110
@SQ SN:hsa-mir-181c LN:110
@SQ SN:hsa-mir-182 LN:110
@SQ SN:hsa-mir-183 LN:110
@SQ SN:hsa-mir-187 LN:109
@SQ SN:hsa-mir-196a-2 LN:110
@SQ SN:hsa-mir-199a-2 LN:110
@SQ SN:hsa-mir-199b LN:110
@SQ SN:hsa-mir-203a LN:110
@SQ SN:hsa-mir-204 LN:110
@SQ SN:hsa-mir-205 LN:110
@SQ SN:hsa-mir-210 LN:110
@SQ SN:hsa-mir-211 LN:110
@SQ SN:hsa-mir-212 LN:110
@SQ SN:hsa-mir-181a-1 LN:110
@SQ SN:hsa-mir-214 LN:110
@SQ SN:hsa-mir-215 LN:110
@SQ SN:hsa-mir-216a LN:110
@SQ SN:hsa-mir-217 LN:110
@SQ SN:hsa-mir-218-1 LN:110
@SQ SN:hsa-mir-218-2 LN:110
@SQ SN:hsa-mir-219a-1 LN:110
@SQ SN:hsa-mir-221 LN:110
@SQ SN:hsa-mir-222 LN:110
@SQ SN:hsa-mir-223 LN:110
@SQ SN:hsa-mir-224 LN:81
@SQ SN:hsa-mir-200b LN:95
@SQ SN:hsa-let-7g LN:84
@SQ SN:hsa-let-7i LN:84
@SQ SN:hsa-mir-1-2 LN:85
@SQ SN:hsa-mir-15b LN:98
@SQ SN:hsa-mir-23b LN:97
@SQ SN:hsa-mir-27b LN:97
@SQ SN:hsa-mir-30b LN:88
@SQ SN:hsa-mir-122 LN:85
@SQ SN:hsa-mir-124-1 LN:85
@SQ SN:hsa-mir-124-2 LN:109
@SQ SN:hsa-mir-124-3 LN:87
@SQ SN:hsa-mir-125b-1 LN:88
@SQ SN:hsa-mir-128-1 LN:82
@SQ SN:hsa-mir-130a LN:89
@SQ SN:hsa-mir-132 LN:101
@SQ SN:hsa-mir-133a-1 LN:88
@SQ SN:hsa-mir-133a-2 LN:102
@SQ SN:hsa-mir-135a-1 LN:90
@SQ SN:hsa-mir-135a-2 LN:100
@SQ SN:hsa-mir-137 LN:102
@SQ SN:hsa-mir-138-2 LN:84
@SQ SN:hsa-mir-140 LN:100
@SQ SN:hsa-mir-141 LN:95
@SQ SN:hsa-mir-142 LN:87
@SQ SN:hsa-mir-143 LN:106
@SQ SN:hsa-mir-144 LN:86
@SQ SN:hsa-mir-145 LN:88
@SQ SN:hsa-mir-152 LN:87
@SQ SN:hsa-mir-153-1 LN:90
@SQ SN:hsa-mir-153-2 LN:87
@SQ SN:hsa-mir-191 LN:92
@SQ SN:hsa-mir-9-1 LN:89
@SQ SN:hsa-mir-9-2 LN:87
@SQ SN:hsa-mir-9-3 LN:90
@SQ SN:hsa-mir-125a LN:86
@SQ SN:hsa-mir-125b-2 LN:89
@SQ SN:hsa-mir-126 LN:85
@SQ SN:hsa-mir-127 LN:97
@SQ SN:hsa-mir-129-2 LN:90
@SQ SN:hsa-mir-134 LN:73
@SQ SN:hsa-mir-136 LN:82
@SQ SN:hsa-mir-138-1 LN:99
@SQ SN:hsa-mir-146a LN:99
@SQ SN:hsa-mir-149 LN:89
@SQ SN:hsa-mir-150 LN:84
@SQ SN:hsa-mir-154 LN:84
@SQ SN:hsa-mir-184 LN:84
@SQ SN:hsa-mir-185 LN:82
@SQ SN:hsa-mir-186 LN:86
@SQ SN:hsa-mir-188 LN:86
@SQ SN:hsa-mir-190a LN:85
@SQ SN:hsa-mir-193a LN:88
@SQ SN:hsa-mir-194-1 LN:85
@SQ SN:hsa-mir-195 LN:87
@SQ SN:hsa-mir-206 LN:86
@SQ SN:hsa-mir-320a LN:82
@SQ SN:hsa-mir-200c LN:68
@SQ SN:hsa-mir-1-1 LN:71
@SQ SN:hsa-mir-155 LN:65
@SQ SN:hsa-mir-181b-2 LN:89
@SQ SN:hsa-mir-128-2 LN:84
@SQ SN:hsa-mir-194-2 LN:85
@SQ SN:hsa-mir-106b LN:82
@SQ SN:hsa-mir-29c LN:88
@SQ SN:hsa-mir-30c-1 LN:89
@SQ SN:hsa-mir-200a LN:90
@SQ SN:hsa-mir-302a LN:69
@SQ SN:hsa-mir-101-2 LN:79
@SQ SN:hsa-mir-219a-2 LN:97
@SQ SN:hsa-mir-34b LN:84
@SQ SN:hsa-mir-34c LN:77
@SQ SN:hsa-mir-299 LN:63
@SQ SN:hsa-mir-301a LN:86
@SQ SN:hsa-mir-99b LN:70
@SQ SN:hsa-mir-296 LN:80
@SQ SN:hsa-mir-130b LN:82
@SQ SN:hsa-mir-30e LN:92
@SQ SN:hsa-mir-26a-2 LN:84
@SQ SN:hsa-mir-361 LN:72
@SQ SN:hsa-mir-362 LN:65
@SQ SN:hsa-mir-363 LN:75
@SQ SN:hsa-mir-365a LN:87
@SQ SN:hsa-mir-365b LN:111
@SQ SN:hsa-mir-302b LN:73
@SQ SN:hsa-mir-302c LN:68
@SQ SN:hsa-mir-302d LN:68
@SQ SN:hsa-mir-367 LN:68
@SQ SN:hsa-mir-376c LN:66
@SQ SN:hsa-mir-369 LN:70
@SQ SN:hsa-mir-370 LN:75
@SQ SN:hsa-mir-371a LN:67
@SQ SN:hsa-mir-372 LN:67
@SQ SN:hsa-mir-373 LN:69
@SQ SN:hsa-mir-374a LN:72
@SQ SN:hsa-mir-375 LN:64
@SQ SN:hsa-mir-376a-1 LN:68
@SQ SN:hsa-mir-377 LN:69
@SQ SN:hsa-mir-378a LN:66
@SQ SN:hsa-mir-379 LN:67
@SQ SN:hsa-mir-380 LN:61
@SQ SN:hsa-mir-381 LN:75
@SQ SN:hsa-mir-382 LN:76
@SQ SN:hsa-mir-383 LN:73
@SQ SN:hsa-mir-340 LN:95
@SQ SN:hsa-mir-330 LN:94
@SQ SN:hsa-mir-328 LN:75
@SQ SN:hsa-mir-342 LN:99
@SQ SN:hsa-mir-337 LN:93
@SQ SN:hsa-mir-323a LN:86
@SQ SN:hsa-mir-326 LN:95
@SQ SN:hsa-mir-151a LN:90
@SQ SN:hsa-mir-135b LN:97
@SQ SN:hsa-mir-148b LN:99
@SQ SN:hsa-mir-331 LN:94
@SQ SN:hsa-mir-324 LN:83
@SQ SN:hsa-mir-338 LN:67
@SQ SN:hsa-mir-339 LN:94
@SQ SN:hsa-mir-335 LN:94
@SQ SN:hsa-mir-133b LN:119
@SQ SN:hsa-mir-325 LN:98
@SQ SN:hsa-mir-345 LN:98
@SQ SN:hsa-mir-346 LN:95
@SQ SN:hsa-mir-384 LN:88
@SQ SN:hsa-mir-196b LN:84
@SQ SN:hsa-mir-422a LN:90
@SQ SN:hsa-mir-423 LN:94
@SQ SN:hsa-mir-424 LN:98
@SQ SN:hsa-mir-425 LN:87
@SQ SN:hsa-mir-18b LN:71
@SQ SN:hsa-mir-20b LN:69
@SQ SN:hsa-mir-448 LN:111
@SQ SN:hsa-mir-429 LN:83
@SQ SN:hsa-mir-449a LN:91
@SQ SN:hsa-mir-450a-1 LN:91
@SQ SN:hsa-mir-431 LN:114
@SQ SN:hsa-mir-433 LN:93
@SQ SN:hsa-mir-329-1 LN:80
@SQ SN:hsa-mir-329-2 LN:84
@SQ SN:hsa-mir-451a LN:72
@SQ SN:hsa-mir-452 LN:85
@SQ SN:hsa-mir-409 LN:79
@SQ SN:hsa-mir-412 LN:91
@SQ SN:hsa-mir-410 LN:80
@SQ SN:hsa-mir-376b LN:100
@SQ SN:hsa-mir-483 LN:76
@SQ SN:hsa-mir-484 LN:79
@SQ SN:hsa-mir-485 LN:73
@SQ SN:hsa-mir-486-1 LN:68
@SQ SN:hsa-mir-487a LN:80
@SQ SN:hsa-mir-488 LN:83
@SQ SN:hsa-mir-489 LN:84
@SQ SN:hsa-mir-490 LN:128
@SQ SN:hsa-mir-491 LN:84
@SQ SN:hsa-mir-511 LN:87
@SQ SN:hsa-mir-146b LN:73
@SQ SN:hsa-mir-202 LN:110
@SQ SN:hsa-mir-492 LN:116
@SQ SN:hsa-mir-493 LN:89
@SQ SN:hsa-mir-432 LN:94
@SQ SN:hsa-mir-494 LN:81
@SQ SN:hsa-mir-495 LN:82
@SQ SN:hsa-mir-496 LN:102
@SQ SN:hsa-mir-193b LN:83
@SQ SN:hsa-mir-497 LN:112
@SQ SN:hsa-mir-181d LN:137
@SQ SN:hsa-mir-512-1 LN:84
@SQ SN:hsa-mir-512-2 LN:98
@SQ SN:hsa-mir-498 LN:124
@SQ SN:hsa-mir-520e LN:87
@SQ SN:hsa-mir-515-1 LN:83
@SQ SN:hsa-mir-519e LN:84
@SQ SN:hsa-mir-520f LN:87
@SQ SN:hsa-mir-515-2 LN:83
@SQ SN:hsa-mir-519c LN:87
@SQ SN:hsa-mir-520a LN:85
@SQ SN:hsa-mir-526b LN:83
@SQ SN:hsa-mir-519b LN:81
@SQ SN:hsa-mir-525 LN:85
@SQ SN:hsa-mir-523 LN:87
@SQ SN:hsa-mir-518f LN:87
@SQ SN:hsa-mir-520b LN:61
@SQ SN:hsa-mir-518b LN:83
@SQ SN:hsa-mir-526a-1 LN:85
@SQ SN:hsa-mir-520c LN:87
@SQ SN:hsa-mir-518c LN:101
@SQ SN:hsa-mir-524 LN:87
@SQ SN:hsa-mir-517a LN:87
@SQ SN:hsa-mir-519d LN:88
@SQ SN:hsa-mir-521-2 LN:87
@SQ SN:hsa-mir-520d LN:87
@SQ SN:hsa-mir-517b LN:67
@SQ SN:hsa-mir-520g LN:90
@SQ SN:hsa-mir-516b-2 LN:85
@SQ SN:hsa-mir-526a-2 LN:65
@SQ SN:hsa-mir-518e LN:88
@SQ SN:hsa-mir-518a-1 LN:85
@SQ SN:hsa-mir-518d LN:87
@SQ SN:hsa-mir-516b-1 LN:90
@SQ SN:hsa-mir-518a-2 LN:87
@SQ SN:hsa-mir-517c LN:95
@SQ SN:hsa-mir-520h LN:88
@SQ SN:hsa-mir-521-1 LN:87
@SQ SN:hsa-mir-522 LN:87
@SQ SN:hsa-mir-519a-1 LN:85
@SQ SN:hsa-mir-527 LN:85
@SQ SN:hsa-mir-516a-1 LN:90
@SQ SN:hsa-mir-516a-2 LN:90
@SQ SN:hsa-mir-519a-2 LN:87
@SQ SN:hsa-mir-499a LN:122
@SQ SN:hsa-mir-500a LN:84
@SQ SN:hsa-mir-501 LN:84
@SQ SN:hsa-mir-502 LN:86
@SQ SN:hsa-mir-450a-2 LN:100
@SQ SN:hsa-mir-503 LN:71
@SQ SN:hsa-mir-504 LN:83
@SQ SN:hsa-mir-505 LN:84
@SQ SN:hsa-mir-513a-1 LN:129
@SQ SN:hsa-mir-513a-2 LN:127
@SQ SN:hsa-mir-506 LN:124
@SQ SN:hsa-mir-507 LN:94
@SQ SN:hsa-mir-508 LN:115
@SQ SN:hsa-mir-509-1 LN:94
@SQ SN:hsa-mir-510 LN:74
@SQ SN:hsa-mir-514a-1 LN:98
@SQ SN:hsa-mir-514a-2 LN:88
@SQ SN:hsa-mir-514a-3 LN:88
@SQ SN:hsa-mir-532 LN:91
@SQ SN:hsa-mir-455 LN:96
@SQ SN:hsa-mir-539 LN:78
@SQ SN:hsa-mir-544a LN:91
@SQ SN:hsa-mir-545 LN:106
@SQ SN:hsa-mir-376a-2 LN:80
@SQ SN:hsa-mir-487b LN:84
@SQ SN:hsa-mir-551a LN:96
@SQ SN:hsa-mir-552 LN:96
@SQ SN:hsa-mir-553 LN:68
@SQ SN:hsa-mir-554 LN:96
@SQ SN:hsa-mir-92b LN:96
@SQ SN:hsa-mir-555 LN:96
@SQ SN:hsa-mir-556 LN:95
@SQ SN:hsa-mir-557 LN:98
@SQ SN:hsa-mir-558 LN:94
@SQ SN:hsa-mir-559 LN:96
@SQ SN:hsa-mir-561 LN:97
@SQ SN:hsa-mir-562 LN:95
@SQ SN:hsa-mir-563 LN:79
@SQ SN:hsa-mir-564 LN:94
@SQ SN:hsa-mir-566 LN:94
@SQ SN:hsa-mir-567 LN:98
@SQ SN:hsa-mir-568 LN:95
@SQ SN:hsa-mir-551b LN:96
@SQ SN:hsa-mir-569 LN:96
@SQ SN:hsa-mir-570 LN:97
@SQ SN:hsa-mir-571 LN:96
@SQ SN:hsa-mir-572 LN:95
@SQ SN:hsa-mir-573 LN:99
@SQ SN:hsa-mir-574 LN:96
@SQ SN:hsa-mir-575 LN:94
@SQ SN:hsa-mir-576 LN:98
@SQ SN:hsa-mir-577 LN:96
@SQ SN:hsa-mir-578 LN:96
@SQ SN:hsa-mir-579 LN:98
@SQ SN:hsa-mir-580 LN:97
@SQ SN:hsa-mir-581 LN:96
@SQ SN:hsa-mir-582 LN:98
@SQ SN:hsa-mir-583 LN:75
@SQ SN:hsa-mir-584 LN:97
@SQ SN:hsa-mir-585 LN:94
@SQ SN:hsa-mir-548a-1 LN:97
@SQ SN:hsa-mir-586 LN:97
@SQ SN:hsa-mir-587 LN:96
@SQ SN:hsa-mir-548b LN:97
@SQ SN:hsa-mir-588 LN:83
@SQ SN:hsa-mir-548a-2 LN:97
@SQ SN:hsa-mir-589 LN:99
@SQ SN:hsa-mir-550a-1 LN:97
@SQ SN:hsa-mir-550a-2 LN:97
@SQ SN:hsa-mir-590 LN:97
@SQ SN:hsa-mir-591 LN:95
@SQ SN:hsa-mir-592 LN:97
@SQ SN:hsa-mir-593 LN:100
@SQ SN:hsa-mir-595 LN:96
@SQ SN:hsa-mir-596 LN:77
@SQ SN:hsa-mir-597 LN:97
@SQ SN:hsa-mir-598 LN:97
@SQ SN:hsa-mir-599 LN:95
@SQ SN:hsa-mir-548a-3 LN:97
@SQ SN:hsa-mir-600 LN:98
@SQ SN:hsa-mir-601 LN:79
@SQ SN:hsa-mir-602 LN:98
@SQ SN:hsa-mir-603 LN:97
@SQ SN:hsa-mir-604 LN:94
@SQ SN:hsa-mir-605 LN:83
@SQ SN:hsa-mir-606 LN:96
@SQ SN:hsa-mir-607 LN:96
@SQ SN:hsa-mir-608 LN:100
@SQ SN:hsa-mir-609 LN:95
@SQ SN:hsa-mir-610 LN:96
@SQ SN:hsa-mir-611 LN:67
@SQ SN:hsa-mir-612 LN:100
@SQ SN:hsa-mir-613 LN:95
@SQ SN:hsa-mir-614 LN:90
@SQ SN:hsa-mir-615 LN:96
@SQ SN:hsa-mir-616 LN:97
@SQ SN:hsa-mir-548c LN:97
@SQ SN:hsa-mir-617 LN:97
@SQ SN:hsa-mir-618 LN:98
@SQ SN:hsa-mir-619 LN:99
@SQ SN:hsa-mir-620 LN:95
@SQ SN:hsa-mir-621 LN:96
@SQ SN:hsa-mir-622 LN:96
@SQ SN:hsa-mir-623 LN:98
@SQ SN:hsa-mir-624 LN:97
@SQ SN:hsa-mir-625 LN:85
@SQ SN:hsa-mir-626 LN:94
@SQ SN:hsa-mir-627 LN:97
@SQ SN:hsa-mir-628 LN:95
@SQ SN:hsa-mir-629 LN:97
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@SQ SN:hsa-mir-454 LN:115
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@SQ SN:hsa-mir-297 LN:66
@SQ SN:hsa-mir-1178 LN:91
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@SQ SN:hsa-mir-1229 LN:69
@SQ SN:hsa-mir-1231 LN:92
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@SQ SN:hsa-mir-1234 LN:80
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@SQ SN:hsa-mir-1200 LN:76
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@SQ SN:hsa-mir-663b LN:115
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@SQ SN:hsa-mir-1207 LN:87
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@SQ SN:hsa-mir-548e LN:88
@SQ SN:hsa-mir-548j LN:112
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@SQ SN:hsa-mir-1285-2 LN:88
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@SQ SN:hsa-mir-1289-1 LN:144
@SQ SN:hsa-mir-1289-2 LN:111
@SQ SN:hsa-mir-1290 LN:78
@SQ SN:hsa-mir-1291 LN:87
@SQ SN:hsa-mir-548k LN:116
@SQ SN:hsa-mir-1293 LN:71
@SQ SN:hsa-mir-1294 LN:142
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@SQ SN:hsa-mir-1302-1 LN:143
@SQ SN:hsa-mir-1302-2 LN:138
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@SQ SN:hsa-mir-1302-4 LN:150
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@SQ SN:hsa-mir-1302-6 LN:90
@SQ SN:hsa-mir-1302-7 LN:72
@SQ SN:hsa-mir-1302-8 LN:128
@SQ SN:hsa-mir-1303 LN:86
@SQ SN:hsa-mir-1304 LN:91
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@SQ SN:hsa-mir-548f-1 LN:84
@SQ SN:hsa-mir-548f-2 LN:98
@SQ SN:hsa-mir-548f-3 LN:87
@SQ SN:hsa-mir-548f-4 LN:105
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@SQ SN:hsa-mir-1247 LN:136
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@SQ SN:hsa-mir-1250 LN:113
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@SQ SN:hsa-mir-1254-1 LN:97
@SQ SN:hsa-mir-1255a LN:113
@SQ SN:hsa-mir-1256 LN:119
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@SQ SN:hsa-mir-548g LN:89
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@SQ SN:hsa-mir-548n LN:75
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@SQ SN:hsa-mir-548o LN:114
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@SQ SN:hsa-mir-1272 LN:129
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@SQ SN:hsa-mir-548h-2 LN:88
@SQ SN:hsa-mir-548h-3 LN:118
@SQ SN:hsa-mir-548h-4 LN:111
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@SQ SN:hsa-mir-302e LN:72
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@SQ SN:hsa-mir-548i-1 LN:149
@SQ SN:hsa-mir-548i-2 LN:149
@SQ SN:hsa-mir-548i-3 LN:149
@SQ SN:hsa-mir-548i-4 LN:77
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@SQ SN:hsa-mir-1282 LN:101
@SQ SN:hsa-mir-1283-2 LN:87
@SQ SN:hsa-mir-1284 LN:120
@SQ SN:hsa-mir-1288 LN:75
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@SQ SN:hsa-mir-1255b-1 LN:63
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@SQ SN:hsa-mir-1307 LN:149
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@SQ SN:hsa-mir-1321 LN:79
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@SQ SN:hsa-mir-103b-1 LN:62
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@SQ SN:hsa-mir-1972-1 LN:77
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@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-3118-4 LN:75
@SQ SN:hsa-mir-3174 LN:87
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@SQ SN:hsa-mir-3180-3 LN:94
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@SQ SN:hsa-mir-3156-3 LN:77
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@SQ SN:hsa-mir-1233-2 LN:82
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@SQ SN:hsa-mir-1244-3 LN:85
@SQ SN:hsa-mir-1972-2 LN:77
@SQ SN:hsa-mir-1302-9 LN:138
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@SQ SN:hsa-mir-548aa-1 LN:97
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@SQ SN:hsa-mir-1254-2 LN:63
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@SQ SN:hsa-mir-548ae-1 LN:70
@SQ SN:hsa-mir-548ae-2 LN:67
@SQ SN:hsa-mir-4438 LN:93
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@SQ SN:hsa-mir-4447 LN:91
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@SQ SN:hsa-mir-548ag-1 LN:66
@SQ SN:hsa-mir-548ag-2 LN:64
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@SQ SN:hsa-mir-4464 LN:92
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@SQ SN:hsa-mir-548aj-1 LN:72
@SQ SN:hsa-mir-548aj-2 LN:92
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@SQ SN:hsa-mir-548al LN:97
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@SQ SN:hsa-mir-548ao LN:96
@SQ SN:hsa-mir-5006 LN:110
@SQ SN:hsa-mir-5007 LN:95
@SQ SN:hsa-mir-548ap LN:96
@SQ SN:hsa-mir-5008 LN:94
@SQ SN:hsa-mir-5009 LN:100
@SQ SN:hsa-mir-5010 LN:120
@SQ SN:hsa-mir-5011 LN:103
@SQ SN:hsa-mir-5047 LN:100
@SQ SN:hsa-mir-5087 LN:76
@SQ SN:hsa-mir-5088 LN:79
@SQ SN:hsa-mir-5089 LN:84
@SQ SN:hsa-mir-5090 LN:85
@SQ SN:hsa-mir-5091 LN:93
@SQ SN:hsa-mir-5092 LN:88
@SQ SN:hsa-mir-5093 LN:100
@SQ SN:hsa-mir-5094 LN:85
@SQ SN:hsa-mir-5095 LN:88
@SQ SN:hsa-mir-1273f LN:99
@SQ SN:hsa-mir-1273g LN:100
@SQ SN:hsa-mir-5096 LN:70
@SQ SN:hsa-mir-5186 LN:120
@SQ SN:hsa-mir-5187 LN:76
@SQ SN:hsa-mir-5188 LN:113
@SQ SN:hsa-mir-5189 LN:114
@SQ SN:hsa-mir-5190 LN:80
@SQ SN:hsa-mir-5191 LN:120
@SQ SN:hsa-mir-5192 LN:92
@SQ SN:hsa-mir-5193 LN:109
@SQ SN:hsa-mir-5194 LN:120
@SQ SN:hsa-mir-5195 LN:115
@SQ SN:hsa-mir-5196 LN:115
@SQ SN:hsa-mir-5197 LN:112
@SQ SN:hsa-mir-4436b-2 LN:91
@SQ SN:hsa-mir-4444-2 LN:74
@SQ SN:hsa-mir-3670-2 LN:65
@SQ SN:hsa-mir-3680-2 LN:87
@SQ SN:hsa-mir-4524b LN:115
@SQ SN:hsa-mir-5571 LN:113
@SQ SN:hsa-mir-5100 LN:119
@SQ SN:hsa-mir-5572 LN:137
@SQ SN:hsa-mir-548aq LN:58
@SQ SN:hsa-mir-548ar LN:57
@SQ SN:hsa-mir-548as LN:58
@SQ SN:hsa-mir-5579 LN:58
@SQ SN:hsa-mir-664b LN:61
@SQ SN:hsa-mir-5580 LN:58
@SQ SN:hsa-mir-5581 LN:60
@SQ SN:hsa-mir-548at LN:58
@SQ SN:hsa-mir-5582 LN:68
@SQ SN:hsa-mir-5583-1 LN:59
@SQ SN:hsa-mir-5583-2 LN:59
@SQ SN:hsa-mir-5584 LN:60
@SQ SN:hsa-mir-5585 LN:59
@SQ SN:hsa-mir-5586 LN:59
@SQ SN:hsa-mir-5587 LN:53
@SQ SN:hsa-mir-548au LN:54
@SQ SN:hsa-mir-1295b LN:60
@SQ SN:hsa-mir-5588 LN:63
@SQ SN:hsa-mir-5589 LN:60
@SQ SN:hsa-mir-4536-2 LN:88
@SQ SN:hsa-mir-5590 LN:54
@SQ SN:hsa-mir-5591 LN:65
@SQ SN:hsa-mir-548av LN:62
@SQ SN:hsa-mir-5680 LN:84
@SQ SN:hsa-mir-5681a LN:75
@SQ SN:hsa-mir-5682 LN:76
@SQ SN:hsa-mir-548aw LN:65
@SQ SN:hsa-mir-5683 LN:76
@SQ SN:hsa-mir-5684 LN:65
@SQ SN:hsa-mir-548ax LN:73
@SQ SN:hsa-mir-5685 LN:79
@SQ SN:hsa-mir-5692c-1 LN:91
@SQ SN:hsa-mir-5692c-2 LN:77
@SQ SN:hsa-mir-5687 LN:77
@SQ SN:hsa-mir-5688 LN:83
@SQ SN:hsa-mir-5681b LN:60
@SQ SN:hsa-mir-5689 LN:78
@SQ SN:hsa-mir-5690 LN:73
@SQ SN:hsa-mir-5691 LN:68
@SQ SN:hsa-mir-5692a-1 LN:69
@SQ SN:hsa-mir-5692a-2 LN:59
@SQ SN:hsa-mir-4666b LN:81
@SQ SN:hsa-mir-5693 LN:73
@SQ SN:hsa-mir-5694 LN:76
@SQ SN:hsa-mir-5695 LN:85
@SQ SN:hsa-mir-5696 LN:85
@SQ SN:hsa-mir-5697 LN:78
@SQ SN:hsa-mir-5698 LN:72
@SQ SN:hsa-mir-5699 LN:90
@SQ SN:hsa-mir-5700 LN:71
@SQ SN:hsa-mir-5701-1 LN:82
@SQ SN:hsa-mir-5702 LN:84
@SQ SN:hsa-mir-5703 LN:56
@SQ SN:hsa-mir-5692b LN:87
@SQ SN:hsa-mir-5704 LN:77
@SQ SN:hsa-mir-5705 LN:89
@SQ SN:hsa-mir-5706 LN:80
@SQ SN:hsa-mir-5707 LN:81
@SQ SN:hsa-mir-5708 LN:85
@SQ SN:hsa-mir-5739 LN:80
@SQ SN:hsa-mir-5701-2 LN:82
@SQ SN:hsa-mir-5787 LN:55
@SQ SN:hsa-mir-1199 LN:119
@SQ SN:hsa-mir-6068 LN:60
@SQ SN:hsa-mir-6069 LN:79
@SQ SN:hsa-mir-6070 LN:103
@SQ SN:hsa-mir-6071 LN:78
@SQ SN:hsa-mir-6072 LN:71
@SQ SN:hsa-mir-6073 LN:89
@SQ SN:hsa-mir-6074 LN:107
@SQ SN:hsa-mir-6075 LN:95
@SQ SN:hsa-mir-6076 LN:113
@SQ SN:hsa-mir-6077 LN:82
@SQ SN:hsa-mir-6078 LN:100
@SQ SN:hsa-mir-6079 LN:62
@SQ SN:hsa-mir-6080 LN:66
@SQ SN:hsa-mir-6081 LN:97
@SQ SN:hsa-mir-6082 LN:109
@SQ SN:hsa-mir-6083 LN:106
@SQ SN:hsa-mir-6084 LN:110
@SQ SN:hsa-mir-6085 LN:110
@SQ SN:hsa-mir-6086 LN:55
@SQ SN:hsa-mir-6087 LN:49
@SQ SN:hsa-mir-6088 LN:51
@SQ SN:hsa-mir-6089-1 LN:64
@SQ SN:hsa-mir-6090 LN:60
@SQ SN:hsa-mir-6124 LN:85
@SQ SN:hsa-mir-6125 LN:96
@SQ SN:hsa-mir-6126 LN:89
@SQ SN:hsa-mir-6127 LN:109
@SQ SN:hsa-mir-6128 LN:109
@SQ SN:hsa-mir-378j LN:109
@SQ SN:hsa-mir-6129 LN:109
@SQ SN:hsa-mir-6130 LN:109
@SQ SN:hsa-mir-6131 LN:109
@SQ SN:hsa-mir-6132 LN:109
@SQ SN:hsa-mir-6133 LN:108
@SQ SN:hsa-mir-6134 LN:109
@SQ SN:hsa-mir-6165 LN:84
@SQ SN:hsa-mir-6499 LN:62
@SQ SN:hsa-mir-548ay LN:107
@SQ SN:hsa-mir-6500 LN:86
@SQ SN:hsa-mir-548az LN:95
@SQ SN:hsa-mir-6501 LN:67
@SQ SN:hsa-mir-6502 LN:76
@SQ SN:hsa-mir-6503 LN:86
@SQ SN:hsa-mir-6504 LN:61
@SQ SN:hsa-mir-6505 LN:71
@SQ SN:hsa-mir-6506 LN:66
@SQ SN:hsa-mir-6507 LN:70
@SQ SN:hsa-mir-6508 LN:60
@SQ SN:hsa-mir-6509 LN:85
@SQ SN:hsa-mir-6510 LN:54
@SQ SN:hsa-mir-6511a-1 LN:67
@SQ SN:hsa-mir-6512 LN:77
@SQ SN:hsa-mir-6513 LN:64
@SQ SN:hsa-mir-6514 LN:70
@SQ SN:hsa-mir-6515 LN:57
@SQ SN:hsa-mir-6715a LN:79
@SQ SN:hsa-mir-6715b LN:77
@SQ SN:hsa-mir-6716 LN:80
@SQ SN:hsa-mir-6717 LN:73
@SQ SN:hsa-mir-6511b-1 LN:85
@SQ SN:hsa-mir-6718 LN:80
@SQ SN:hsa-mir-6719 LN:87
@SQ SN:hsa-mir-6720 LN:98
@SQ SN:hsa-mir-6721 LN:87
@SQ SN:hsa-mir-6722 LN:78
@SQ SN:hsa-mir-6723 LN:89
@SQ SN:hsa-mir-6724-1 LN:92
@SQ SN:hsa-mir-892c LN:77
@SQ SN:hsa-mir-6726 LN:61
@SQ SN:hsa-mir-6727 LN:65
@SQ SN:hsa-mir-6728 LN:89
@SQ SN:hsa-mir-6729 LN:65
@SQ SN:hsa-mir-6730 LN:67
@SQ SN:hsa-mir-6731 LN:72
@SQ SN:hsa-mir-6732 LN:60
@SQ SN:hsa-mir-6733 LN:61
@SQ SN:hsa-mir-6734 LN:68
@SQ SN:hsa-mir-6735 LN:73
@SQ SN:hsa-mir-6736 LN:59
@SQ SN:hsa-mir-6737 LN:70
@SQ SN:hsa-mir-6738 LN:64
@SQ SN:hsa-mir-6739 LN:75
@SQ SN:hsa-mir-6740 LN:113
@SQ SN:hsa-mir-6741 LN:63
@SQ SN:hsa-mir-6742 LN:62
@SQ SN:hsa-mir-6743 LN:71
@SQ SN:hsa-mir-6744 LN:66
@SQ SN:hsa-mir-6745 LN:127
@SQ SN:hsa-mir-6746 LN:63
@SQ SN:hsa-mir-6747 LN:61
@SQ SN:hsa-mir-6748 LN:71
@SQ SN:hsa-mir-6749 LN:69
@SQ SN:hsa-mir-6750 LN:75
@SQ SN:hsa-mir-6751 LN:63
@SQ SN:hsa-mir-6752 LN:71
@SQ SN:hsa-mir-6753 LN:164
@SQ SN:hsa-mir-6754 LN:66
@SQ SN:hsa-mir-6755 LN:66
@SQ SN:hsa-mir-6756 LN:63
@SQ SN:hsa-mir-6757 LN:69
@SQ SN:hsa-mir-6758 LN:63
@SQ SN:hsa-mir-6759 LN:65
@SQ SN:hsa-mir-6760 LN:68
@SQ SN:hsa-mir-6761 LN:72
@SQ SN:hsa-mir-6762 LN:86
@SQ SN:hsa-mir-6763 LN:65
@SQ SN:hsa-mir-6764 LN:61
@SQ SN:hsa-mir-6765 LN:87
@SQ SN:hsa-mir-6766 LN:72
@SQ SN:hsa-mir-6767 LN:66
@SQ SN:hsa-mir-6768 LN:72
@SQ SN:hsa-mir-6769a LN:73
@SQ SN:hsa-mir-6770-1 LN:60
@SQ SN:hsa-mir-6771 LN:60
@SQ SN:hsa-mir-6772 LN:64
@SQ SN:hsa-mir-6773 LN:74
@SQ SN:hsa-mir-6774 LN:70
@SQ SN:hsa-mir-6775 LN:69
@SQ SN:hsa-mir-6776 LN:59
@SQ SN:hsa-mir-6777 LN:66
@SQ SN:hsa-mir-6778 LN:73
@SQ SN:hsa-mir-6779 LN:64
@SQ SN:hsa-mir-6780a LN:68
@SQ SN:hsa-mir-6781 LN:64
@SQ SN:hsa-mir-6782 LN:69
@SQ SN:hsa-mir-6783 LN:64
@SQ SN:hsa-mir-6784 LN:67
@SQ SN:hsa-mir-6785 LN:81
@SQ SN:hsa-mir-6786 LN:113
@SQ SN:hsa-mir-6787 LN:61
@SQ SN:hsa-mir-6788 LN:66
@SQ SN:hsa-mir-6789 LN:98
@SQ SN:hsa-mir-6790 LN:63
@SQ SN:hsa-mir-6791 LN:67
@SQ SN:hsa-mir-6792 LN:67
@SQ SN:hsa-mir-6793 LN:63
@SQ SN:hsa-mir-6794 LN:68
@SQ SN:hsa-mir-6795 LN:68
@SQ SN:hsa-mir-6796 LN:62
@SQ SN:hsa-mir-6797 LN:72
@SQ SN:hsa-mir-6798 LN:67
@SQ SN:hsa-mir-6799 LN:69
@SQ SN:hsa-mir-6800 LN:82
@SQ SN:hsa-mir-6801 LN:79
@SQ SN:hsa-mir-6802 LN:65
@SQ SN:hsa-mir-6803 LN:65
@SQ SN:hsa-mir-6804 LN:68
@SQ SN:hsa-mir-6805 LN:62
@SQ SN:hsa-mir-6806 LN:64
@SQ SN:hsa-mir-6807 LN:92
@SQ SN:hsa-mir-6808 LN:59
@SQ SN:hsa-mir-6809 LN:116
@SQ SN:hsa-mir-6810 LN:70
@SQ SN:hsa-mir-6811 LN:58
@SQ SN:hsa-mir-6812 LN:64
@SQ SN:hsa-mir-6813 LN:56
@SQ SN:hsa-mir-6814 LN:70
@SQ SN:hsa-mir-6815 LN:61
@SQ SN:hsa-mir-6816 LN:66
@SQ SN:hsa-mir-6817 LN:66
@SQ SN:hsa-mir-6818 LN:65
@SQ SN:hsa-mir-6819 LN:61
@SQ SN:hsa-mir-6820 LN:62
@SQ SN:hsa-mir-6821 LN:74
@SQ SN:hsa-mir-6822 LN:61
@SQ SN:hsa-mir-6823 LN:61
@SQ SN:hsa-mir-6824 LN:63
@SQ SN:hsa-mir-6825 LN:66
@SQ SN:hsa-mir-6826 LN:98
@SQ SN:hsa-mir-6827 LN:59
@SQ SN:hsa-mir-6828 LN:60
@SQ SN:hsa-mir-6829 LN:67
@SQ SN:hsa-mir-6830 LN:70
@SQ SN:hsa-mir-6831 LN:81
@SQ SN:hsa-mir-6832 LN:72
@SQ SN:hsa-mir-6833 LN:61
@SQ SN:hsa-mir-6834 LN:81
@SQ SN:hsa-mir-6835 LN:64
@SQ SN:hsa-mir-6780b LN:79
@SQ SN:hsa-mir-6836 LN:63
@SQ SN:hsa-mir-6837 LN:64
@SQ SN:hsa-mir-6838 LN:56
@SQ SN:hsa-mir-6839 LN:113
@SQ SN:hsa-mir-6840 LN:71
@SQ SN:hsa-mir-6841 LN:72
@SQ SN:hsa-mir-6842 LN:65
@SQ SN:hsa-mir-6843 LN:151
@SQ SN:hsa-mir-6844 LN:62
@SQ SN:hsa-mir-6845 LN:61
@SQ SN:hsa-mir-6846 LN:60
@SQ SN:hsa-mir-6847 LN:69
@SQ SN:hsa-mir-6848 LN:70
@SQ SN:hsa-mir-6849 LN:69
@SQ SN:hsa-mir-6850 LN:61
@SQ SN:hsa-mir-6851 LN:67
@SQ SN:hsa-mir-6852 LN:66
@SQ SN:hsa-mir-6853 LN:74
@SQ SN:hsa-mir-6854 LN:69
@SQ SN:hsa-mir-6855 LN:67
@SQ SN:hsa-mir-6856 LN:67
@SQ SN:hsa-mir-6857 LN:93
@SQ SN:hsa-mir-6858 LN:67
@SQ SN:hsa-mir-6859-1 LN:68
@SQ SN:hsa-mir-6769b LN:62
@SQ SN:hsa-mir-6860 LN:66
@SQ SN:hsa-mir-6861 LN:64
@SQ SN:hsa-mir-6862-1 LN:70
@SQ SN:hsa-mir-6863 LN:90
@SQ SN:hsa-mir-6864 LN:70
@SQ SN:hsa-mir-6865 LN:65
@SQ SN:hsa-mir-6866 LN:69
@SQ SN:hsa-mir-6867 LN:67
@SQ SN:hsa-mir-6868 LN:58
@SQ SN:hsa-mir-6869 LN:62
@SQ SN:hsa-mir-6870 LN:60
@SQ SN:hsa-mir-6871 LN:56
@SQ SN:hsa-mir-6872 LN:62
@SQ SN:hsa-mir-6873 LN:63
@SQ SN:hsa-mir-6874 LN:71
@SQ SN:hsa-mir-6875 LN:72
@SQ SN:hsa-mir-6876 LN:73
@SQ SN:hsa-mir-6877 LN:64
@SQ SN:hsa-mir-6878 LN:66
@SQ SN:hsa-mir-6879 LN:66
@SQ SN:hsa-mir-6880 LN:62
@SQ SN:hsa-mir-6881 LN:76
@SQ SN:hsa-mir-6882 LN:66
@SQ SN:hsa-mir-6883 LN:78
@SQ SN:hsa-mir-6884 LN:78
@SQ SN:hsa-mir-6885 LN:66
@SQ SN:hsa-mir-6886 LN:61
@SQ SN:hsa-mir-6887 LN:65
@SQ SN:hsa-mir-6888 LN:67
@SQ SN:hsa-mir-6889 LN:59
@SQ SN:hsa-mir-6890 LN:61
@SQ SN:hsa-mir-6891 LN:93
@SQ SN:hsa-mir-6892 LN:115
@SQ SN:hsa-mir-6893 LN:69
@SQ SN:hsa-mir-6894 LN:57
@SQ SN:hsa-mir-6895 LN:78
@SQ SN:hsa-mir-7106 LN:65
@SQ SN:hsa-mir-7107 LN:80
@SQ SN:hsa-mir-7108 LN:87
@SQ SN:hsa-mir-7109 LN:65
@SQ SN:hsa-mir-7110 LN:86
@SQ SN:hsa-mir-7111 LN:72
@SQ SN:hsa-mir-7112 LN:65
@SQ SN:hsa-mir-7113 LN:59
@SQ SN:hsa-mir-7114 LN:61
@SQ SN:hsa-mir-6511b-2 LN:71
@SQ SN:hsa-mir-3690-2 LN:75
@SQ SN:hsa-mir-6089-2 LN:64
@SQ SN:hsa-mir-6511a-2 LN:67
@SQ SN:hsa-mir-6511a-3 LN:67
@SQ SN:hsa-mir-6511a-4 LN:67
@SQ SN:hsa-mir-7150 LN:94
@SQ SN:hsa-mir-7151 LN:60
@SQ SN:hsa-mir-7152 LN:54
@SQ SN:hsa-mir-7153 LN:57
@SQ SN:hsa-mir-7154 LN:73
@SQ SN:hsa-mir-7155 LN:56
@SQ SN:hsa-mir-7156 LN:60
@SQ SN:hsa-mir-7157 LN:60
@SQ SN:hsa-mir-7158 LN:71
@SQ SN:hsa-mir-7161 LN:84
@SQ SN:hsa-mir-7159 LN:66
@SQ SN:hsa-mir-7160 LN:52
@SQ SN:hsa-mir-486-2 LN:64
@SQ SN:hsa-mir-7162 LN:69
@SQ SN:hsa-mir-7515 LN:67
@SQ SN:hsa-mir-7641-1 LN:61
@SQ SN:hsa-mir-7641-2 LN:53
@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_17del3t_x2 0 hsa-let-7a-1 6 255 17M1D3M * 0 0 TGAGGTAGTAGGTTGTAAGT ____________________ NM:i:1 MD:Z:17^T3 mirtop-0.4.23/data/aligments/let7-perfect-genome.sam 0000664 0000000 0000000 00000000213 13547635037 0022272 0 ustar 00root root 0000000 0000000 @SQ SN:chr9 LN:222146522
seq_perfect_x2 0 hsa-let-7a-1 94175956 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT NM:i:2 MD:Z:22
mirtop-0.4.23/data/aligments/let7-perfect.sam 0000664 0000000 0000000 00000140535 13547635037 0021036 0 ustar 00root root 0000000 0000000 @SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
@SQ SN:hsa-let-7b LN:83
@SQ SN:hsa-let-7c LN:84
@SQ SN:hsa-let-7d LN:87
@SQ SN:hsa-let-7e LN:79
@SQ SN:hsa-let-7f-1 LN:87
@SQ SN:hsa-let-7f-2 LN:83
@SQ SN:hsa-mir-15a LN:83
@SQ SN:hsa-mir-16-1 LN:89
@SQ SN:hsa-mir-17 LN:84
@SQ SN:hsa-mir-18a LN:71
@SQ SN:hsa-mir-19a LN:82
@SQ SN:hsa-mir-19b-1 LN:87
@SQ SN:hsa-mir-19b-2 LN:96
@SQ SN:hsa-mir-20a LN:71
@SQ SN:hsa-mir-21 LN:72
@SQ SN:hsa-mir-22 LN:85
@SQ SN:hsa-mir-23a LN:73
@SQ SN:hsa-mir-24-1 LN:68
@SQ SN:hsa-mir-24-2 LN:73
@SQ SN:hsa-mir-25 LN:84
@SQ SN:hsa-mir-26a-1 LN:77
@SQ SN:hsa-mir-26b LN:77
@SQ SN:hsa-mir-27a LN:78
@SQ SN:hsa-mir-28 LN:86
@SQ SN:hsa-mir-29a LN:64
@SQ SN:hsa-mir-30a LN:71
@SQ SN:hsa-mir-31 LN:71
@SQ SN:hsa-mir-32 LN:70
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@SQ SN:hsa-mir-92a-1 LN:78
@SQ SN:hsa-mir-92a-2 LN:75
@SQ SN:hsa-mir-93 LN:80
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@SQ SN:hsa-mir-96 LN:78
@SQ SN:hsa-mir-98 LN:119
@SQ SN:hsa-mir-99a LN:81
@SQ SN:hsa-mir-100 LN:80
@SQ SN:hsa-mir-101-1 LN:75
@SQ SN:hsa-mir-29b-1 LN:81
@SQ SN:hsa-mir-29b-2 LN:81
@SQ SN:hsa-mir-103a-2 LN:78
@SQ SN:hsa-mir-103a-1 LN:78
@SQ SN:hsa-mir-105-1 LN:81
@SQ SN:hsa-mir-105-2 LN:81
@SQ SN:hsa-mir-106a LN:81
@SQ SN:hsa-mir-107 LN:81
@SQ SN:hsa-mir-16-2 LN:81
@SQ SN:hsa-mir-192 LN:110
@SQ SN:hsa-mir-196a-1 LN:70
@SQ SN:hsa-mir-197 LN:75
@SQ SN:hsa-mir-198 LN:62
@SQ SN:hsa-mir-199a-1 LN:71
@SQ SN:hsa-mir-208a LN:71
@SQ SN:hsa-mir-129-1 LN:72
@SQ SN:hsa-mir-148a LN:68
@SQ SN:hsa-mir-30c-2 LN:72
@SQ SN:hsa-mir-30d LN:70
@SQ SN:hsa-mir-139 LN:68
@SQ SN:hsa-mir-147a LN:72
@SQ SN:hsa-mir-7-1 LN:110
@SQ SN:hsa-mir-7-2 LN:110
@SQ SN:hsa-mir-7-3 LN:110
@SQ SN:hsa-mir-10a LN:110
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@SQ SN:hsa-mir-34a LN:110
@SQ SN:hsa-mir-181a-2 LN:110
@SQ SN:hsa-mir-181b-1 LN:110
@SQ SN:hsa-mir-181c LN:110
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@SQ SN:hsa-mir-187 LN:109
@SQ SN:hsa-mir-196a-2 LN:110
@SQ SN:hsa-mir-199a-2 LN:110
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@SQ SN:hsa-mir-203a LN:110
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@SQ SN:hsa-mir-214 LN:110
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@SQ SN:hsa-mir-218-2 LN:110
@SQ SN:hsa-mir-219a-1 LN:110
@SQ SN:hsa-mir-221 LN:110
@SQ SN:hsa-mir-222 LN:110
@SQ SN:hsa-mir-223 LN:110
@SQ SN:hsa-mir-224 LN:81
@SQ SN:hsa-mir-200b LN:95
@SQ SN:hsa-let-7g LN:84
@SQ SN:hsa-let-7i LN:84
@SQ SN:hsa-mir-1-2 LN:85
@SQ SN:hsa-mir-15b LN:98
@SQ SN:hsa-mir-23b LN:97
@SQ SN:hsa-mir-27b LN:97
@SQ SN:hsa-mir-30b LN:88
@SQ SN:hsa-mir-122 LN:85
@SQ SN:hsa-mir-124-1 LN:85
@SQ SN:hsa-mir-124-2 LN:109
@SQ SN:hsa-mir-124-3 LN:87
@SQ SN:hsa-mir-125b-1 LN:88
@SQ SN:hsa-mir-128-1 LN:82
@SQ SN:hsa-mir-130a LN:89
@SQ SN:hsa-mir-132 LN:101
@SQ SN:hsa-mir-133a-1 LN:88
@SQ SN:hsa-mir-133a-2 LN:102
@SQ SN:hsa-mir-135a-1 LN:90
@SQ SN:hsa-mir-135a-2 LN:100
@SQ SN:hsa-mir-137 LN:102
@SQ SN:hsa-mir-138-2 LN:84
@SQ SN:hsa-mir-140 LN:100
@SQ SN:hsa-mir-141 LN:95
@SQ SN:hsa-mir-142 LN:87
@SQ SN:hsa-mir-143 LN:106
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@SQ SN:hsa-mir-153-1 LN:90
@SQ SN:hsa-mir-153-2 LN:87
@SQ SN:hsa-mir-191 LN:92
@SQ SN:hsa-mir-9-1 LN:89
@SQ SN:hsa-mir-9-2 LN:87
@SQ SN:hsa-mir-9-3 LN:90
@SQ SN:hsa-mir-125a LN:86
@SQ SN:hsa-mir-125b-2 LN:89
@SQ SN:hsa-mir-126 LN:85
@SQ SN:hsa-mir-127 LN:97
@SQ SN:hsa-mir-129-2 LN:90
@SQ SN:hsa-mir-134 LN:73
@SQ SN:hsa-mir-136 LN:82
@SQ SN:hsa-mir-138-1 LN:99
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@SQ SN:hsa-mir-149 LN:89
@SQ SN:hsa-mir-150 LN:84
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@SQ SN:hsa-mir-185 LN:82
@SQ SN:hsa-mir-186 LN:86
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@SQ SN:hsa-mir-193a LN:88
@SQ SN:hsa-mir-194-1 LN:85
@SQ SN:hsa-mir-195 LN:87
@SQ SN:hsa-mir-206 LN:86
@SQ SN:hsa-mir-320a LN:82
@SQ SN:hsa-mir-200c LN:68
@SQ SN:hsa-mir-1-1 LN:71
@SQ SN:hsa-mir-155 LN:65
@SQ SN:hsa-mir-181b-2 LN:89
@SQ SN:hsa-mir-128-2 LN:84
@SQ SN:hsa-mir-194-2 LN:85
@SQ SN:hsa-mir-106b LN:82
@SQ SN:hsa-mir-29c LN:88
@SQ SN:hsa-mir-30c-1 LN:89
@SQ SN:hsa-mir-200a LN:90
@SQ SN:hsa-mir-302a LN:69
@SQ SN:hsa-mir-101-2 LN:79
@SQ SN:hsa-mir-219a-2 LN:97
@SQ SN:hsa-mir-34b LN:84
@SQ SN:hsa-mir-34c LN:77
@SQ SN:hsa-mir-299 LN:63
@SQ SN:hsa-mir-301a LN:86
@SQ SN:hsa-mir-99b LN:70
@SQ SN:hsa-mir-296 LN:80
@SQ SN:hsa-mir-130b LN:82
@SQ SN:hsa-mir-30e LN:92
@SQ SN:hsa-mir-26a-2 LN:84
@SQ SN:hsa-mir-361 LN:72
@SQ SN:hsa-mir-362 LN:65
@SQ SN:hsa-mir-363 LN:75
@SQ SN:hsa-mir-365a LN:87
@SQ SN:hsa-mir-365b LN:111
@SQ SN:hsa-mir-302b LN:73
@SQ SN:hsa-mir-302c LN:68
@SQ SN:hsa-mir-302d LN:68
@SQ SN:hsa-mir-367 LN:68
@SQ SN:hsa-mir-376c LN:66
@SQ SN:hsa-mir-369 LN:70
@SQ SN:hsa-mir-370 LN:75
@SQ SN:hsa-mir-371a LN:67
@SQ SN:hsa-mir-372 LN:67
@SQ SN:hsa-mir-373 LN:69
@SQ SN:hsa-mir-374a LN:72
@SQ SN:hsa-mir-375 LN:64
@SQ SN:hsa-mir-376a-1 LN:68
@SQ SN:hsa-mir-377 LN:69
@SQ SN:hsa-mir-378a LN:66
@SQ SN:hsa-mir-379 LN:67
@SQ SN:hsa-mir-380 LN:61
@SQ SN:hsa-mir-381 LN:75
@SQ SN:hsa-mir-382 LN:76
@SQ SN:hsa-mir-383 LN:73
@SQ SN:hsa-mir-340 LN:95
@SQ SN:hsa-mir-330 LN:94
@SQ SN:hsa-mir-328 LN:75
@SQ SN:hsa-mir-342 LN:99
@SQ SN:hsa-mir-337 LN:93
@SQ SN:hsa-mir-323a LN:86
@SQ SN:hsa-mir-326 LN:95
@SQ SN:hsa-mir-151a LN:90
@SQ SN:hsa-mir-135b LN:97
@SQ SN:hsa-mir-148b LN:99
@SQ SN:hsa-mir-331 LN:94
@SQ SN:hsa-mir-324 LN:83
@SQ SN:hsa-mir-338 LN:67
@SQ SN:hsa-mir-339 LN:94
@SQ SN:hsa-mir-335 LN:94
@SQ SN:hsa-mir-133b LN:119
@SQ SN:hsa-mir-325 LN:98
@SQ SN:hsa-mir-345 LN:98
@SQ SN:hsa-mir-346 LN:95
@SQ SN:hsa-mir-384 LN:88
@SQ SN:hsa-mir-196b LN:84
@SQ SN:hsa-mir-422a LN:90
@SQ SN:hsa-mir-423 LN:94
@SQ SN:hsa-mir-424 LN:98
@SQ SN:hsa-mir-425 LN:87
@SQ SN:hsa-mir-18b LN:71
@SQ SN:hsa-mir-20b LN:69
@SQ SN:hsa-mir-448 LN:111
@SQ SN:hsa-mir-429 LN:83
@SQ SN:hsa-mir-449a LN:91
@SQ SN:hsa-mir-450a-1 LN:91
@SQ SN:hsa-mir-431 LN:114
@SQ SN:hsa-mir-433 LN:93
@SQ SN:hsa-mir-329-1 LN:80
@SQ SN:hsa-mir-329-2 LN:84
@SQ SN:hsa-mir-451a LN:72
@SQ SN:hsa-mir-452 LN:85
@SQ SN:hsa-mir-409 LN:79
@SQ SN:hsa-mir-412 LN:91
@SQ SN:hsa-mir-410 LN:80
@SQ SN:hsa-mir-376b LN:100
@SQ SN:hsa-mir-483 LN:76
@SQ SN:hsa-mir-484 LN:79
@SQ SN:hsa-mir-485 LN:73
@SQ SN:hsa-mir-486-1 LN:68
@SQ SN:hsa-mir-487a LN:80
@SQ SN:hsa-mir-488 LN:83
@SQ SN:hsa-mir-489 LN:84
@SQ SN:hsa-mir-490 LN:128
@SQ SN:hsa-mir-491 LN:84
@SQ SN:hsa-mir-511 LN:87
@SQ SN:hsa-mir-146b LN:73
@SQ SN:hsa-mir-202 LN:110
@SQ SN:hsa-mir-492 LN:116
@SQ SN:hsa-mir-493 LN:89
@SQ SN:hsa-mir-432 LN:94
@SQ SN:hsa-mir-494 LN:81
@SQ SN:hsa-mir-495 LN:82
@SQ SN:hsa-mir-496 LN:102
@SQ SN:hsa-mir-193b LN:83
@SQ SN:hsa-mir-497 LN:112
@SQ SN:hsa-mir-181d LN:137
@SQ SN:hsa-mir-512-1 LN:84
@SQ SN:hsa-mir-512-2 LN:98
@SQ SN:hsa-mir-498 LN:124
@SQ SN:hsa-mir-520e LN:87
@SQ SN:hsa-mir-515-1 LN:83
@SQ SN:hsa-mir-519e LN:84
@SQ SN:hsa-mir-520f LN:87
@SQ SN:hsa-mir-515-2 LN:83
@SQ SN:hsa-mir-519c LN:87
@SQ SN:hsa-mir-520a LN:85
@SQ SN:hsa-mir-526b LN:83
@SQ SN:hsa-mir-519b LN:81
@SQ SN:hsa-mir-525 LN:85
@SQ SN:hsa-mir-523 LN:87
@SQ SN:hsa-mir-518f LN:87
@SQ SN:hsa-mir-520b LN:61
@SQ SN:hsa-mir-518b LN:83
@SQ SN:hsa-mir-526a-1 LN:85
@SQ SN:hsa-mir-520c LN:87
@SQ SN:hsa-mir-518c LN:101
@SQ SN:hsa-mir-524 LN:87
@SQ SN:hsa-mir-517a LN:87
@SQ SN:hsa-mir-519d LN:88
@SQ SN:hsa-mir-521-2 LN:87
@SQ SN:hsa-mir-520d LN:87
@SQ SN:hsa-mir-517b LN:67
@SQ SN:hsa-mir-520g LN:90
@SQ SN:hsa-mir-516b-2 LN:85
@SQ SN:hsa-mir-526a-2 LN:65
@SQ SN:hsa-mir-518e LN:88
@SQ SN:hsa-mir-518a-1 LN:85
@SQ SN:hsa-mir-518d LN:87
@SQ SN:hsa-mir-516b-1 LN:90
@SQ SN:hsa-mir-518a-2 LN:87
@SQ SN:hsa-mir-517c LN:95
@SQ SN:hsa-mir-520h LN:88
@SQ SN:hsa-mir-521-1 LN:87
@SQ SN:hsa-mir-522 LN:87
@SQ SN:hsa-mir-519a-1 LN:85
@SQ SN:hsa-mir-527 LN:85
@SQ SN:hsa-mir-516a-1 LN:90
@SQ SN:hsa-mir-516a-2 LN:90
@SQ SN:hsa-mir-519a-2 LN:87
@SQ SN:hsa-mir-499a LN:122
@SQ SN:hsa-mir-500a LN:84
@SQ SN:hsa-mir-501 LN:84
@SQ SN:hsa-mir-502 LN:86
@SQ SN:hsa-mir-450a-2 LN:100
@SQ SN:hsa-mir-503 LN:71
@SQ SN:hsa-mir-504 LN:83
@SQ SN:hsa-mir-505 LN:84
@SQ SN:hsa-mir-513a-1 LN:129
@SQ SN:hsa-mir-513a-2 LN:127
@SQ SN:hsa-mir-506 LN:124
@SQ SN:hsa-mir-507 LN:94
@SQ SN:hsa-mir-508 LN:115
@SQ SN:hsa-mir-509-1 LN:94
@SQ SN:hsa-mir-510 LN:74
@SQ SN:hsa-mir-514a-1 LN:98
@SQ SN:hsa-mir-514a-2 LN:88
@SQ SN:hsa-mir-514a-3 LN:88
@SQ SN:hsa-mir-532 LN:91
@SQ SN:hsa-mir-455 LN:96
@SQ SN:hsa-mir-539 LN:78
@SQ SN:hsa-mir-544a LN:91
@SQ SN:hsa-mir-545 LN:106
@SQ SN:hsa-mir-376a-2 LN:80
@SQ SN:hsa-mir-487b LN:84
@SQ SN:hsa-mir-551a LN:96
@SQ SN:hsa-mir-552 LN:96
@SQ SN:hsa-mir-553 LN:68
@SQ SN:hsa-mir-554 LN:96
@SQ SN:hsa-mir-92b LN:96
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@SQ SN:hsa-mir-563 LN:79
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@SQ SN:hsa-mir-568 LN:95
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@SQ SN:hsa-mir-569 LN:96
@SQ SN:hsa-mir-570 LN:97
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@SQ SN:hsa-mir-583 LN:75
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@SQ SN:hsa-mir-548a-1 LN:97
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@SQ SN:hsa-mir-588 LN:83
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@SQ SN:hsa-mir-593 LN:100
@SQ SN:hsa-mir-595 LN:96
@SQ SN:hsa-mir-596 LN:77
@SQ SN:hsa-mir-597 LN:97
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@SQ SN:hsa-mir-599 LN:95
@SQ SN:hsa-mir-548a-3 LN:97
@SQ SN:hsa-mir-600 LN:98
@SQ SN:hsa-mir-601 LN:79
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@SQ SN:hsa-mir-605 LN:83
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@SQ SN:hsa-mir-608 LN:100
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@SQ SN:hsa-mir-610 LN:96
@SQ SN:hsa-mir-611 LN:67
@SQ SN:hsa-mir-612 LN:100
@SQ SN:hsa-mir-613 LN:95
@SQ SN:hsa-mir-614 LN:90
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@SQ SN:hsa-mir-617 LN:97
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@SQ SN:hsa-mir-631 LN:75
@SQ SN:hsa-mir-33b LN:96
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@SQ SN:hsa-mir-644a LN:94
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@SQ SN:hsa-mir-548d-1 LN:97
@SQ SN:hsa-mir-661 LN:89
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@SQ SN:hsa-mir-663a LN:93
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@SQ SN:hsa-mir-654 LN:81
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@SQ SN:hsa-mir-549a LN:96
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@SQ SN:hsa-mir-421 LN:85
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@SQ SN:hsa-mir-758 LN:88
@SQ SN:hsa-mir-1264 LN:69
@SQ SN:hsa-mir-671 LN:118
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@SQ SN:hsa-mir-550a-3 LN:95
@SQ SN:hsa-mir-767 LN:109
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@SQ SN:hsa-mir-320b-1 LN:79
@SQ SN:hsa-mir-320c-1 LN:88
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@SQ SN:hsa-mir-769 LN:118
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@SQ SN:hsa-mir-320b-2 LN:138
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@SQ SN:hsa-mir-509-2 LN:91
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@SQ SN:hsa-mir-941-1 LN:72
@SQ SN:hsa-mir-941-2 LN:72
@SQ SN:hsa-mir-941-3 LN:72
@SQ SN:hsa-mir-941-4 LN:72
@SQ SN:hsa-mir-942 LN:86
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@SQ SN:hsa-mir-1231 LN:92
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@SQ SN:hsa-mir-1302-4 LN:150
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@SQ SN:hsa-mir-1302-7 LN:72
@SQ SN:hsa-mir-1302-8 LN:128
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@SQ SN:hsa-mir-1304 LN:91
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@SQ SN:hsa-mir-548f-2 LN:98
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@SQ SN:hsa-mir-548h-2 LN:88
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@SQ SN:hsa-mir-548i-1 LN:149
@SQ SN:hsa-mir-548i-2 LN:149
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@SQ SN:hsa-mir-1307 LN:149
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@SQ SN:hsa-mir-103b-1 LN:62
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@SQ SN:hsa-mir-1825 LN:53
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@SQ SN:hsa-mir-1911 LN:80
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@SQ SN:hsa-mir-1972-1 LN:77
@SQ SN:hsa-mir-1973 LN:44
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@SQ SN:hsa-mir-2052 LN:55
@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-2276 LN:89
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@SQ SN:hsa-mir-2681 LN:105
@SQ SN:hsa-mir-2682 LN:110
@SQ SN:hsa-mir-711 LN:76
@SQ SN:hsa-mir-718 LN:70
@SQ SN:hsa-mir-2861 LN:90
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@SQ SN:hsa-mir-3116-1 LN:74
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@SQ SN:hsa-mir-3119-1 LN:85
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@SQ SN:hsa-mir-3120 LN:81
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@SQ SN:hsa-mir-3137 LN:75
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@SQ SN:hsa-mir-3159 LN:74
@SQ SN:hsa-mir-3160-1 LN:85
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@SQ SN:hsa-mir-3161 LN:77
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@SQ SN:hsa-mir-3118-4 LN:75
@SQ SN:hsa-mir-3174 LN:87
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@SQ SN:hsa-mir-3180-3 LN:94
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@SQ SN:hsa-mir-3156-3 LN:77
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@SQ SN:hsa-mir-4314 LN:92
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@SQ SN:hsa-mir-4286 LN:93
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@SQ SN:hsa-mir-4290 LN:95
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@SQ SN:hsa-mir-4329 LN:71
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@SQ SN:hsa-mir-1184-2 LN:99
@SQ SN:hsa-mir-1184-3 LN:99
@SQ SN:hsa-mir-1233-2 LN:82
@SQ SN:hsa-mir-1244-2 LN:85
@SQ SN:hsa-mir-1244-3 LN:85
@SQ SN:hsa-mir-1972-2 LN:77
@SQ SN:hsa-mir-1302-9 LN:138
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@SQ SN:hsa-mir-1302-11 LN:138
@SQ SN:hsa-mir-4283-2 LN:80
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@SQ SN:hsa-mir-3605 LN:100
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@SQ SN:hsa-mir-3648-1 LN:180
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@SQ SN:hsa-mir-3652 LN:131
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@SQ SN:hsa-mir-3944 LN:108
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@SQ SN:hsa-mir-4536-1 LN:88
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@SQ SN:hsa-mir-6081 LN:97
@SQ SN:hsa-mir-6082 LN:109
@SQ SN:hsa-mir-6083 LN:106
@SQ SN:hsa-mir-6084 LN:110
@SQ SN:hsa-mir-6085 LN:110
@SQ SN:hsa-mir-6086 LN:55
@SQ SN:hsa-mir-6087 LN:49
@SQ SN:hsa-mir-6088 LN:51
@SQ SN:hsa-mir-6089-1 LN:64
@SQ SN:hsa-mir-6090 LN:60
@SQ SN:hsa-mir-6124 LN:85
@SQ SN:hsa-mir-6125 LN:96
@SQ SN:hsa-mir-6126 LN:89
@SQ SN:hsa-mir-6127 LN:109
@SQ SN:hsa-mir-6128 LN:109
@SQ SN:hsa-mir-378j LN:109
@SQ SN:hsa-mir-6129 LN:109
@SQ SN:hsa-mir-6130 LN:109
@SQ SN:hsa-mir-6131 LN:109
@SQ SN:hsa-mir-6132 LN:109
@SQ SN:hsa-mir-6133 LN:108
@SQ SN:hsa-mir-6134 LN:109
@SQ SN:hsa-mir-6165 LN:84
@SQ SN:hsa-mir-6499 LN:62
@SQ SN:hsa-mir-548ay LN:107
@SQ SN:hsa-mir-6500 LN:86
@SQ SN:hsa-mir-548az LN:95
@SQ SN:hsa-mir-6501 LN:67
@SQ SN:hsa-mir-6502 LN:76
@SQ SN:hsa-mir-6503 LN:86
@SQ SN:hsa-mir-6504 LN:61
@SQ SN:hsa-mir-6505 LN:71
@SQ SN:hsa-mir-6506 LN:66
@SQ SN:hsa-mir-6507 LN:70
@SQ SN:hsa-mir-6508 LN:60
@SQ SN:hsa-mir-6509 LN:85
@SQ SN:hsa-mir-6510 LN:54
@SQ SN:hsa-mir-6511a-1 LN:67
@SQ SN:hsa-mir-6512 LN:77
@SQ SN:hsa-mir-6513 LN:64
@SQ SN:hsa-mir-6514 LN:70
@SQ SN:hsa-mir-6515 LN:57
@SQ SN:hsa-mir-6715a LN:79
@SQ SN:hsa-mir-6715b LN:77
@SQ SN:hsa-mir-6716 LN:80
@SQ SN:hsa-mir-6717 LN:73
@SQ SN:hsa-mir-6511b-1 LN:85
@SQ SN:hsa-mir-6718 LN:80
@SQ SN:hsa-mir-6719 LN:87
@SQ SN:hsa-mir-6720 LN:98
@SQ SN:hsa-mir-6721 LN:87
@SQ SN:hsa-mir-6722 LN:78
@SQ SN:hsa-mir-6723 LN:89
@SQ SN:hsa-mir-6724-1 LN:92
@SQ SN:hsa-mir-892c LN:77
@SQ SN:hsa-mir-6726 LN:61
@SQ SN:hsa-mir-6727 LN:65
@SQ SN:hsa-mir-6728 LN:89
@SQ SN:hsa-mir-6729 LN:65
@SQ SN:hsa-mir-6730 LN:67
@SQ SN:hsa-mir-6731 LN:72
@SQ SN:hsa-mir-6732 LN:60
@SQ SN:hsa-mir-6733 LN:61
@SQ SN:hsa-mir-6734 LN:68
@SQ SN:hsa-mir-6735 LN:73
@SQ SN:hsa-mir-6736 LN:59
@SQ SN:hsa-mir-6737 LN:70
@SQ SN:hsa-mir-6738 LN:64
@SQ SN:hsa-mir-6739 LN:75
@SQ SN:hsa-mir-6740 LN:113
@SQ SN:hsa-mir-6741 LN:63
@SQ SN:hsa-mir-6742 LN:62
@SQ SN:hsa-mir-6743 LN:71
@SQ SN:hsa-mir-6744 LN:66
@SQ SN:hsa-mir-6745 LN:127
@SQ SN:hsa-mir-6746 LN:63
@SQ SN:hsa-mir-6747 LN:61
@SQ SN:hsa-mir-6748 LN:71
@SQ SN:hsa-mir-6749 LN:69
@SQ SN:hsa-mir-6750 LN:75
@SQ SN:hsa-mir-6751 LN:63
@SQ SN:hsa-mir-6752 LN:71
@SQ SN:hsa-mir-6753 LN:164
@SQ SN:hsa-mir-6754 LN:66
@SQ SN:hsa-mir-6755 LN:66
@SQ SN:hsa-mir-6756 LN:63
@SQ SN:hsa-mir-6757 LN:69
@SQ SN:hsa-mir-6758 LN:63
@SQ SN:hsa-mir-6759 LN:65
@SQ SN:hsa-mir-6760 LN:68
@SQ SN:hsa-mir-6761 LN:72
@SQ SN:hsa-mir-6762 LN:86
@SQ SN:hsa-mir-6763 LN:65
@SQ SN:hsa-mir-6764 LN:61
@SQ SN:hsa-mir-6765 LN:87
@SQ SN:hsa-mir-6766 LN:72
@SQ SN:hsa-mir-6767 LN:66
@SQ SN:hsa-mir-6768 LN:72
@SQ SN:hsa-mir-6769a LN:73
@SQ SN:hsa-mir-6770-1 LN:60
@SQ SN:hsa-mir-6771 LN:60
@SQ SN:hsa-mir-6772 LN:64
@SQ SN:hsa-mir-6773 LN:74
@SQ SN:hsa-mir-6774 LN:70
@SQ SN:hsa-mir-6775 LN:69
@SQ SN:hsa-mir-6776 LN:59
@SQ SN:hsa-mir-6777 LN:66
@SQ SN:hsa-mir-6778 LN:73
@SQ SN:hsa-mir-6779 LN:64
@SQ SN:hsa-mir-6780a LN:68
@SQ SN:hsa-mir-6781 LN:64
@SQ SN:hsa-mir-6782 LN:69
@SQ SN:hsa-mir-6783 LN:64
@SQ SN:hsa-mir-6784 LN:67
@SQ SN:hsa-mir-6785 LN:81
@SQ SN:hsa-mir-6786 LN:113
@SQ SN:hsa-mir-6787 LN:61
@SQ SN:hsa-mir-6788 LN:66
@SQ SN:hsa-mir-6789 LN:98
@SQ SN:hsa-mir-6790 LN:63
@SQ SN:hsa-mir-6791 LN:67
@SQ SN:hsa-mir-6792 LN:67
@SQ SN:hsa-mir-6793 LN:63
@SQ SN:hsa-mir-6794 LN:68
@SQ SN:hsa-mir-6795 LN:68
@SQ SN:hsa-mir-6796 LN:62
@SQ SN:hsa-mir-6797 LN:72
@SQ SN:hsa-mir-6798 LN:67
@SQ SN:hsa-mir-6799 LN:69
@SQ SN:hsa-mir-6800 LN:82
@SQ SN:hsa-mir-6801 LN:79
@SQ SN:hsa-mir-6802 LN:65
@SQ SN:hsa-mir-6803 LN:65
@SQ SN:hsa-mir-6804 LN:68
@SQ SN:hsa-mir-6805 LN:62
@SQ SN:hsa-mir-6806 LN:64
@SQ SN:hsa-mir-6807 LN:92
@SQ SN:hsa-mir-6808 LN:59
@SQ SN:hsa-mir-6809 LN:116
@SQ SN:hsa-mir-6810 LN:70
@SQ SN:hsa-mir-6811 LN:58
@SQ SN:hsa-mir-6812 LN:64
@SQ SN:hsa-mir-6813 LN:56
@SQ SN:hsa-mir-6814 LN:70
@SQ SN:hsa-mir-6815 LN:61
@SQ SN:hsa-mir-6816 LN:66
@SQ SN:hsa-mir-6817 LN:66
@SQ SN:hsa-mir-6818 LN:65
@SQ SN:hsa-mir-6819 LN:61
@SQ SN:hsa-mir-6820 LN:62
@SQ SN:hsa-mir-6821 LN:74
@SQ SN:hsa-mir-6822 LN:61
@SQ SN:hsa-mir-6823 LN:61
@SQ SN:hsa-mir-6824 LN:63
@SQ SN:hsa-mir-6825 LN:66
@SQ SN:hsa-mir-6826 LN:98
@SQ SN:hsa-mir-6827 LN:59
@SQ SN:hsa-mir-6828 LN:60
@SQ SN:hsa-mir-6829 LN:67
@SQ SN:hsa-mir-6830 LN:70
@SQ SN:hsa-mir-6831 LN:81
@SQ SN:hsa-mir-6832 LN:72
@SQ SN:hsa-mir-6833 LN:61
@SQ SN:hsa-mir-6834 LN:81
@SQ SN:hsa-mir-6835 LN:64
@SQ SN:hsa-mir-6780b LN:79
@SQ SN:hsa-mir-6836 LN:63
@SQ SN:hsa-mir-6837 LN:64
@SQ SN:hsa-mir-6838 LN:56
@SQ SN:hsa-mir-6839 LN:113
@SQ SN:hsa-mir-6840 LN:71
@SQ SN:hsa-mir-6841 LN:72
@SQ SN:hsa-mir-6842 LN:65
@SQ SN:hsa-mir-6843 LN:151
@SQ SN:hsa-mir-6844 LN:62
@SQ SN:hsa-mir-6845 LN:61
@SQ SN:hsa-mir-6846 LN:60
@SQ SN:hsa-mir-6847 LN:69
@SQ SN:hsa-mir-6848 LN:70
@SQ SN:hsa-mir-6849 LN:69
@SQ SN:hsa-mir-6850 LN:61
@SQ SN:hsa-mir-6851 LN:67
@SQ SN:hsa-mir-6852 LN:66
@SQ SN:hsa-mir-6853 LN:74
@SQ SN:hsa-mir-6854 LN:69
@SQ SN:hsa-mir-6855 LN:67
@SQ SN:hsa-mir-6856 LN:67
@SQ SN:hsa-mir-6857 LN:93
@SQ SN:hsa-mir-6858 LN:67
@SQ SN:hsa-mir-6859-1 LN:68
@SQ SN:hsa-mir-6769b LN:62
@SQ SN:hsa-mir-6860 LN:66
@SQ SN:hsa-mir-6861 LN:64
@SQ SN:hsa-mir-6862-1 LN:70
@SQ SN:hsa-mir-6863 LN:90
@SQ SN:hsa-mir-6864 LN:70
@SQ SN:hsa-mir-6865 LN:65
@SQ SN:hsa-mir-6866 LN:69
@SQ SN:hsa-mir-6867 LN:67
@SQ SN:hsa-mir-6868 LN:58
@SQ SN:hsa-mir-6869 LN:62
@SQ SN:hsa-mir-6870 LN:60
@SQ SN:hsa-mir-6871 LN:56
@SQ SN:hsa-mir-6872 LN:62
@SQ SN:hsa-mir-6873 LN:63
@SQ SN:hsa-mir-6874 LN:71
@SQ SN:hsa-mir-6875 LN:72
@SQ SN:hsa-mir-6876 LN:73
@SQ SN:hsa-mir-6877 LN:64
@SQ SN:hsa-mir-6878 LN:66
@SQ SN:hsa-mir-6879 LN:66
@SQ SN:hsa-mir-6880 LN:62
@SQ SN:hsa-mir-6881 LN:76
@SQ SN:hsa-mir-6882 LN:66
@SQ SN:hsa-mir-6883 LN:78
@SQ SN:hsa-mir-6884 LN:78
@SQ SN:hsa-mir-6885 LN:66
@SQ SN:hsa-mir-6886 LN:61
@SQ SN:hsa-mir-6887 LN:65
@SQ SN:hsa-mir-6888 LN:67
@SQ SN:hsa-mir-6889 LN:59
@SQ SN:hsa-mir-6890 LN:61
@SQ SN:hsa-mir-6891 LN:93
@SQ SN:hsa-mir-6892 LN:115
@SQ SN:hsa-mir-6893 LN:69
@SQ SN:hsa-mir-6894 LN:57
@SQ SN:hsa-mir-6895 LN:78
@SQ SN:hsa-mir-7106 LN:65
@SQ SN:hsa-mir-7107 LN:80
@SQ SN:hsa-mir-7108 LN:87
@SQ SN:hsa-mir-7109 LN:65
@SQ SN:hsa-mir-7110 LN:86
@SQ SN:hsa-mir-7111 LN:72
@SQ SN:hsa-mir-7112 LN:65
@SQ SN:hsa-mir-7113 LN:59
@SQ SN:hsa-mir-7114 LN:61
@SQ SN:hsa-mir-6511b-2 LN:71
@SQ SN:hsa-mir-3690-2 LN:75
@SQ SN:hsa-mir-6089-2 LN:64
@SQ SN:hsa-mir-6511a-2 LN:67
@SQ SN:hsa-mir-6511a-3 LN:67
@SQ SN:hsa-mir-6511a-4 LN:67
@SQ SN:hsa-mir-7150 LN:94
@SQ SN:hsa-mir-7151 LN:60
@SQ SN:hsa-mir-7152 LN:54
@SQ SN:hsa-mir-7153 LN:57
@SQ SN:hsa-mir-7154 LN:73
@SQ SN:hsa-mir-7155 LN:56
@SQ SN:hsa-mir-7156 LN:60
@SQ SN:hsa-mir-7157 LN:60
@SQ SN:hsa-mir-7158 LN:71
@SQ SN:hsa-mir-7161 LN:84
@SQ SN:hsa-mir-7159 LN:66
@SQ SN:hsa-mir-7160 LN:52
@SQ SN:hsa-mir-486-2 LN:64
@SQ SN:hsa-mir-7162 LN:69
@SQ SN:hsa-mir-7515 LN:67
@SQ SN:hsa-mir-7641-1 LN:61
@SQ SN:hsa-mir-7641-2 LN:53
@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_perfect_x2 0 hsa-let-7a-1 6 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT NM:i:2 MD:Z:22
mirtop-0.4.23/data/aligments/let7-triming.sam 0000664 0000000 0000000 00000141212 13547635037 0021050 0 ustar 00root root 0000000 0000000 @SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
@SQ SN:hsa-let-7b LN:83
@SQ SN:hsa-let-7c LN:84
@SQ SN:hsa-let-7d LN:87
@SQ SN:hsa-let-7e LN:79
@SQ SN:hsa-let-7f-1 LN:87
@SQ SN:hsa-let-7f-2 LN:83
@SQ SN:hsa-mir-15a LN:83
@SQ SN:hsa-mir-16-1 LN:89
@SQ SN:hsa-mir-17 LN:84
@SQ SN:hsa-mir-18a LN:71
@SQ SN:hsa-mir-19a LN:82
@SQ SN:hsa-mir-19b-1 LN:87
@SQ SN:hsa-mir-19b-2 LN:96
@SQ SN:hsa-mir-20a LN:71
@SQ SN:hsa-mir-21 LN:72
@SQ SN:hsa-mir-22 LN:85
@SQ SN:hsa-mir-23a LN:73
@SQ SN:hsa-mir-24-1 LN:68
@SQ SN:hsa-mir-24-2 LN:73
@SQ SN:hsa-mir-25 LN:84
@SQ SN:hsa-mir-26a-1 LN:77
@SQ SN:hsa-mir-26b LN:77
@SQ SN:hsa-mir-27a LN:78
@SQ SN:hsa-mir-28 LN:86
@SQ SN:hsa-mir-29a LN:64
@SQ SN:hsa-mir-30a LN:71
@SQ SN:hsa-mir-31 LN:71
@SQ SN:hsa-mir-32 LN:70
@SQ SN:hsa-mir-33a LN:69
@SQ SN:hsa-mir-92a-1 LN:78
@SQ SN:hsa-mir-92a-2 LN:75
@SQ SN:hsa-mir-93 LN:80
@SQ SN:hsa-mir-95 LN:81
@SQ SN:hsa-mir-96 LN:78
@SQ SN:hsa-mir-98 LN:119
@SQ SN:hsa-mir-99a LN:81
@SQ SN:hsa-mir-100 LN:80
@SQ SN:hsa-mir-101-1 LN:75
@SQ SN:hsa-mir-29b-1 LN:81
@SQ SN:hsa-mir-29b-2 LN:81
@SQ SN:hsa-mir-103a-2 LN:78
@SQ SN:hsa-mir-103a-1 LN:78
@SQ SN:hsa-mir-105-1 LN:81
@SQ SN:hsa-mir-105-2 LN:81
@SQ SN:hsa-mir-106a LN:81
@SQ SN:hsa-mir-107 LN:81
@SQ SN:hsa-mir-16-2 LN:81
@SQ SN:hsa-mir-192 LN:110
@SQ SN:hsa-mir-196a-1 LN:70
@SQ SN:hsa-mir-197 LN:75
@SQ SN:hsa-mir-198 LN:62
@SQ SN:hsa-mir-199a-1 LN:71
@SQ SN:hsa-mir-208a LN:71
@SQ SN:hsa-mir-129-1 LN:72
@SQ SN:hsa-mir-148a LN:68
@SQ SN:hsa-mir-30c-2 LN:72
@SQ SN:hsa-mir-30d LN:70
@SQ SN:hsa-mir-139 LN:68
@SQ SN:hsa-mir-147a LN:72
@SQ SN:hsa-mir-7-1 LN:110
@SQ SN:hsa-mir-7-2 LN:110
@SQ SN:hsa-mir-7-3 LN:110
@SQ SN:hsa-mir-10a LN:110
@SQ SN:hsa-mir-10b LN:110
@SQ SN:hsa-mir-34a LN:110
@SQ SN:hsa-mir-181a-2 LN:110
@SQ SN:hsa-mir-181b-1 LN:110
@SQ SN:hsa-mir-181c LN:110
@SQ SN:hsa-mir-182 LN:110
@SQ SN:hsa-mir-183 LN:110
@SQ SN:hsa-mir-187 LN:109
@SQ SN:hsa-mir-196a-2 LN:110
@SQ SN:hsa-mir-199a-2 LN:110
@SQ SN:hsa-mir-199b LN:110
@SQ SN:hsa-mir-203a LN:110
@SQ SN:hsa-mir-204 LN:110
@SQ SN:hsa-mir-205 LN:110
@SQ SN:hsa-mir-210 LN:110
@SQ SN:hsa-mir-211 LN:110
@SQ SN:hsa-mir-212 LN:110
@SQ SN:hsa-mir-181a-1 LN:110
@SQ SN:hsa-mir-214 LN:110
@SQ SN:hsa-mir-215 LN:110
@SQ SN:hsa-mir-216a LN:110
@SQ SN:hsa-mir-217 LN:110
@SQ SN:hsa-mir-218-1 LN:110
@SQ SN:hsa-mir-218-2 LN:110
@SQ SN:hsa-mir-219a-1 LN:110
@SQ SN:hsa-mir-221 LN:110
@SQ SN:hsa-mir-222 LN:110
@SQ SN:hsa-mir-223 LN:110
@SQ SN:hsa-mir-224 LN:81
@SQ SN:hsa-mir-200b LN:95
@SQ SN:hsa-let-7g LN:84
@SQ SN:hsa-let-7i LN:84
@SQ SN:hsa-mir-1-2 LN:85
@SQ SN:hsa-mir-15b LN:98
@SQ SN:hsa-mir-23b LN:97
@SQ SN:hsa-mir-27b LN:97
@SQ SN:hsa-mir-30b LN:88
@SQ SN:hsa-mir-122 LN:85
@SQ SN:hsa-mir-124-1 LN:85
@SQ SN:hsa-mir-124-2 LN:109
@SQ SN:hsa-mir-124-3 LN:87
@SQ SN:hsa-mir-125b-1 LN:88
@SQ SN:hsa-mir-128-1 LN:82
@SQ SN:hsa-mir-130a LN:89
@SQ SN:hsa-mir-132 LN:101
@SQ SN:hsa-mir-133a-1 LN:88
@SQ SN:hsa-mir-133a-2 LN:102
@SQ SN:hsa-mir-135a-1 LN:90
@SQ SN:hsa-mir-135a-2 LN:100
@SQ SN:hsa-mir-137 LN:102
@SQ SN:hsa-mir-138-2 LN:84
@SQ SN:hsa-mir-140 LN:100
@SQ SN:hsa-mir-141 LN:95
@SQ SN:hsa-mir-142 LN:87
@SQ SN:hsa-mir-143 LN:106
@SQ SN:hsa-mir-144 LN:86
@SQ SN:hsa-mir-145 LN:88
@SQ SN:hsa-mir-152 LN:87
@SQ SN:hsa-mir-153-1 LN:90
@SQ SN:hsa-mir-153-2 LN:87
@SQ SN:hsa-mir-191 LN:92
@SQ SN:hsa-mir-9-1 LN:89
@SQ SN:hsa-mir-9-2 LN:87
@SQ SN:hsa-mir-9-3 LN:90
@SQ SN:hsa-mir-125a LN:86
@SQ SN:hsa-mir-125b-2 LN:89
@SQ SN:hsa-mir-126 LN:85
@SQ SN:hsa-mir-127 LN:97
@SQ SN:hsa-mir-129-2 LN:90
@SQ SN:hsa-mir-134 LN:73
@SQ SN:hsa-mir-136 LN:82
@SQ SN:hsa-mir-138-1 LN:99
@SQ SN:hsa-mir-146a LN:99
@SQ SN:hsa-mir-149 LN:89
@SQ SN:hsa-mir-150 LN:84
@SQ SN:hsa-mir-154 LN:84
@SQ SN:hsa-mir-184 LN:84
@SQ SN:hsa-mir-185 LN:82
@SQ SN:hsa-mir-186 LN:86
@SQ SN:hsa-mir-188 LN:86
@SQ SN:hsa-mir-190a LN:85
@SQ SN:hsa-mir-193a LN:88
@SQ SN:hsa-mir-194-1 LN:85
@SQ SN:hsa-mir-195 LN:87
@SQ SN:hsa-mir-206 LN:86
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@SQ SN:hsa-mir-181b-2 LN:89
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@SQ SN:hsa-mir-302a LN:69
@SQ SN:hsa-mir-101-2 LN:79
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@SQ SN:hsa-mir-361 LN:72
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@SQ SN:hsa-mir-302b LN:73
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@SQ SN:hsa-mir-367 LN:68
@SQ SN:hsa-mir-376c LN:66
@SQ SN:hsa-mir-369 LN:70
@SQ SN:hsa-mir-370 LN:75
@SQ SN:hsa-mir-371a LN:67
@SQ SN:hsa-mir-372 LN:67
@SQ SN:hsa-mir-373 LN:69
@SQ SN:hsa-mir-374a LN:72
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@SQ SN:hsa-mir-377 LN:69
@SQ SN:hsa-mir-378a LN:66
@SQ SN:hsa-mir-379 LN:67
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@SQ SN:hsa-mir-448 LN:111
@SQ SN:hsa-mir-429 LN:83
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@SQ SN:hsa-mir-450a-1 LN:91
@SQ SN:hsa-mir-431 LN:114
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@SQ SN:hsa-mir-329-1 LN:80
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@SQ SN:hsa-mir-409 LN:79
@SQ SN:hsa-mir-412 LN:91
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@SQ SN:hsa-mir-376b LN:100
@SQ SN:hsa-mir-483 LN:76
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@SQ SN:hsa-mir-490 LN:128
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@SQ SN:hsa-mir-202 LN:110
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@SQ SN:hsa-mir-496 LN:102
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@SQ SN:hsa-mir-497 LN:112
@SQ SN:hsa-mir-181d LN:137
@SQ SN:hsa-mir-512-1 LN:84
@SQ SN:hsa-mir-512-2 LN:98
@SQ SN:hsa-mir-498 LN:124
@SQ SN:hsa-mir-520e LN:87
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@SQ SN:hsa-mir-519b LN:81
@SQ SN:hsa-mir-525 LN:85
@SQ SN:hsa-mir-523 LN:87
@SQ SN:hsa-mir-518f LN:87
@SQ SN:hsa-mir-520b LN:61
@SQ SN:hsa-mir-518b LN:83
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@SQ SN:hsa-mir-520c LN:87
@SQ SN:hsa-mir-518c LN:101
@SQ SN:hsa-mir-524 LN:87
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@SQ SN:hsa-mir-519d LN:88
@SQ SN:hsa-mir-521-2 LN:87
@SQ SN:hsa-mir-520d LN:87
@SQ SN:hsa-mir-517b LN:67
@SQ SN:hsa-mir-520g LN:90
@SQ SN:hsa-mir-516b-2 LN:85
@SQ SN:hsa-mir-526a-2 LN:65
@SQ SN:hsa-mir-518e LN:88
@SQ SN:hsa-mir-518a-1 LN:85
@SQ SN:hsa-mir-518d LN:87
@SQ SN:hsa-mir-516b-1 LN:90
@SQ SN:hsa-mir-518a-2 LN:87
@SQ SN:hsa-mir-517c LN:95
@SQ SN:hsa-mir-520h LN:88
@SQ SN:hsa-mir-521-1 LN:87
@SQ SN:hsa-mir-522 LN:87
@SQ SN:hsa-mir-519a-1 LN:85
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@SQ SN:hsa-mir-516a-1 LN:90
@SQ SN:hsa-mir-516a-2 LN:90
@SQ SN:hsa-mir-519a-2 LN:87
@SQ SN:hsa-mir-499a LN:122
@SQ SN:hsa-mir-500a LN:84
@SQ SN:hsa-mir-501 LN:84
@SQ SN:hsa-mir-502 LN:86
@SQ SN:hsa-mir-450a-2 LN:100
@SQ SN:hsa-mir-503 LN:71
@SQ SN:hsa-mir-504 LN:83
@SQ SN:hsa-mir-505 LN:84
@SQ SN:hsa-mir-513a-1 LN:129
@SQ SN:hsa-mir-513a-2 LN:127
@SQ SN:hsa-mir-506 LN:124
@SQ SN:hsa-mir-507 LN:94
@SQ SN:hsa-mir-508 LN:115
@SQ SN:hsa-mir-509-1 LN:94
@SQ SN:hsa-mir-510 LN:74
@SQ SN:hsa-mir-514a-1 LN:98
@SQ SN:hsa-mir-514a-2 LN:88
@SQ SN:hsa-mir-514a-3 LN:88
@SQ SN:hsa-mir-532 LN:91
@SQ SN:hsa-mir-455 LN:96
@SQ SN:hsa-mir-539 LN:78
@SQ SN:hsa-mir-544a LN:91
@SQ SN:hsa-mir-545 LN:106
@SQ SN:hsa-mir-376a-2 LN:80
@SQ SN:hsa-mir-487b LN:84
@SQ SN:hsa-mir-551a LN:96
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@SQ SN:hsa-mir-553 LN:68
@SQ SN:hsa-mir-554 LN:96
@SQ SN:hsa-mir-92b LN:96
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@SQ SN:hsa-mir-563 LN:79
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@SQ SN:hsa-mir-596 LN:77
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@SQ SN:hsa-mir-601 LN:79
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@SQ SN:hsa-mir-611 LN:67
@SQ SN:hsa-mir-612 LN:100
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@SQ SN:hsa-mir-614 LN:90
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@SQ SN:hsa-mir-661 LN:89
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@SQ SN:hsa-mir-654 LN:81
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@SQ SN:hsa-mir-421 LN:85
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@SQ SN:hsa-mir-758 LN:88
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@SQ SN:hsa-mir-671 LN:118
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@SQ SN:hsa-mir-550a-3 LN:95
@SQ SN:hsa-mir-767 LN:109
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@SQ SN:hsa-mir-320b-1 LN:79
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@SQ SN:hsa-mir-1296 LN:92
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@SQ SN:hsa-mir-1301 LN:82
@SQ SN:hsa-mir-454 LN:115
@SQ SN:hsa-mir-1185-2 LN:86
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@SQ SN:hsa-mir-1283-1 LN:87
@SQ SN:hsa-mir-769 LN:118
@SQ SN:hsa-mir-766 LN:111
@SQ SN:hsa-mir-320b-2 LN:138
@SQ SN:hsa-mir-378d-2 LN:98
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@SQ SN:hsa-mir-762 LN:83
@SQ SN:hsa-mir-802 LN:94
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@SQ SN:hsa-mir-2113 LN:91
@SQ SN:hsa-mir-761 LN:59
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@SQ SN:hsa-mir-759 LN:91
@SQ SN:hsa-mir-765 LN:114
@SQ SN:hsa-mir-770 LN:98
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@SQ SN:hsa-mir-298 LN:88
@SQ SN:hsa-mir-891a LN:79
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@SQ SN:hsa-mir-892a LN:75
@SQ SN:hsa-mir-509-2 LN:91
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@SQ SN:hsa-mir-874 LN:78
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@SQ SN:hsa-mir-541 LN:84
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@SQ SN:hsa-mir-744 LN:98
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@SQ SN:hsa-mir-940 LN:94
@SQ SN:hsa-mir-941-1 LN:72
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@SQ SN:hsa-mir-297 LN:66
@SQ SN:hsa-mir-1178 LN:91
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@SQ SN:hsa-mir-1180 LN:69
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@SQ SN:hsa-mir-1225 LN:90
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@SQ SN:hsa-mir-1227 LN:88
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@SQ SN:hsa-mir-1231 LN:92
@SQ SN:hsa-mir-1233-1 LN:82
@SQ SN:hsa-mir-1234 LN:80
@SQ SN:hsa-mir-1236 LN:102
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@SQ SN:hsa-mir-1200 LN:76
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@SQ SN:hsa-mir-663b LN:115
@SQ SN:hsa-mir-1204 LN:67
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@SQ SN:hsa-mir-1285-2 LN:88
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@SQ SN:hsa-mir-1289-1 LN:144
@SQ SN:hsa-mir-1289-2 LN:111
@SQ SN:hsa-mir-1290 LN:78
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@SQ SN:hsa-mir-1302-1 LN:143
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@SQ SN:hsa-mir-1302-4 LN:150
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@SQ SN:hsa-mir-1302-8 LN:128
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@SQ SN:hsa-mir-664a LN:82
@SQ SN:hsa-mir-1306 LN:85
@SQ SN:hsa-mir-1307 LN:149
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@SQ SN:hsa-mir-1911 LN:80
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@SQ SN:hsa-mir-1972-1 LN:77
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@SQ SN:hsa-mir-2053 LN:91
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@SQ SN:hsa-mir-2110 LN:75
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@SQ SN:hsa-mir-3648-1 LN:180
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@SQ SN:hsa-mir-3180-4 LN:153
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@SQ SN:hsa-mir-3908 LN:126
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@SQ SN:hsa-mir-3934 LN:107
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@SQ SN:hsa-mir-3945 LN:98
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@SQ SN:hsa-mir-548o-2 LN:70
@SQ SN:hsa-mir-1254-2 LN:63
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@SQ SN:hsa-mir-4419b LN:68
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@SQ SN:hsa-mir-4708 LN:67
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@SQ SN:hsa-mir-4737 LN:81
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@SQ SN:hsa-mir-5692c-1 LN:91
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@SQ SN:hsa-mir-6798 LN:67
@SQ SN:hsa-mir-6799 LN:69
@SQ SN:hsa-mir-6800 LN:82
@SQ SN:hsa-mir-6801 LN:79
@SQ SN:hsa-mir-6802 LN:65
@SQ SN:hsa-mir-6803 LN:65
@SQ SN:hsa-mir-6804 LN:68
@SQ SN:hsa-mir-6805 LN:62
@SQ SN:hsa-mir-6806 LN:64
@SQ SN:hsa-mir-6807 LN:92
@SQ SN:hsa-mir-6808 LN:59
@SQ SN:hsa-mir-6809 LN:116
@SQ SN:hsa-mir-6810 LN:70
@SQ SN:hsa-mir-6811 LN:58
@SQ SN:hsa-mir-6812 LN:64
@SQ SN:hsa-mir-6813 LN:56
@SQ SN:hsa-mir-6814 LN:70
@SQ SN:hsa-mir-6815 LN:61
@SQ SN:hsa-mir-6816 LN:66
@SQ SN:hsa-mir-6817 LN:66
@SQ SN:hsa-mir-6818 LN:65
@SQ SN:hsa-mir-6819 LN:61
@SQ SN:hsa-mir-6820 LN:62
@SQ SN:hsa-mir-6821 LN:74
@SQ SN:hsa-mir-6822 LN:61
@SQ SN:hsa-mir-6823 LN:61
@SQ SN:hsa-mir-6824 LN:63
@SQ SN:hsa-mir-6825 LN:66
@SQ SN:hsa-mir-6826 LN:98
@SQ SN:hsa-mir-6827 LN:59
@SQ SN:hsa-mir-6828 LN:60
@SQ SN:hsa-mir-6829 LN:67
@SQ SN:hsa-mir-6830 LN:70
@SQ SN:hsa-mir-6831 LN:81
@SQ SN:hsa-mir-6832 LN:72
@SQ SN:hsa-mir-6833 LN:61
@SQ SN:hsa-mir-6834 LN:81
@SQ SN:hsa-mir-6835 LN:64
@SQ SN:hsa-mir-6780b LN:79
@SQ SN:hsa-mir-6836 LN:63
@SQ SN:hsa-mir-6837 LN:64
@SQ SN:hsa-mir-6838 LN:56
@SQ SN:hsa-mir-6839 LN:113
@SQ SN:hsa-mir-6840 LN:71
@SQ SN:hsa-mir-6841 LN:72
@SQ SN:hsa-mir-6842 LN:65
@SQ SN:hsa-mir-6843 LN:151
@SQ SN:hsa-mir-6844 LN:62
@SQ SN:hsa-mir-6845 LN:61
@SQ SN:hsa-mir-6846 LN:60
@SQ SN:hsa-mir-6847 LN:69
@SQ SN:hsa-mir-6848 LN:70
@SQ SN:hsa-mir-6849 LN:69
@SQ SN:hsa-mir-6850 LN:61
@SQ SN:hsa-mir-6851 LN:67
@SQ SN:hsa-mir-6852 LN:66
@SQ SN:hsa-mir-6853 LN:74
@SQ SN:hsa-mir-6854 LN:69
@SQ SN:hsa-mir-6855 LN:67
@SQ SN:hsa-mir-6856 LN:67
@SQ SN:hsa-mir-6857 LN:93
@SQ SN:hsa-mir-6858 LN:67
@SQ SN:hsa-mir-6859-1 LN:68
@SQ SN:hsa-mir-6769b LN:62
@SQ SN:hsa-mir-6860 LN:66
@SQ SN:hsa-mir-6861 LN:64
@SQ SN:hsa-mir-6862-1 LN:70
@SQ SN:hsa-mir-6863 LN:90
@SQ SN:hsa-mir-6864 LN:70
@SQ SN:hsa-mir-6865 LN:65
@SQ SN:hsa-mir-6866 LN:69
@SQ SN:hsa-mir-6867 LN:67
@SQ SN:hsa-mir-6868 LN:58
@SQ SN:hsa-mir-6869 LN:62
@SQ SN:hsa-mir-6870 LN:60
@SQ SN:hsa-mir-6871 LN:56
@SQ SN:hsa-mir-6872 LN:62
@SQ SN:hsa-mir-6873 LN:63
@SQ SN:hsa-mir-6874 LN:71
@SQ SN:hsa-mir-6875 LN:72
@SQ SN:hsa-mir-6876 LN:73
@SQ SN:hsa-mir-6877 LN:64
@SQ SN:hsa-mir-6878 LN:66
@SQ SN:hsa-mir-6879 LN:66
@SQ SN:hsa-mir-6880 LN:62
@SQ SN:hsa-mir-6881 LN:76
@SQ SN:hsa-mir-6882 LN:66
@SQ SN:hsa-mir-6883 LN:78
@SQ SN:hsa-mir-6884 LN:78
@SQ SN:hsa-mir-6885 LN:66
@SQ SN:hsa-mir-6886 LN:61
@SQ SN:hsa-mir-6887 LN:65
@SQ SN:hsa-mir-6888 LN:67
@SQ SN:hsa-mir-6889 LN:59
@SQ SN:hsa-mir-6890 LN:61
@SQ SN:hsa-mir-6891 LN:93
@SQ SN:hsa-mir-6892 LN:115
@SQ SN:hsa-mir-6893 LN:69
@SQ SN:hsa-mir-6894 LN:57
@SQ SN:hsa-mir-6895 LN:78
@SQ SN:hsa-mir-7106 LN:65
@SQ SN:hsa-mir-7107 LN:80
@SQ SN:hsa-mir-7108 LN:87
@SQ SN:hsa-mir-7109 LN:65
@SQ SN:hsa-mir-7110 LN:86
@SQ SN:hsa-mir-7111 LN:72
@SQ SN:hsa-mir-7112 LN:65
@SQ SN:hsa-mir-7113 LN:59
@SQ SN:hsa-mir-7114 LN:61
@SQ SN:hsa-mir-6511b-2 LN:71
@SQ SN:hsa-mir-3690-2 LN:75
@SQ SN:hsa-mir-6089-2 LN:64
@SQ SN:hsa-mir-6511a-2 LN:67
@SQ SN:hsa-mir-6511a-3 LN:67
@SQ SN:hsa-mir-6511a-4 LN:67
@SQ SN:hsa-mir-7150 LN:94
@SQ SN:hsa-mir-7151 LN:60
@SQ SN:hsa-mir-7152 LN:54
@SQ SN:hsa-mir-7153 LN:57
@SQ SN:hsa-mir-7154 LN:73
@SQ SN:hsa-mir-7155 LN:56
@SQ SN:hsa-mir-7156 LN:60
@SQ SN:hsa-mir-7157 LN:60
@SQ SN:hsa-mir-7158 LN:71
@SQ SN:hsa-mir-7161 LN:84
@SQ SN:hsa-mir-7159 LN:66
@SQ SN:hsa-mir-7160 LN:52
@SQ SN:hsa-mir-486-2 LN:64
@SQ SN:hsa-mir-7162 LN:69
@SQ SN:hsa-mir-7515 LN:67
@SQ SN:hsa-mir-7641-1 LN:61
@SQ SN:hsa-mir-7641-2 LN:53
@SQ SN:hsa-mir-7702 LN:59
@SQ SN:hsa-mir-7703 LN:77
@SQ SN:hsa-mir-7704 LN:59
@SQ SN:hsa-mir-7705 LN:57
@SQ SN:hsa-mir-7706 LN:67
@SQ SN:hsa-mir-7843 LN:79
@SQ SN:hsa-mir-4433b LN:102
@SQ SN:hsa-mir-1273h LN:116
@SQ SN:hsa-mir-6516 LN:81
@SQ SN:hsa-mir-7844 LN:122
@SQ SN:hsa-mir-7845 LN:99
@SQ SN:hsa-mir-7846 LN:96
@SQ SN:hsa-mir-7847 LN:103
@SQ SN:hsa-mir-7848 LN:101
@SQ SN:hsa-mir-7849 LN:106
@SQ SN:hsa-mir-7850 LN:79
@SQ SN:hsa-mir-7851 LN:160
@SQ SN:hsa-mir-7852 LN:82
@SQ SN:hsa-mir-7853 LN:132
@SQ SN:hsa-mir-7854 LN:65
@SQ SN:hsa-mir-7855 LN:61
@SQ SN:hsa-mir-7856 LN:56
@SQ SN:hsa-mir-548ba LN:56
@SQ SN:hsa-mir-7973-1 LN:76
@SQ SN:hsa-mir-7973-2 LN:76
@SQ SN:hsa-mir-7974 LN:79
@SQ SN:hsa-mir-7975 LN:68
@SQ SN:hsa-mir-7976 LN:66
@SQ SN:hsa-mir-7977 LN:49
@SQ SN:hsa-mir-7978 LN:59
@SQ SN:hsa-mir-8052 LN:69
@SQ SN:hsa-mir-8053 LN:75
@SQ SN:hsa-mir-8054 LN:86
@SQ SN:hsa-mir-8055 LN:97
@SQ SN:hsa-mir-8056 LN:82
@SQ SN:hsa-mir-8057 LN:69
@SQ SN:hsa-mir-8058 LN:89
@SQ SN:hsa-mir-8059 LN:81
@SQ SN:hsa-mir-8060 LN:76
@SQ SN:hsa-mir-8061 LN:75
@SQ SN:hsa-mir-8062 LN:85
@SQ SN:hsa-mir-8063 LN:81
@SQ SN:hsa-mir-8064 LN:90
@SQ SN:hsa-mir-8065 LN:100
@SQ SN:hsa-mir-8066 LN:78
@SQ SN:hsa-mir-8067 LN:77
@SQ SN:hsa-mir-8068 LN:68
@SQ SN:hsa-mir-8069-1 LN:86
@SQ SN:hsa-mir-8070 LN:88
@SQ SN:hsa-mir-8071-1 LN:65
@SQ SN:hsa-mir-8072 LN:80
@SQ SN:hsa-mir-8073 LN:72
@SQ SN:hsa-mir-8074 LN:81
@SQ SN:hsa-mir-8075 LN:80
@SQ SN:hsa-mir-8076 LN:83
@SQ SN:hsa-mir-8077 LN:75
@SQ SN:hsa-mir-8078 LN:84
@SQ SN:hsa-mir-8079 LN:72
@SQ SN:hsa-mir-8080 LN:89
@SQ SN:hsa-mir-8081 LN:95
@SQ SN:hsa-mir-8082 LN:81
@SQ SN:hsa-mir-8083 LN:89
@SQ SN:hsa-mir-8084 LN:89
@SQ SN:hsa-mir-8085 LN:65
@SQ SN:hsa-mir-8086 LN:93
@SQ SN:hsa-mir-8087 LN:78
@SQ SN:hsa-mir-8088 LN:86
@SQ SN:hsa-mir-8089 LN:82
@SQ SN:hsa-mir-6862-2 LN:70
@SQ SN:hsa-mir-8071-2 LN:65
@SQ SN:hsa-mir-6770-2 LN:60
@SQ SN:hsa-mir-6770-3 LN:60
@SQ SN:hsa-mir-6859-2 LN:68
@SQ SN:hsa-mir-6859-3 LN:68
@SQ SN:hsa-mir-8485 LN:91
@SQ SN:hsa-mir-9500 LN:65
@SQ SN:hsa-mir-548bb LN:66
@SQ SN:hsa-mir-3179-4 LN:84
@SQ SN:hsa-mir-1244-4 LN:85
@SQ SN:hsa-mir-3648-2 LN:180
@SQ SN:hsa-mir-3670-3 LN:65
@SQ SN:hsa-mir-3670-4 LN:65
@SQ SN:hsa-mir-3687-2 LN:61
@SQ SN:hsa-mir-6724-2 LN:92
@SQ SN:hsa-mir-6724-3 LN:92
@SQ SN:hsa-mir-6724-4 LN:92
@SQ SN:hsa-mir-8069-2 LN:86
@SQ SN:hsa-mir-941-5 LN:72
@SQ SN:hsa-mir-6859-4 LN:68
@SQ SN:hsa-mir-5701-3 LN:82
seq_3tt_x2 0 hsa-let-7a-1 6 255 20M * 0 0 TGAGGTAGTAGGTTGTATAG TGAGGTAGTAGGTTGTATAG NM:i:2 MD:Z:20
seq_3TT_x2 0 hsa-let-7a-1 6 255 24M * 0 0 TGAGGTAGTAGGTTGTATAGTTTT TGAGGTAGTAGGTTGTATAGTTTT NM:i:2 MD:Z:24
seq_5A_x2 0 hsa-let-7a-1 5 255 23M * 0 0 ATGAGGTAGTAGGTTGTATAGTT ATGAGGTAGTAGGTTGTATAGTT NM:i:2 MD:Z:23
seq_5t3gtt_x2 0 hsa-let-7a-1 7 255 18M * 0 0 GAGGTAGTAGGTTGTATA GAGGTAGTAGGTTGTATA NM:i:2 MD:Z:18
mirtop-0.4.23/data/db/ 0000775 0000000 0000000 00000000000 13547635037 0014425 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/db/mature/ 0000775 0000000 0000000 00000000000 13547635037 0015722 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/db/mature/mature.fa 0000664 0000000 0000000 00000000212 13547635037 0017522 0 ustar 00root root 0000000 0000000 >hsa-let-7a-1
TGGGATGAGGTAGTAGGTTGTA
>hsa-let-7a-2
TGGGATGAGCTAGTAGGTTGTA
>fake-3
GGGTGACCGCCCCAGGGTCCCAT
>fake-4
GGGTGATTTTTTTAGGGTCCCAT
mirtop-0.4.23/data/db/mature/universe.fa 0000664 0000000 0000000 00000000044 13547635037 0020070 0 ustar 00root root 0000000 0000000 >universe-4
GGGTGATTTTTTTAGGGTCCCAT
mirtop-0.4.23/data/db/mirbase/ 0000775 0000000 0000000 00000000000 13547635037 0016047 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/db/mirbase/hsa.gff3 0000664 0000000 0000000 00000002155 13547635037 0017374 0 ustar 00root root 0000000 0000000 ##gff-version 3
##date 2018-3-5
#
# Chromosomal coordinates of Homo sapiens microRNAs
# microRNAs: miRBase v22
# genome-build-id: GRCh38
# genome-build-accession: NCBI_Assembly:GCA_000001405.15
#
# Hairpin precursor sequences have type "miRNA_primary_transcript".
# Note, these sequences do not represent the full primary transcript,
# rather a predicted stem-loop portion that includes the precursor
# miRNA. Mature sequences have type "miRNA".
#
11 . miRNA_primary_transcript 122146522 122146593 . - . ID=MI0000061;Alias=MI0000061;Name=hsa-let-7a-2
11 . miRNA 122146568 122146589 . - . ID=MIMAT0000062;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000061
11 . miRNA 122146523 122146544 . - . ID=MIMAT0010195;Alias=MIMAT0010195;Name=hsa-let-7a-2-3p;Derives_from=MI0000061
9 . miRNA_primary_transcript 94175957 94176036 . + . ID=MI0000060;Alias=MI0000060;Name=hsa-let-7a-1
9 . miRNA 94175962 94175983 . + . ID=MIMAT0000062_2;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000060
9 . miRNA 94176013 94176033 . + . ID=MIMAT0004481_1;Alias=MIMAT0004481;Name=hsa-let-7a-3p;Derives_from=MI0000060
mirtop-0.4.23/data/db/mirgenedb/ 0000775 0000000 0000000 00000000000 13547635037 0016361 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/db/mirgenedb/hsa-hg38-pri-30-30.fas 0000664 0000000 0000000 00000000222 13547635037 0021622 0 ustar 00root root 0000000 0000000 >Hsa-Let-7-P1_pri
TCCAGCCATTGTGACTGCATGCTCCCAGGTTGAGGTAGTAGGTTGTATAGTTTAGAATTACATCAAGGGAGATAACTGTACAGCCTCCTAGCTTTCCTTGGGTCTTGCACTAAACAACATGGTGAGA
mirtop-0.4.23/data/db/mirgenedb/hsa.gff 0000664 0000000 0000000 00000000465 13547635037 0017625 0 ustar 00root root 0000000 0000000 ##gff-version 3
# microRNAs: MirGeneDB v2.0
# genome-build-id: hg38
chr11 . pre_miRNA 122146523 122146589 . - . ID=Hsa-Let-7-P1_pre;Alias=MI0000061
chr11 . miRNA 122146523 122146544 . - . ID=Hsa-Let-7-P1_5p;Alias=MIMAT0000062
chr11 . miRNA 122146568 122146589 . - . ID=Hsa-Let-7-P1_3p*;Alias=MIMAT0010195
mirtop-0.4.23/data/examples/ 0000775 0000000 0000000 00000000000 13547635037 0015656 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/annotate/ 0000775 0000000 0000000 00000000000 13547635037 0017467 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/annotate/hairpin.fa 0000664 0000000 0000000 00000000640 13547635037 0021431 0 ustar 00root root 0000000 0000000 >hsa-let-7a-1
TGGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTA
>hsa-let-7a-2
AGGTTGAGGTAGTAGGTTGTATAGTTTAGAATTACATCAAGGGAGATAACTGTACAGCCTCCTAGCTTTCCT
>hsa-let-7a-3
GGGTGAGGTAGTAGGTTGTATAGTTTGGGGCTCTGCCCTGCTATGGGATAACTATACAATCTACTGTCTTTCCT
>hsa-let-7f-1 MI0000067 Homo sapiens let-7f-1 stem-loop
UCAGAGUGAGGUAGUAGAUUGUAUAGUUGUGGGGUAGUGAUUUUACCCUGUUCAGGAGAU
AACUAUACAAUCUAUUGCCUUCCCUGA
mirtop-0.4.23/data/examples/annotate/hsa-let-7a-3ploss1.sam 0000664 0000000 0000000 00000012353 13547635037 0023341 0 ustar 00root root 0000000 0000000 @SQ SN:1 LN:248956422
@SQ SN:10 LN:133797422
@SQ SN:11 LN:135086622
@SQ SN:12 LN:133275309
@SQ SN:13 LN:114364328
@SQ SN:14 LN:107043718
@SQ SN:15 LN:101991189
@SQ SN:16 LN:90338345
@SQ SN:17 LN:83257441
@SQ SN:18 LN:80373285
@SQ SN:19 LN:58617616
@SQ SN:2 LN:242193529
@SQ SN:20 LN:64444167
@SQ SN:21 LN:46709983
@SQ SN:22 LN:50818468
@SQ SN:3 LN:198295559
@SQ SN:4 LN:190214555
@SQ SN:5 LN:181538259
@SQ SN:6 LN:170805979
@SQ SN:7 LN:159345973
@SQ SN:8 LN:145138636
@SQ SN:9 LN:138394717
@SQ SN:MT LN:16569
@SQ SN:X LN:156040895
@SQ SN:Y LN:57227415
@SQ SN:KI270728.1 LN:1872759
@SQ SN:KI270727.1 LN:448248
@SQ SN:KI270442.1 LN:392061
@SQ SN:KI270729.1 LN:280839
@SQ SN:GL000225.1 LN:211173
@SQ SN:KI270743.1 LN:210658
@SQ SN:GL000008.2 LN:209709
@SQ SN:GL000009.2 LN:201709
@SQ SN:KI270747.1 LN:198735
@SQ SN:KI270722.1 LN:194050
@SQ SN:GL000194.1 LN:191469
@SQ SN:KI270742.1 LN:186739
@SQ SN:GL000205.2 LN:185591
@SQ SN:GL000195.1 LN:182896
@SQ SN:KI270736.1 LN:181920
@SQ SN:KI270733.1 LN:179772
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000219.1 LN:179198
@SQ SN:KI270719.1 LN:176845
@SQ SN:GL000216.2 LN:176608
@SQ SN:KI270712.1 LN:176043
@SQ SN:KI270706.1 LN:175055
@SQ SN:KI270725.1 LN:172810
@SQ SN:KI270744.1 LN:168472
@SQ SN:KI270734.1 LN:165050
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000220.1 LN:161802
@SQ SN:KI270715.1 LN:161471
@SQ SN:GL000218.1 LN:161147
@SQ SN:KI270749.1 LN:158759
@SQ SN:KI270741.1 LN:157432
@SQ SN:GL000221.1 LN:155397
@SQ SN:KI270716.1 LN:153799
@SQ SN:KI270731.1 LN:150754
@SQ SN:KI270751.1 LN:150742
@SQ SN:KI270750.1 LN:148850
@SQ SN:KI270519.1 LN:138126
@SQ SN:GL000214.1 LN:137718
@SQ SN:KI270708.1 LN:127682
@SQ SN:KI270730.1 LN:112551
@SQ SN:KI270438.1 LN:112505
@SQ SN:KI270737.1 LN:103838
@SQ SN:KI270721.1 LN:100316
@SQ SN:KI270738.1 LN:99375
@SQ SN:KI270748.1 LN:93321
@SQ SN:KI270435.1 LN:92983
@SQ SN:GL000208.1 LN:92689
@SQ SN:KI270538.1 LN:91309
@SQ SN:KI270756.1 LN:79590
@SQ SN:KI270739.1 LN:73985
@SQ SN:KI270757.1 LN:71251
@SQ SN:KI270709.1 LN:66860
@SQ SN:KI270746.1 LN:66486
@SQ SN:KI270753.1 LN:62944
@SQ SN:KI270589.1 LN:44474
@SQ SN:KI270726.1 LN:43739
@SQ SN:KI270735.1 LN:42811
@SQ SN:KI270711.1 LN:42210
@SQ SN:KI270745.1 LN:41891
@SQ SN:KI270714.1 LN:41717
@SQ SN:KI270732.1 LN:41543
@SQ SN:KI270713.1 LN:40745
@SQ SN:KI270754.1 LN:40191
@SQ SN:KI270710.1 LN:40176
@SQ SN:KI270717.1 LN:40062
@SQ SN:KI270724.1 LN:39555
@SQ SN:KI270720.1 LN:39050
@SQ SN:KI270723.1 LN:38115
@SQ SN:KI270718.1 LN:38054
@SQ SN:KI270317.1 LN:37690
@SQ SN:KI270740.1 LN:37240
@SQ SN:KI270755.1 LN:36723
@SQ SN:KI270707.1 LN:32032
@SQ SN:KI270579.1 LN:31033
@SQ SN:KI270752.1 LN:27745
@SQ SN:KI270512.1 LN:22689
@SQ SN:KI270322.1 LN:21476
@SQ SN:GL000226.1 LN:15008
@SQ SN:KI270311.1 LN:12399
@SQ SN:KI270366.1 LN:8320
@SQ SN:KI270511.1 LN:8127
@SQ SN:KI270448.1 LN:7992
@SQ SN:KI270521.1 LN:7642
@SQ SN:KI270581.1 LN:7046
@SQ SN:KI270582.1 LN:6504
@SQ SN:KI270515.1 LN:6361
@SQ SN:KI270588.1 LN:6158
@SQ SN:KI270591.1 LN:5796
@SQ SN:KI270522.1 LN:5674
@SQ SN:KI270507.1 LN:5353
@SQ SN:KI270590.1 LN:4685
@SQ SN:KI270584.1 LN:4513
@SQ SN:KI270320.1 LN:4416
@SQ SN:KI270382.1 LN:4215
@SQ SN:KI270468.1 LN:4055
@SQ SN:KI270467.1 LN:3920
@SQ SN:KI270362.1 LN:3530
@SQ SN:KI270517.1 LN:3253
@SQ SN:KI270593.1 LN:3041
@SQ SN:KI270528.1 LN:2983
@SQ SN:KI270587.1 LN:2969
@SQ SN:KI270364.1 LN:2855
@SQ SN:KI270371.1 LN:2805
@SQ SN:KI270333.1 LN:2699
@SQ SN:KI270374.1 LN:2656
@SQ SN:KI270411.1 LN:2646
@SQ SN:KI270414.1 LN:2489
@SQ SN:KI270510.1 LN:2415
@SQ SN:KI270390.1 LN:2387
@SQ SN:KI270375.1 LN:2378
@SQ SN:KI270420.1 LN:2321
@SQ SN:KI270509.1 LN:2318
@SQ SN:KI270315.1 LN:2276
@SQ SN:KI270302.1 LN:2274
@SQ SN:KI270518.1 LN:2186
@SQ SN:KI270530.1 LN:2168
@SQ SN:KI270304.1 LN:2165
@SQ SN:KI270418.1 LN:2145
@SQ SN:KI270424.1 LN:2140
@SQ SN:KI270417.1 LN:2043
@SQ SN:KI270508.1 LN:1951
@SQ SN:KI270303.1 LN:1942
@SQ SN:KI270381.1 LN:1930
@SQ SN:KI270529.1 LN:1899
@SQ SN:KI270425.1 LN:1884
@SQ SN:KI270396.1 LN:1880
@SQ SN:KI270363.1 LN:1803
@SQ SN:KI270386.1 LN:1788
@SQ SN:KI270465.1 LN:1774
@SQ SN:KI270383.1 LN:1750
@SQ SN:KI270384.1 LN:1658
@SQ SN:KI270330.1 LN:1652
@SQ SN:KI270372.1 LN:1650
@SQ SN:KI270548.1 LN:1599
@SQ SN:KI270580.1 LN:1553
@SQ SN:KI270387.1 LN:1537
@SQ SN:KI270391.1 LN:1484
@SQ SN:KI270305.1 LN:1472
@SQ SN:KI270373.1 LN:1451
@SQ SN:KI270422.1 LN:1445
@SQ SN:KI270316.1 LN:1444
@SQ SN:KI270340.1 LN:1428
@SQ SN:KI270338.1 LN:1428
@SQ SN:KI270583.1 LN:1400
@SQ SN:KI270334.1 LN:1368
@SQ SN:KI270429.1 LN:1361
@SQ SN:KI270393.1 LN:1308
@SQ SN:KI270516.1 LN:1300
@SQ SN:KI270389.1 LN:1298
@SQ SN:KI270466.1 LN:1233
@SQ SN:KI270388.1 LN:1216
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@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa samse /work/Genomes/GRCh38/Sequence_91/Homo_sapiens.GRCh38.dna.primary_assembly.fa reads.sai simulated_miRNA_BF.fa
hsa-let-7a-5p_3prime_loss_T_2 0 9 94175962 0 21M * 0 0 TGAGGTAGTAGGTTGTATAGT * XT:A:R NM:i:0 X0:i:3 X1:i:4 XM:i:0 XO:i:0 XG:i:0 MD:Z:21
mirtop-0.4.23/data/examples/annotate/hsa-let-7a-5ploss1.sam 0000664 0000000 0000000 00000012565 13547635037 0023350 0 ustar 00root root 0000000 0000000 @SQ SN:1 LN:248956422
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@SQ SN:KI270582.1 LN:6504
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@SQ SN:KI270591.1 LN:5796
@SQ SN:KI270522.1 LN:5674
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@SQ SN:KI270590.1 LN:4685
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@SQ SN:KI270593.1 LN:3041
@SQ SN:KI270528.1 LN:2983
@SQ SN:KI270587.1 LN:2969
@SQ SN:KI270364.1 LN:2855
@SQ SN:KI270371.1 LN:2805
@SQ SN:KI270333.1 LN:2699
@SQ SN:KI270374.1 LN:2656
@SQ SN:KI270411.1 LN:2646
@SQ SN:KI270414.1 LN:2489
@SQ SN:KI270510.1 LN:2415
@SQ SN:KI270390.1 LN:2387
@SQ SN:KI270375.1 LN:2378
@SQ SN:KI270420.1 LN:2321
@SQ SN:KI270509.1 LN:2318
@SQ SN:KI270315.1 LN:2276
@SQ SN:KI270302.1 LN:2274
@SQ SN:KI270518.1 LN:2186
@SQ SN:KI270530.1 LN:2168
@SQ SN:KI270304.1 LN:2165
@SQ SN:KI270418.1 LN:2145
@SQ SN:KI270424.1 LN:2140
@SQ SN:KI270417.1 LN:2043
@SQ SN:KI270508.1 LN:1951
@SQ SN:KI270303.1 LN:1942
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@SQ SN:KI270583.1 LN:1400
@SQ SN:KI270334.1 LN:1368
@SQ SN:KI270429.1 LN:1361
@SQ SN:KI270393.1 LN:1308
@SQ SN:KI270516.1 LN:1300
@SQ SN:KI270389.1 LN:1298
@SQ SN:KI270466.1 LN:1233
@SQ SN:KI270388.1 LN:1216
@SQ SN:KI270544.1 LN:1202
@SQ SN:KI270310.1 LN:1201
@SQ SN:KI270412.1 LN:1179
@SQ SN:KI270395.1 LN:1143
@SQ SN:KI270376.1 LN:1136
@SQ SN:KI270337.1 LN:1121
@SQ SN:KI270335.1 LN:1048
@SQ SN:KI270378.1 LN:1048
@SQ SN:KI270379.1 LN:1045
@SQ SN:KI270329.1 LN:1040
@SQ SN:KI270419.1 LN:1029
@SQ SN:KI270336.1 LN:1026
@SQ SN:KI270312.1 LN:998
@SQ SN:KI270539.1 LN:993
@SQ SN:KI270385.1 LN:990
@SQ SN:KI270423.1 LN:981
@SQ SN:KI270392.1 LN:971
@SQ SN:KI270394.1 LN:970
@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa samse /work/Genomes/GRCh38/Sequence_91/Homo_sapiens.GRCh38.dna.primary_assembly.fa reads.sai simulated_miRNA_BF.fa
hsa-let-7a-5p_5prime_loss_T_1 0 9 94175963 0 21M * 0 0 GAGGTAGTAGGTTGTATAGTT * XT:A:R NM:i:0 X0:i:3 X1:i:5 XM:i:0 XO:i:0 XG:i:0 MD:Z:21
hsa-let-7a-5p_5prime_loss_T_10 0 22 46112753 0 21M * 0 0 GAGGTAGTAGGTTGTATAGTT * XT:A:R NM:i:0 X0:i:3 X1:i:5 XM:i:0 XO:i:0 XG:i:0 MD:Z:21
mirtop-0.4.23/data/examples/annotate/hsa-let-7a-5ploss1_neg.sam 0000664 0000000 0000000 00000012356 13547635037 0024177 0 ustar 00root root 0000000 0000000 @SQ SN:1 LN:248956422
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@SQ SN:11 LN:135086622
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@SQ SN:13 LN:114364328
@SQ SN:14 LN:107043718
@SQ SN:15 LN:101991189
@SQ SN:16 LN:90338345
@SQ SN:17 LN:83257441
@SQ SN:18 LN:80373285
@SQ SN:19 LN:58617616
@SQ SN:2 LN:242193529
@SQ SN:20 LN:64444167
@SQ SN:21 LN:46709983
@SQ SN:22 LN:50818468
@SQ SN:3 LN:198295559
@SQ SN:4 LN:190214555
@SQ SN:5 LN:181538259
@SQ SN:6 LN:170805979
@SQ SN:7 LN:159345973
@SQ SN:8 LN:145138636
@SQ SN:9 LN:138394717
@SQ SN:MT LN:16569
@SQ SN:X LN:156040895
@SQ SN:Y LN:57227415
@SQ SN:KI270728.1 LN:1872759
@SQ SN:KI270727.1 LN:448248
@SQ SN:KI270442.1 LN:392061
@SQ SN:KI270729.1 LN:280839
@SQ SN:GL000225.1 LN:211173
@SQ SN:KI270743.1 LN:210658
@SQ SN:GL000008.2 LN:209709
@SQ SN:GL000009.2 LN:201709
@SQ SN:KI270747.1 LN:198735
@SQ SN:KI270722.1 LN:194050
@SQ SN:GL000194.1 LN:191469
@SQ SN:KI270742.1 LN:186739
@SQ SN:GL000205.2 LN:185591
@SQ SN:GL000195.1 LN:182896
@SQ SN:KI270736.1 LN:181920
@SQ SN:KI270733.1 LN:179772
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000219.1 LN:179198
@SQ SN:KI270719.1 LN:176845
@SQ SN:GL000216.2 LN:176608
@SQ SN:KI270712.1 LN:176043
@SQ SN:KI270706.1 LN:175055
@SQ SN:KI270725.1 LN:172810
@SQ SN:KI270744.1 LN:168472
@SQ SN:KI270734.1 LN:165050
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000220.1 LN:161802
@SQ SN:KI270715.1 LN:161471
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@SQ SN:KI270749.1 LN:158759
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@SQ SN:KI270750.1 LN:148850
@SQ SN:KI270519.1 LN:138126
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@SQ SN:KI270708.1 LN:127682
@SQ SN:KI270730.1 LN:112551
@SQ SN:KI270438.1 LN:112505
@SQ SN:KI270737.1 LN:103838
@SQ SN:KI270721.1 LN:100316
@SQ SN:KI270738.1 LN:99375
@SQ SN:KI270748.1 LN:93321
@SQ SN:KI270435.1 LN:92983
@SQ SN:GL000208.1 LN:92689
@SQ SN:KI270538.1 LN:91309
@SQ SN:KI270756.1 LN:79590
@SQ SN:KI270739.1 LN:73985
@SQ SN:KI270757.1 LN:71251
@SQ SN:KI270709.1 LN:66860
@SQ SN:KI270746.1 LN:66486
@SQ SN:KI270753.1 LN:62944
@SQ SN:KI270589.1 LN:44474
@SQ SN:KI270726.1 LN:43739
@SQ SN:KI270735.1 LN:42811
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@SQ SN:KI270745.1 LN:41891
@SQ SN:KI270714.1 LN:41717
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@SQ SN:KI270713.1 LN:40745
@SQ SN:KI270754.1 LN:40191
@SQ SN:KI270710.1 LN:40176
@SQ SN:KI270717.1 LN:40062
@SQ SN:KI270724.1 LN:39555
@SQ SN:KI270720.1 LN:39050
@SQ SN:KI270723.1 LN:38115
@SQ SN:KI270718.1 LN:38054
@SQ SN:KI270317.1 LN:37690
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@SQ SN:KI270752.1 LN:27745
@SQ SN:KI270512.1 LN:22689
@SQ SN:KI270322.1 LN:21476
@SQ SN:GL000226.1 LN:15008
@SQ SN:KI270311.1 LN:12399
@SQ SN:KI270366.1 LN:8320
@SQ SN:KI270511.1 LN:8127
@SQ SN:KI270448.1 LN:7992
@SQ SN:KI270521.1 LN:7642
@SQ SN:KI270581.1 LN:7046
@SQ SN:KI270582.1 LN:6504
@SQ SN:KI270515.1 LN:6361
@SQ SN:KI270588.1 LN:6158
@SQ SN:KI270591.1 LN:5796
@SQ SN:KI270522.1 LN:5674
@SQ SN:KI270507.1 LN:5353
@SQ SN:KI270590.1 LN:4685
@SQ SN:KI270584.1 LN:4513
@SQ SN:KI270320.1 LN:4416
@SQ SN:KI270382.1 LN:4215
@SQ SN:KI270468.1 LN:4055
@SQ SN:KI270467.1 LN:3920
@SQ SN:KI270362.1 LN:3530
@SQ SN:KI270517.1 LN:3253
@SQ SN:KI270593.1 LN:3041
@SQ SN:KI270528.1 LN:2983
@SQ SN:KI270587.1 LN:2969
@SQ SN:KI270364.1 LN:2855
@SQ SN:KI270371.1 LN:2805
@SQ SN:KI270333.1 LN:2699
@SQ SN:KI270374.1 LN:2656
@SQ SN:KI270411.1 LN:2646
@SQ SN:KI270414.1 LN:2489
@SQ SN:KI270510.1 LN:2415
@SQ SN:KI270390.1 LN:2387
@SQ SN:KI270375.1 LN:2378
@SQ SN:KI270420.1 LN:2321
@SQ SN:KI270509.1 LN:2318
@SQ SN:KI270315.1 LN:2276
@SQ SN:KI270302.1 LN:2274
@SQ SN:KI270518.1 LN:2186
@SQ SN:KI270530.1 LN:2168
@SQ SN:KI270304.1 LN:2165
@SQ SN:KI270418.1 LN:2145
@SQ SN:KI270424.1 LN:2140
@SQ SN:KI270417.1 LN:2043
@SQ SN:KI270508.1 LN:1951
@SQ SN:KI270303.1 LN:1942
@SQ SN:KI270381.1 LN:1930
@SQ SN:KI270529.1 LN:1899
@SQ SN:KI270425.1 LN:1884
@SQ SN:KI270396.1 LN:1880
@SQ SN:KI270363.1 LN:1803
@SQ SN:KI270386.1 LN:1788
@SQ SN:KI270465.1 LN:1774
@SQ SN:KI270383.1 LN:1750
@SQ SN:KI270384.1 LN:1658
@SQ SN:KI270330.1 LN:1652
@SQ SN:KI270372.1 LN:1650
@SQ SN:KI270548.1 LN:1599
@SQ SN:KI270580.1 LN:1553
@SQ SN:KI270387.1 LN:1537
@SQ SN:KI270391.1 LN:1484
@SQ SN:KI270305.1 LN:1472
@SQ SN:KI270373.1 LN:1451
@SQ SN:KI270422.1 LN:1445
@SQ SN:KI270316.1 LN:1444
@SQ SN:KI270340.1 LN:1428
@SQ SN:KI270338.1 LN:1428
@SQ SN:KI270583.1 LN:1400
@SQ SN:KI270334.1 LN:1368
@SQ SN:KI270429.1 LN:1361
@SQ SN:KI270393.1 LN:1308
@SQ SN:KI270516.1 LN:1300
@SQ SN:KI270389.1 LN:1298
@SQ SN:KI270466.1 LN:1233
@SQ SN:KI270388.1 LN:1216
@SQ SN:KI270544.1 LN:1202
@SQ SN:KI270310.1 LN:1201
@SQ SN:KI270412.1 LN:1179
@SQ SN:KI270395.1 LN:1143
@SQ SN:KI270376.1 LN:1136
@SQ SN:KI270337.1 LN:1121
@SQ SN:KI270335.1 LN:1048
@SQ SN:KI270378.1 LN:1048
@SQ SN:KI270379.1 LN:1045
@SQ SN:KI270329.1 LN:1040
@SQ SN:KI270419.1 LN:1029
@SQ SN:KI270336.1 LN:1026
@SQ SN:KI270312.1 LN:998
@SQ SN:KI270539.1 LN:993
@SQ SN:KI270385.1 LN:990
@SQ SN:KI270423.1 LN:981
@SQ SN:KI270392.1 LN:971
@SQ SN:KI270394.1 LN:970
@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa samse /work/Genomes/GRCh38/Sequence_91/Homo_sapiens.GRCh38.dna.primary_assembly.fa reads.sai simulated_miRNA_BF.fa
hsa-let-7a-5p_5prime_loss_T_2 16 11 122146568 0 21M * 0 0 AACTATACAACCTACTACCTC * XT:A:R NM:i:0 X0:i:3 X1:i:5 XM:i:0 XO:i:0 XG:i:0 MD:Z:21
mirtop-0.4.23/data/examples/annotate/hsa-let-7a-nm.sam 0000664 0000000 0000000 00000013035 13547635037 0022445 0 ustar 00root root 0000000 0000000 @SQ SN:1 LN:248956422
@SQ SN:10 LN:133797422
@SQ SN:11 LN:135086622
@SQ SN:12 LN:133275309
@SQ SN:13 LN:114364328
@SQ SN:14 LN:107043718
@SQ SN:15 LN:101991189
@SQ SN:16 LN:90338345
@SQ SN:17 LN:83257441
@SQ SN:18 LN:80373285
@SQ SN:19 LN:58617616
@SQ SN:2 LN:242193529
@SQ SN:20 LN:64444167
@SQ SN:21 LN:46709983
@SQ SN:22 LN:50818468
@SQ SN:3 LN:198295559
@SQ SN:4 LN:190214555
@SQ SN:5 LN:181538259
@SQ SN:6 LN:170805979
@SQ SN:7 LN:159345973
@SQ SN:8 LN:145138636
@SQ SN:9 LN:138394717
@SQ SN:MT LN:16569
@SQ SN:X LN:156040895
@SQ SN:Y LN:57227415
@SQ SN:KI270728.1 LN:1872759
@SQ SN:KI270727.1 LN:448248
@SQ SN:KI270442.1 LN:392061
@SQ SN:KI270729.1 LN:280839
@SQ SN:GL000225.1 LN:211173
@SQ SN:KI270743.1 LN:210658
@SQ SN:GL000008.2 LN:209709
@SQ SN:GL000009.2 LN:201709
@SQ SN:KI270747.1 LN:198735
@SQ SN:KI270722.1 LN:194050
@SQ SN:GL000194.1 LN:191469
@SQ SN:KI270742.1 LN:186739
@SQ SN:GL000205.2 LN:185591
@SQ SN:GL000195.1 LN:182896
@SQ SN:KI270736.1 LN:181920
@SQ SN:KI270733.1 LN:179772
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000219.1 LN:179198
@SQ SN:KI270719.1 LN:176845
@SQ SN:GL000216.2 LN:176608
@SQ SN:KI270712.1 LN:176043
@SQ SN:KI270706.1 LN:175055
@SQ SN:KI270725.1 LN:172810
@SQ SN:KI270744.1 LN:168472
@SQ SN:KI270734.1 LN:165050
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000220.1 LN:161802
@SQ SN:KI270715.1 LN:161471
@SQ SN:GL000218.1 LN:161147
@SQ SN:KI270749.1 LN:158759
@SQ SN:KI270741.1 LN:157432
@SQ SN:GL000221.1 LN:155397
@SQ SN:KI270716.1 LN:153799
@SQ SN:KI270731.1 LN:150754
@SQ SN:KI270751.1 LN:150742
@SQ SN:KI270750.1 LN:148850
@SQ SN:KI270519.1 LN:138126
@SQ SN:GL000214.1 LN:137718
@SQ SN:KI270708.1 LN:127682
@SQ SN:KI270730.1 LN:112551
@SQ SN:KI270438.1 LN:112505
@SQ SN:KI270737.1 LN:103838
@SQ SN:KI270721.1 LN:100316
@SQ SN:KI270738.1 LN:99375
@SQ SN:KI270748.1 LN:93321
@SQ SN:KI270435.1 LN:92983
@SQ SN:GL000208.1 LN:92689
@SQ SN:KI270538.1 LN:91309
@SQ SN:KI270756.1 LN:79590
@SQ SN:KI270739.1 LN:73985
@SQ SN:KI270757.1 LN:71251
@SQ SN:KI270709.1 LN:66860
@SQ SN:KI270746.1 LN:66486
@SQ SN:KI270753.1 LN:62944
@SQ SN:KI270589.1 LN:44474
@SQ SN:KI270726.1 LN:43739
@SQ SN:KI270735.1 LN:42811
@SQ SN:KI270711.1 LN:42210
@SQ SN:KI270745.1 LN:41891
@SQ SN:KI270714.1 LN:41717
@SQ SN:KI270732.1 LN:41543
@SQ SN:KI270713.1 LN:40745
@SQ SN:KI270754.1 LN:40191
@SQ SN:KI270710.1 LN:40176
@SQ SN:KI270717.1 LN:40062
@SQ SN:KI270724.1 LN:39555
@SQ SN:KI270720.1 LN:39050
@SQ SN:KI270723.1 LN:38115
@SQ SN:KI270718.1 LN:38054
@SQ SN:KI270317.1 LN:37690
@SQ SN:KI270740.1 LN:37240
@SQ SN:KI270755.1 LN:36723
@SQ SN:KI270707.1 LN:32032
@SQ SN:KI270579.1 LN:31033
@SQ SN:KI270752.1 LN:27745
@SQ SN:KI270512.1 LN:22689
@SQ SN:KI270322.1 LN:21476
@SQ SN:GL000226.1 LN:15008
@SQ SN:KI270311.1 LN:12399
@SQ SN:KI270366.1 LN:8320
@SQ SN:KI270511.1 LN:8127
@SQ SN:KI270448.1 LN:7992
@SQ SN:KI270521.1 LN:7642
@SQ SN:KI270581.1 LN:7046
@SQ SN:KI270582.1 LN:6504
@SQ SN:KI270515.1 LN:6361
@SQ SN:KI270588.1 LN:6158
@SQ SN:KI270591.1 LN:5796
@SQ SN:KI270522.1 LN:5674
@SQ SN:KI270507.1 LN:5353
@SQ SN:KI270590.1 LN:4685
@SQ SN:KI270584.1 LN:4513
@SQ SN:KI270320.1 LN:4416
@SQ SN:KI270382.1 LN:4215
@SQ SN:KI270468.1 LN:4055
@SQ SN:KI270467.1 LN:3920
@SQ SN:KI270362.1 LN:3530
@SQ SN:KI270517.1 LN:3253
@SQ SN:KI270593.1 LN:3041
@SQ SN:KI270528.1 LN:2983
@SQ SN:KI270587.1 LN:2969
@SQ SN:KI270364.1 LN:2855
@SQ SN:KI270371.1 LN:2805
@SQ SN:KI270333.1 LN:2699
@SQ SN:KI270374.1 LN:2656
@SQ SN:KI270411.1 LN:2646
@SQ SN:KI270414.1 LN:2489
@SQ SN:KI270510.1 LN:2415
@SQ SN:KI270390.1 LN:2387
@SQ SN:KI270375.1 LN:2378
@SQ SN:KI270420.1 LN:2321
@SQ SN:KI270509.1 LN:2318
@SQ SN:KI270315.1 LN:2276
@SQ SN:KI270302.1 LN:2274
@SQ SN:KI270518.1 LN:2186
@SQ SN:KI270530.1 LN:2168
@SQ SN:KI270304.1 LN:2165
@SQ SN:KI270418.1 LN:2145
@SQ SN:KI270424.1 LN:2140
@SQ SN:KI270417.1 LN:2043
@SQ SN:KI270508.1 LN:1951
@SQ SN:KI270303.1 LN:1942
@SQ SN:KI270381.1 LN:1930
@SQ SN:KI270529.1 LN:1899
@SQ SN:KI270425.1 LN:1884
@SQ SN:KI270396.1 LN:1880
@SQ SN:KI270363.1 LN:1803
@SQ SN:KI270386.1 LN:1788
@SQ SN:KI270465.1 LN:1774
@SQ SN:KI270383.1 LN:1750
@SQ SN:KI270384.1 LN:1658
@SQ SN:KI270330.1 LN:1652
@SQ SN:KI270372.1 LN:1650
@SQ SN:KI270548.1 LN:1599
@SQ SN:KI270580.1 LN:1553
@SQ SN:KI270387.1 LN:1537
@SQ SN:KI270391.1 LN:1484
@SQ SN:KI270305.1 LN:1472
@SQ SN:KI270373.1 LN:1451
@SQ SN:KI270422.1 LN:1445
@SQ SN:KI270316.1 LN:1444
@SQ SN:KI270340.1 LN:1428
@SQ SN:KI270338.1 LN:1428
@SQ SN:KI270583.1 LN:1400
@SQ SN:KI270334.1 LN:1368
@SQ SN:KI270429.1 LN:1361
@SQ SN:KI270393.1 LN:1308
@SQ SN:KI270516.1 LN:1300
@SQ SN:KI270389.1 LN:1298
@SQ SN:KI270466.1 LN:1233
@SQ SN:KI270388.1 LN:1216
@SQ SN:KI270544.1 LN:1202
@SQ SN:KI270310.1 LN:1201
@SQ SN:KI270412.1 LN:1179
@SQ SN:KI270395.1 LN:1143
@SQ SN:KI270376.1 LN:1136
@SQ SN:KI270337.1 LN:1121
@SQ SN:KI270335.1 LN:1048
@SQ SN:KI270378.1 LN:1048
@SQ SN:KI270379.1 LN:1045
@SQ SN:KI270329.1 LN:1040
@SQ SN:KI270419.1 LN:1029
@SQ SN:KI270336.1 LN:1026
@SQ SN:KI270312.1 LN:998
@SQ SN:KI270539.1 LN:993
@SQ SN:KI270385.1 LN:990
@SQ SN:KI270423.1 LN:981
@SQ SN:KI270392.1 LN:971
@SQ SN:KI270394.1 LN:970
@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa samse /work/Genomes/GRCh38/Sequence_91/Homo_sapiens.GRCh38.dna.primary_assembly.fa reads.sai simulated_miRNA_BF.fa
hsa-let-7a-5p_no_modification_nm_6 0 9 94175962 0 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT * XT:A:R NM:i:0 X0:i:3 X1:i:4 XM:i:0 XO:i:0 XG:i:0 MD:Z:22
hsa-let-7a-5p_no_modification_nm_6 0 3 94175962 0 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT * XT:A:R NM:i:0 X0:i:3 X1:i:4 XM:i:0 XO:i:0 XG:i:0 MD:Z:22
hsa-let-7a-5p_3prime_templated_addition_TGG_128 0 9 94175962 0 25M * 0 0 TGAGGTAGTAGGTTGTATAGTTTGG * XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:25
mirtop-0.4.23/data/examples/annotate/hsa.gff3 0000664 0000000 0000000 00000003253 13547635037 0021014 0 ustar 00root root 0000000 0000000 ##gff-version 3
##date 2014-6-22
#
# Chromosomal coordinates of Homo sapiens microRNAs
# microRNAs: miRBase v21
# genome-build-id: GRCh38
# genome-build-accession: NCBI_Assembly:GCA_000001405.15
#
# Hairpin precursor sequences have type "miRNA_primary_transcript".
# Note, these sequences do not represent the full primary transcript,
# rather a predicted stem-loop portion that includes the precursor
# miRNA. Mature sequences have type "miRNA".
#
chr11 . miRNA_primary_transcript 122146522 122146593 . - . ID=MI0000061;Alias=MI0000061;Name=hsa-let-7a-2
chr11 . miRNA 122146568 122146589 . - . ID=MIMAT0000062;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000061
chr11 . miRNA 122146523 122146544 . - . ID=MIMAT0010195;Alias=MIMAT0010195;Name=hsa-let-7a-2-3p;Derives_from=MI0000061
chr22 . miRNA_primary_transcript 46112749 46112822 . + . ID=MI0000062;Alias=MI0000062;Name=hsa-let-7a-3
chr22 . miRNA 46112752 46112773 . + . ID=MIMAT0000062_1;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000062
chr22 . miRNA 46112800 46112820 . + . ID=MIMAT0004481;Alias=MIMAT0004481;Name=hsa-let-7a-3p;Derives_from=MI0000062
chr9 . miRNA_primary_transcript 94175957 94176036 . + . ID=MI0000060;Alias=MI0000060;Name=hsa-let-7a-1
chr9 . miRNA 94175962 94175983 . + . ID=MIMAT0000062_2;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000060
chr9 . miRNA 94176013 94176033 . + . ID=MIMAT0004481_1;Alias=MIMAT0004481;Name=hsa-let-7a-3p;Derives_from=MI0000060
chr9 . miRNA_primary_transcript 94176347 94176433 . + . ID=MI0000067;Alias=MI0000067;Name=hsa-let-7f-1
chr9 . miRNA 94176409 94176430 . + . ID=MIMAT0004486;Alias=MIMAT0004486;Name=hsa-let-7f-1-3p;Derives_from=MI0000067
mirtop-0.4.23/data/examples/annotate/miRNA.str 0000664 0000000 0000000 00000000316 13547635037 0021167 0 ustar 00root root 0000000 0000000 >hsa-let-7a-1 (-35.60) [hsa-let-7a-5p:6-27] [hsa-let-7a-3p:57-77]
>hsa-let-7a-2 (-25.20) [hsa-let-7a-5p:5-26] [hsa-let-7a-2-3p:50-71]
>hsa-let-7a-3 (-34.40) [hsa-let-7a-5p:4-25] [hsa-let-7a-3p:52-72]
mirtop-0.4.23/data/examples/annotate/sim_isomir.sam 0000664 0000000 0000000 00000022254 13547635037 0022350 0 ustar 00root root 0000000 0000000 @HD VN:1.4 SO:coordinate
@PG ID:razers3 VN:3.2 [af3f84e] PN:razers3 CL:hairpin.fa sim_isomir.fa -o sim_isomir.sam
@SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null 0 hsa-let-7a-1 9 255 18M * 0 0 GGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:18
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null 256 hsa-let-7a-2 8 255 18M * 0 0 * * NM:i:0 MD:Z:18
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null 256 hsa-let-7a-2 8 255 18M * 0 0 * * NM:i:0 MD:Z:18
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null 256 hsa-let-7a-3 7 255 18M * 0 0 * * NM:i:0 MD:Z:18
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TTT 0 hsa-let-7a-1 9 255 21M * 0 0 GGTAGTAGGTTGTATAGTTTT ]]]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:21
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TTT 256 hsa-let-7a-2 8 255 21M * 0 0 * * NM:i:1 MD:Z:20A
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TTT 256 hsa-let-7a-2 8 255 21M * 0 0 * * NM:i:1 MD:Z:20A
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TTT 256 hsa-let-7a-3 7 255 21M * 0 0 * * NM:i:1 MD:Z:20G
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:1A_add:null 0 hsa-let-7a-1 5 255 1D21M * 0 0 AGAGGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:AT20
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:1A_add:null 256 hsa-let-7a-2 5 255 21M * 0 0 * * NM:i:1 MD:Z:T20
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:1A_add:null 256 hsa-let-7a-2 5 255 21M * 0 0 * * NM:i:1 MD:Z:T20
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:1A_add:null 256 hsa-let-7a-3 4 255 21M * 0 0 * * NM:i:1 MD:Z:T20
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:18G_add:null 0 hsa-let-7a-1 7 255 20M * 0 0 GAGGTAGTAGGTTGTATGGT ]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:17A2
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:18G_add:null 256 hsa-let-7a-2 6 255 20M * 0 0 * * NM:i:1 MD:Z:17A2
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:18G_add:null 256 hsa-let-7a-2 6 255 20M * 0 0 * * NM:i:1 MD:Z:17A2
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:18G_add:null 256 hsa-let-7a-3 5 255 20M * 0 0 * * NM:i:1 MD:Z:17A2
hsa-let-7a-1_hsa-let-7a-5p_8:25_2:-2_mut:null_add:T 0 hsa-let-7a-1 8 255 19M * 0 0 AGGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_8:25_2:-2_mut:null_add:T 256 hsa-let-7a-2 7 255 19M * 0 0 * * NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_8:25_2:-2_mut:null_add:T 256 hsa-let-7a-2 7 255 19M * 0 0 * * NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_8:25_2:-2_mut:null_add:T 256 hsa-let-7a-3 6 255 19M * 0 0 * * NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:10A_add:null 0 hsa-let-7a-1 5 255 22M * 0 0 ATGAGGTAGAAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:9T12
hsa-let-7a-1_hsa-let-7a-5p_4:26_-2:-1_mut:null_add:A 0 hsa-let-7a-1 4 255 24M * 0 0 GATGAGGTAGTAGGTTGTATAGTA ]]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:23T
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:ATA 0 hsa-let-7a-2 6 255 23M * 0 0 GAGGTAGTAGGTTGTATAGTATA ]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:20T2
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:ATA 256 hsa-let-7a-2 6 255 23M * 0 0 * * NM:i:1 MD:Z:20T2
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null 0 hsa-let-7a-1 5 255 23M * 0 0 ATGAGGTAGTAGGTTGTATAGTT ]]]]]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:23
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null 256 hsa-let-7a-2 4 255 23M * 0 0 * * NM:i:1 MD:Z:T22
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null 256 hsa-let-7a-2 4 255 23M * 0 0 * * NM:i:1 MD:Z:T22
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null 256 hsa-let-7a-3 3 255 23M * 0 0 * * NM:i:1 MD:Z:G22
hsa-let-7a-2_hsa-let-7a-5p_7:26_2:0_mut:null_add:null 0 hsa-let-7a-1 8 255 20M * 0 0 AGGTAGTAGGTTGTATAGTT ]]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_7:26_2:0_mut:null_add:null 256 hsa-let-7a-2 7 255 20M * 0 0 * * NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_7:26_2:0_mut:null_add:null 256 hsa-let-7a-2 7 255 20M * 0 0 * * NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_7:26_2:0_mut:null_add:null 256 hsa-let-7a-3 6 255 20M * 0 0 * * NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:AT 0 hsa-let-7a-1 6 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGAT ]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:20T1
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:AT 256 hsa-let-7a-2 5 255 22M * 0 0 * * NM:i:1 MD:Z:20T1
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:AT 256 hsa-let-7a-2 5 255 22M * 0 0 * * NM:i:1 MD:Z:20T1
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:AT 256 hsa-let-7a-3 4 255 22M * 0 0 * * NM:i:1 MD:Z:20T1
hsa-let-7a-2_hsa-let-7a-5p_8:25_3:-1_mut:null_add:ATT 0 hsa-let-7a-1 9 255 21M * 0 0 GGTAGTAGGTTGTATAGTATT ]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:18T2
hsa-let-7a-2_hsa-let-7a-5p_8:25_3:-1_mut:null_add:ATT 256 hsa-let-7a-2 8 255 18M1I2M * 0 0 * * NM:i:1 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_8:25_3:-1_mut:null_add:ATT 256 hsa-let-7a-2 8 255 18M1I2M * 0 0 * * NM:i:1 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_8:25_3:-1_mut:null_add:ATT 256 hsa-let-7a-3 7 255 18M1I2M * 0 0 * * NM:i:1 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_4:26_-1:0_mut:null_add:null 0 hsa-let-7a-1 5 255 23M * 0 0 TTGAGGTAGTAGGTTGTATAGTT ]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:A22
hsa-let-7a-2_hsa-let-7a-5p_4:26_-1:0_mut:null_add:null 256 hsa-let-7a-2 4 255 23M * 0 0 * * NM:i:0 MD:Z:23
hsa-let-7a-2_hsa-let-7a-5p_4:26_-1:0_mut:null_add:null 256 hsa-let-7a-2 4 255 23M * 0 0 * * NM:i:0 MD:Z:23
hsa-let-7a-2_hsa-let-7a-5p_4:26_-1:0_mut:null_add:null 256 hsa-let-7a-3 3 255 23M * 0 0 * * NM:i:1 MD:Z:G22
hsa-let-7a-2_hsa-let-7a-5p_7:25_2:-1_mut:14G_add:TTA 0 hsa-let-7a-2 7 255 22M * 0 0 AGGTAGTAGGTTGGATAGTTTA ]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:13T8
hsa-let-7a-2_hsa-let-7a-5p_7:25_2:-1_mut:14G_add:TTA 256 hsa-let-7a-2 7 255 22M * 0 0 * * NM:i:1 MD:Z:13T8
hsa-let-7a-2_hsa-let-7a-5p_6:25_1:-1_mut:null_add:TAT 0 hsa-let-7a-1 7 255 23M * 0 0 GAGGTAGTAGGTTGTATAGTTAT ]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:21T1
hsa-let-7a-2_hsa-let-7a-5p_6:25_1:-1_mut:null_add:TAT 256 hsa-let-7a-2 6 255 21M1I1M * 0 0 * * NM:i:1 MD:Z:22
hsa-let-7a-2_hsa-let-7a-5p_6:25_1:-1_mut:null_add:TAT 256 hsa-let-7a-2 6 255 21M1I1M * 0 0 * * NM:i:1 MD:Z:22
hsa-let-7a-2_hsa-let-7a-5p_6:25_1:-1_mut:null_add:TAT 256 hsa-let-7a-3 5 255 21M1I1M * 0 0 * * NM:i:1 MD:Z:22
hsa-let-7a-2_hsa-let-7a-5p_3:25_-2:-1_mut:null_add:null 0 hsa-let-7a-1 4 255 23M * 0 0 GTTGAGGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:1A21
hsa-let-7a-2_hsa-let-7a-5p_3:25_-2:-1_mut:null_add:null 256 hsa-let-7a-2 3 255 23M * 0 0 * * NM:i:0 MD:Z:23
hsa-let-7a-2_hsa-let-7a-5p_3:25_-2:-1_mut:null_add:null 256 hsa-let-7a-2 3 255 23M * 0 0 * * NM:i:0 MD:Z:23
hsa-let-7a-2_hsa-let-7a-5p_3:25_-2:-1_mut:null_add:null 256 hsa-let-7a-3 2 255 23M * 0 0 * * NM:i:1 MD:Z:1G21
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:null 0 hsa-let-7a-1 6 255 20M * 0 0 TGAGGTAGTAGGTTGTATAG ]]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:null 256 hsa-let-7a-2 5 255 20M * 0 0 * * NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:null 256 hsa-let-7a-2 5 255 20M * 0 0 * * NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:null 256 hsa-let-7a-3 4 255 20M * 0 0 * * NM:i:0 MD:Z:20
hsa-let-7a-3_hsa-let-7a-5p_8:24_4:-1_mut:null_add:TAA 0 hsa-let-7a-2 9 255 20M * 0 0 GTAGTAGGTTGTATAGTTAA ]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:18T1
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:TTT 0 hsa-let-7a-1 3 255 1D26M * 0 0 GGTGAGGTAGTAGGTTGTATAGTTTT ]]]]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:G1A24
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:TTT 256 hsa-let-7a-3 2 255 25M1I * 0 0 * * NM:i:1 MD:Z:25
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:null 0 hsa-let-7a-1 3 255 1D23M * 0 0 GGTGAGGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:G1A21
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:null 256 hsa-let-7a-2 2 255 1D23M * 0 0 * * NM:i:1 MD:Z:G1T21
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:null 256 hsa-let-7a-2 2 255 1D23M * 0 0 * * NM:i:1 MD:Z:G1T21
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:null 256 hsa-let-7a-3 2 255 23M * 0 0 * * NM:i:0 MD:Z:23
hsa-let-7a-3_hsa-let-7a-5p_3:24_-1:-1_mut:null_add:null 0 hsa-let-7a-1 4 255 1D22M * 0 0 GTGAGGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]]]]] NM:i:1 MD:Z:GA21
hsa-let-7a-3_hsa-let-7a-5p_3:24_-1:-1_mut:null_add:null 256 hsa-let-7a-2 3 255 1D22M * 0 0 * * NM:i:1 MD:Z:GT21
hsa-let-7a-3_hsa-let-7a-5p_3:24_-1:-1_mut:null_add:null 256 hsa-let-7a-2 3 255 1D22M * 0 0 * * NM:i:1 MD:Z:GT21
hsa-let-7a-3_hsa-let-7a-5p_3:24_-1:-1_mut:null_add:null 256 hsa-let-7a-3 3 255 22M * 0 0 * * NM:i:0 MD:Z:22
hsa-let-7a-3_hsa-let-7a-5p_4:24_0:-1_mut:null_add:null 0 hsa-let-7a-1 6 255 21M * 0 0 TGAGGTAGTAGGTTGTATAGT ]]]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_4:24_0:-1_mut:null_add:null 256 hsa-let-7a-2 5 255 21M * 0 0 * * NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_4:24_0:-1_mut:null_add:null 256 hsa-let-7a-2 5 255 21M * 0 0 * * NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_4:24_0:-1_mut:null_add:null 256 hsa-let-7a-3 4 255 21M * 0 0 * * NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_5:24_1:-1_mut:null_add:T 0 hsa-let-7a-1 7 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT ]]]]]]]]]]]]]]]]]]]]] NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_5:24_1:-1_mut:null_add:T 256 hsa-let-7a-2 6 255 21M * 0 0 * * NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_5:24_1:-1_mut:null_add:T 256 hsa-let-7a-2 6 255 21M * 0 0 * * NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_5:24_1:-1_mut:null_add:T 256 hsa-let-7a-3 5 255 21M * 0 0 * * NM:i:0 MD:Z:21
mirtop-0.4.23/data/examples/annotate/sim_isomir_sort.bam 0000664 0000000 0000000 00000002461 13547635037 0023374 0 ustar 00root root 0000000 0000000 BC sregegoUXZTbUXZTl RbgffasH,*KKT(̍,,ts 92usRKtu
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idauj|`CroN)Hn~` 3QVpu)ԬiʈQ 3^v+T" BC mirtop-0.4.23/data/examples/compare/ 0000775 0000000 0000000 00000000000 13547635037 0017304 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/compare/reference.gff 0000664 0000000 0000000 00000001451 13547635037 0021727 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## COLDATA: sampleX
hsa-let-7a-1 miRBase21 isomiR 4 26 0 + . Read hsa-let-7a-5p.sA.t.ATGAGGTAGTAGGTTGTATAGT; UID bhJJ5WJL2; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_5p:-1,iso_3p:-1; Cigar 22M; Expression 11; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 4 30 0 + . Read hsa-let-7a-5p.sA.TT.eT.ATGAGGTAGTAGGTTGTATAGTTTTT; UID bhJJ5WJ%Q1; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_add:+3,iso_5p:-1,iso_3p:+2; Cigar 25MT; Expression 66; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 4 29 0 + . Read hsa-let-7a-5p.sA.T.eA.ATGAGGTAGTAGGTTGTATAGTTTA; UID bhJJ5WJ%@2; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_add:+1,iso_5p:-1,iso_3p:+1; Cigar 24MA; Expression 2; Filter Pass; Hits 1;
mirtop-0.4.23/data/examples/compare/target.gff 0000664 0000000 0000000 00000001402 13547635037 0021253 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## COLDATA: sampleX
hsa-let-7a-1 miRBase21 isomiR 4 26 0 + . Read=hsa-let-7a-5p.sA.t.ATGAGGTAGTAGGTTGTATAGT; UID=bhJJ5WJL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1,iso_3p:-1; Cigar=22M; Expression 11; Filter=Pass; Hits=1;
hsa-let-7a-1 miRBase21 isomiR 4 30 0 + . Read=hsa-let-7a-5p.sA.TT.eT.ATGAGGTAGTAGGTTGTATAGTTTTT; UID=bhJJ5WJ%Q1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+3,iso_5p:-1; Cigar=25MT; Expression=66; Filter=Pass; Hits=1;
hsa-let-7a-1 miRBase21 isomiR 4 27 0 + . Read=hsa-let-7a-5p.sA.ATGAGGTAGTAGGTTGTATAGTT; UID=bhJJ5WJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=56; Filter=Pass; Hits=1;
mirtop-0.4.23/data/examples/gff/ 0000775 0000000 0000000 00000000000 13547635037 0016420 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/gff/2samples.gff 0000664 0000000 0000000 00000001034 13547635037 0020630 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## TOOLS: razers
## COLDATA: samples1,sample2
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=66,33; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=4,2; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/gff/2uid_missing.gff 0000664 0000000 0000000 00000004652 13547635037 0021507 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## TOOLS: razers
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/gff/3wrong_type.gff 0000664 0000000 0000000 00000004731 13547635037 0021371 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## TOOLS: razers
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiRe 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiRe 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/gff/coldata_missing.gff 0000664 0000000 0000000 00000004702 13547635037 0022247 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## TOOLS: razers
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/gff/correct_file.gff 0000664 0000000 0000000 00000004733 13547635037 0021553 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## TOOLS: razers
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add3p:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add3p:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/gff/missing_filter_type.gff 0000664 0000000 0000000 00000004735 13547635037 0023174 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## TOOLS: razers
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=low_counts; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/gff/missing_tools_header.gff 0000664 0000000 0000000 00000004702 13547635037 0023310 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## TOOLS: razers
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/isomir-sea/ 0000775 0000000 0000000 00000000000 13547635037 0017726 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/isomir-sea/tagMir-all.gff 0000664 0000000 0000000 00000002322 13547635037 0022402 0 ustar 00root root 0000000 0000000 chr15 miRBase21 isomiR 107888301 107888322 19 + . TI=6;TS=AUGAGGUAGUAGGUUGUAUAGU;TC=11;PIN=hsa-let-7a-1 MI0000060 Homo sapiens let-7a-1 stem-loop;CI=I21MD;MIN=hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p;ISO=FT1FF-1F;INT=FTTTT;FILTER=Pass
chr15 miRBase21 isomiR 107888300 107888322 20 + . TI=8;TS=AUGAGGUAGUAGGUUGUAUAGUU;TC=56;PIN=hsa-let-7a-1 MI0000060 Homo sapiens let-7a-1 stem-loop;CI=I22M;MIN=hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p;ISO=FT1FF0F;INT=FTTTT;FILTER=Pass
chr15 miRBase21 ref_miRNA 107888301 107888322 22 + . TI=36;TS=UGAGGUAGUAGGUUGUAUAGUU;TC=156;PIN=hsa-let-7a-1 MI0000060 Homo sapiens let-7a-1 stem-loop;CI=22M;MIN=hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p;ISO=TF0FF0F;INT=FTTTT;FILTER=Pass
chr15 miRBase21 isomiR 107888299 107888322 14 + . TI=15;TS=UGAGGUAGUAGGUUGUAUAGUAA;TC=438;PIN=hsa-let-7a-1 MI0000060 Homo sapiens let-7a-1 stem-loop;CI=I4MT16MAI;MIN=hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p;ISO=FT1TF1F;INT=TTTTT;FILTER=Pass
chr15 miRBase21 isomiR 107888296 107888322 16 + . TI=13;TS=ATGAGGTAGTAGGTTGTATAGTTTTTA;TC=112;PIN=hsa-let-7a-1 MI0000060 Homo sapiens let-7a-1 stem-loop;CI=I22M4I;MIN=hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p;ISO=FT1FF4F;INT=FTTTT;FILTER=Pass
mirtop-0.4.23/data/examples/manatee/ 0000775 0000000 0000000 00000000000 13547635037 0017270 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/manatee/simulated.sam 0000664 0000000 0000000 00000000761 13547635037 0021765 0 ustar 00root root 0000000 0000000 @HD VN:1.0 SO:unsorted
@SQ SN:1 LN:248956422
@SQ SN:11 LN:133797422
hsa-let-7a-2-3p_no_modification_nm_1 - chr11 122146523 255 22M * 0 0 GGAAAGCTAGGAGGCTGTACAG IIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22 NM:i:0 1 UAR
hsa-let-7a-2-3p_no_modification_nm_2 - chr11 122146523 255 22M * 0 0 GGAAAGCTAGGAGGCTGTACAG IIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22 NM:i:0 1 UAR
hsa-let-7a-2-3p_no_modification_nm_3 - chr11 122146523 255 22M * 0 0 GGAAAGCTAGGAGGCTGTACAG IIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22 NM:i:0 1 UAR
mirtop-0.4.23/data/examples/mirgenedb/ 0000775 0000000 0000000 00000000000 13547635037 0017612 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/mirgenedb/hairpin.fa 0000664 0000000 0000000 00000000224 13547635037 0021552 0 ustar 00root root 0000000 0000000 >Hsa-Let-7-P6
TTCACCCTGGATGTTCTCTTCACTGTGGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTAACGTGATAGAAAAGTCTGCATCCAGGCG
mirtop-0.4.23/data/examples/mirgenedb/sim.sam 0000664 0000000 0000000 00000007670 13547635037 0021116 0 ustar 00root root 0000000 0000000 @HD VN:1.4 SO:coordinate
@PG ID:razers3 VN:3.3 PN:razers3 CL:-dr 0 -i 80 -rr 90 -f -o sim.sam hairpin.fa ../annotate/sim_isomir.fa
@SQ SN:Hsa-Let-7-P6 LN:133
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null 0 Hsa-Let-7-P6 34 255 18M * 0 0 GGTAGNAGGTTGTATAGT IIIII!IIIIIIIIIIII NM:i:1 MD:Z:5T12
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null 0 Hsa-Let-7-P6 34 255 18M * 0 0 GGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIII NM:i:0 MD:Z:18
hsa-let-7a-1_hsa-let-7a-5p_10:25_4:-2_mut:4C_add:TA 0 Hsa-Let-7-P6 35 255 18M * 0 0 GTACTAGGTTGTATAGTA IIIIIIIIIIIIIIIIII NM:i:2 MD:Z:3G13T
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TTT 0 Hsa-Let-7-P6 34 255 21M * 0 0 GGTAGTAGGTTGTATAGTTTT IIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:21
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:1A_add:null 0 Hsa-Let-7-P6 30 255 1D21M * 0 0 AGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:^A0T20
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:18G_add:null 0 Hsa-Let-7-P6 32 255 20M * 0 0 GAGGTAGTAGGTTGTATGGT IIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:17A2
hsa-let-7a-1_hsa-let-7a-5p_8:25_2:-2_mut:null_add:T 0 Hsa-Let-7-P6 33 255 19M * 0 0 AGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:10A_add:null 0 Hsa-Let-7-P6 30 255 22M * 0 0 ATGAGGTAGAAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:9T12
hsa-let-7a-1_hsa-let-7a-5p_4:26_-2:-1_mut:null_add:A 0 Hsa-Let-7-P6 29 255 24M * 0 0 GATGAGGTAGTAGGTTGTATAGTA IIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:23T
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:ATA 0 Hsa-Let-7-P6 32 255 23M1D * 0 0 GAGGTAGTAGGTTGTATAGTATA IIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:20T1T^A
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null 0 Hsa-Let-7-P6 30 255 23M * 0 0 ATGAGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:23
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:11A_add:AAT 0 Hsa-Let-7-P6 31 255 23M * 0 0 TGAGGTAGTAAGTTGTATAGAAT IIIIIIIIIIIIIIIIIIIIIII NM:i:3 MD:Z:10G9T0T1
hsa-let-7a-2_hsa-let-7a-5p_7:26_2:0_mut:null_add:null 0 Hsa-Let-7-P6 33 255 20M * 0 0 AGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:20
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:AT 0 Hsa-Let-7-P6 31 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGAT IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:20T1
hsa-let-7a-2_hsa-let-7a-5p_8:25_3:-1_mut:null_add:ATT 0 Hsa-Let-7-P6 34 255 21M * 0 0 GGTAGTAGGTTGTATAGTATT IIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:18T2
hsa-let-7a-2_hsa-let-7a-5p_4:26_-1:0_mut:null_add:null 0 Hsa-Let-7-P6 30 255 23M * 0 0 TTGAGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:0A22
hsa-let-7a-2_hsa-let-7a-5p_7:25_2:-1_mut:14G_add:TTA 0 Hsa-Let-7-P6 33 255 22M1D * 0 0 AGGTAGTAGGTTGGATAGTTTA IIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:13T7T^A
hsa-let-7a-2_hsa-let-7a-5p_6:25_1:-1_mut:null_add:TAT 0 Hsa-Let-7-P6 32 255 23M * 0 0 GAGGTAGTAGGTTGTATAGTTAT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:21T1
hsa-let-7a-2_hsa-let-7a-5p_3:25_-2:-1_mut:null_add:null 0 Hsa-Let-7-P6 29 255 23M * 0 0 GTTGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:1A21
hsa-let-7a-2_hsa-let-7a-5p_5:24_0:-2_mut:null_add:null 0 Hsa-Let-7-P6 31 255 20M * 0 0 TGAGGTAGTAGGTTGTATAG IIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:20
hsa-let-7a-3_hsa-let-7a-5p_8:24_4:-1_mut:null_add:TAA 0 Hsa-Let-7-P6 35 255 20M1D * 0 0 GTAGTAGGTTGTATAGTTAA IIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:18T0T^A
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:TTT 0 Hsa-Let-7-P6 28 255 1D26M * 0 0 GGTGAGGTAGTAGGTTGTATAGTTTT IIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:^G1A24
hsa-let-7a-3_hsa-let-7a-5p_2:24_-2:-1_mut:null_add:null 0 Hsa-Let-7-P6 28 255 1D23M * 0 0 GGTGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:^G1A21
hsa-let-7a-3_hsa-let-7a-5p_3:24_-1:-1_mut:null_add:null 0 Hsa-Let-7-P6 29 255 1D22M * 0 0 GTGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:^G0A21
hsa-let-7a-3_hsa-let-7a-5p_4:24_0:-1_mut:null_add:null 0 Hsa-Let-7-P6 31 255 21M * 0 0 TGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:21
hsa-let-7a-3_hsa-let-7a-5p_5:24_1:-1_mut:null_add:T 0 Hsa-Let-7-P6 32 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:21
mirtop-0.4.23/data/examples/optimir/ 0000775 0000000 0000000 00000000000 13547635037 0017341 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/optimir/synthetic_100_full.gff3 0000664 0000000 0000000 00000037617 13547635037 0023542 0 ustar 00root root 0000000 0000000 ## GFF3 adapted for miRNA sequencing data. VERSION 1.1
## Source: miRBasev21 doi:10.25504/fairsharing.hmgte8
## COLDATA: synthetic_100_full
## Processed with OptimiR.
hsa-let-7a-5p mirbase_21 isomiR 1 21 1 + . UID=iso-21-XKVLRYVPE;Read=TGAGGTAGTAGGTTGTATAGT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_3p:-1;Cigar=21M;Alias=MIMAT0000062;Expression=2.0;expression_OptimiR=2.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 21 1 + . UID=iso-22-I0S31NSLN;Read=ATGAGGTAGTAGGTTGTATAGT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_3p:-1;Cigar=A21M;Alias=MIMAT0000062;Expression=11.0;expression_OptimiR=11.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 21 3 + . UID=iso-24-I0S31NSL2F;Read=ATGAGGTAGTAGGTTGTATAGTAA;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_3p:-1,iso_add3p:2;Change=iso_add3p:AA;Cigar=A21MAA;Alias=MIMAT0000062;Expression=35.0;expression_OptimiR=35.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 21 4 + . UID=iso-24-XKVLRYVP26;Read=TGAGGTAGTAGGTTGTATAGTAAA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_3p:-1,iso_add3p:3;Change=iso_add3p:AAA;Cigar=21MAAA;Alias=MIMAT0000062;Expression=1.0;expression_OptimiR=1.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 0 + . UID=iso-23-I0S31NSL0E;Read=ATGAGGTAGTAGGTTGTATAGTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1;Cigar=A22M;Alias=MIMAT0000062;Expression=56.0;expression_OptimiR=56.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 22 0 + . UID=iso-23-XKVLRYVP0Q;Read=TGAGGTAGTAGGTTGTATAGTTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_3p:+1;Cigar=22MT;Alias=MIMAT0000062;Expression=29.0;expression_OptimiR=29.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 0 + . UID=iso-24-XKVLRYVPKQ;Read=TGAGGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_3p:+2;Cigar=22MTT;Alias=MIMAT0000062;Expression=9.0;expression_OptimiR=9.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 0 + . UID=iso-25-I0S31NSL7Z;Read=ATGAGGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_3p:+2;Cigar=A22MTT;Alias=MIMAT0000062;Expression=13.0;expression_OptimiR=13.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 22 1 + . UID=iso-23-XKVLRYVP0O;Read=TGAGGTAGTAGGTTGTATAGTTA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_add3p:1;Change=iso_add3p:A;Cigar=22MA;Alias=MIMAT0000062;Expression=111.0;expression_OptimiR=111.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 1 + . UID=iso-24-I0S31NSL2O;Read=ATGAGGTAGTAGGTTGTATAGTTA;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_add3p:1;Change=iso_add3p:A;Cigar=A22MA;Alias=MIMAT0000062;Expression=5.0;expression_OptimiR=5.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 22 2 + . UID=iso-25-I0S31NSL7X;Read=ATGAGGTAGTAGGTTGTATAGTTTA;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_add3p:2;Change=iso_add3p:TA;Cigar=A22MTA;Alias=MIMAT0000062;Expression=2.0;expression_OptimiR=2.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 22 3 + . UID=iso-25-XKVLRYVPYE;Read=TGAGGTAGTAGGTTGTATAGTTAAT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_add3p:3;Change=iso_add3p:AAT;Cigar=22MAAT;Alias=MIMAT0000062;Expression=29.0;expression_OptimiR=29.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 3 + . UID=iso-25-XKVLRYVPZQ;Read=TGAGGTAGTAGGTTGTATAGTTTAT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_add3p:3;Change=iso_add3p:TAT;Cigar=22MTAT;Alias=MIMAT0000062;Expression=6.0;expression_OptimiR=6.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 3 + . UID=iso-25-XKVLRYVPZZ;Read=TGAGGTAGTAGGTTGTATAGTTTTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_add3p:3;Change=iso_add3p:TTT;Cigar=22MTTT;Alias=MIMAT0000062;Expression=19.0;expression_OptimiR=19.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 1 22 3 + . UID=iso-26-I0S31NSL7ZE;Read=ATGAGGTAGTAGGTTGTATAGTTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_add3p:3;Change=iso_add3p:TTT;Cigar=A22MTTT;Alias=MIMAT0000062;Expression=66.0;expression_OptimiR=66.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 22 4 + . UID=iso-27-I0S31NSL7ZO;Read=ATGAGGTAGTAGGTTGTATAGTTTTTA;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_add3p:4;Change=iso_add3p:TTTA;Cigar=A22MTTTA;Alias=MIMAT0000062;Expression=112.0;expression_OptimiR=112.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 1 22 4 + . UID=iso-27-I0S31NSL7ZQ;Read=ATGAGGTAGTAGGTTGTATAGTTTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:-1,iso_add3p:4;Change=iso_add3p:TTTT;Cigar=A22MTTTT;Alias=MIMAT0000062;Expression=703.0;expression_OptimiR=703.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 2 21 5 + . UID=iso-20-531P7WH3;Read=GAGGTAGTAGGTTGTATAGT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+1,iso_3p:-1;Cigar=20M;Alias=MIMAT0000062;Expression=3.0;expression_OptimiR=3.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 2 22 4 + . UID=iso-21-531P7WH3E;Read=GAGGTAGTAGGTTGTATAGTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+1;Cigar=21M;Alias=MIMAT0000062;Expression=15.0;expression_OptimiR=15.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 2 22 4 + . UID=iso-23-531P7WH30Q;Read=GAGGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:+1,iso_3p:+2;Cigar=21MTT;Alias=MIMAT0000062;Expression=23.0;expression_OptimiR=23.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 2 22 6 + . UID=iso-23-531P7WH30F;Read=GAGGTAGTAGGTTGTATAGTTAA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+1,iso_add3p:2;Change=iso_add3p:AA;Cigar=21MAA;Alias=MIMAT0000062;Expression=273.0;expression_OptimiR=273.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 2 22 7 + . UID=iso-24-531P7WH327;Read=GAGGTAGTAGGTTGTATAGTTAAT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+1,iso_add3p:3;Change=iso_add3p:AAT;Cigar=21MAAT;Alias=MIMAT0000062;Expression=2.0;expression_OptimiR=2.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 2 22 8 + . UID=iso-25-531P7WH3YN;Read=GAGGTAGTAGGTTGTATAGTTTATT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+1,iso_add3p:4;Change=iso_add3p:TATT;Cigar=21MTATT;Alias=MIMAT0000062;Expression=59.0;expression_OptimiR=59.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 2 22 9 + . UID=iso-26-531P7WH3ZXB;Read=GAGGTAGTAGGTTGTATAGTTTTTAA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+1,iso_add3p:5;Change=iso_add3p:TTTAA;Cigar=21MTTTAA;Alias=MIMAT0000062;Expression=50.0;expression_OptimiR=50.0;Filter=PASS;Hits=2;
hsa-let-7a-5p mirbase_21 isomiR 3 21 9 + . UID=iso-19-1LSKZL2Z;Read=AGGTAGTAGGTTGTATAGT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+2,iso_3p:-1;Cigar=19M;Alias=MIMAT0000062;Expression=5.0;expression_OptimiR=5.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 3 22 11 + . UID=iso-23-1LSKZLVN0I;Read=AGGTAGTAGGTTGTATAGTTTAT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+2,iso_add3p:3;Change=iso_add3p:TAT;Cigar=20MTAT;Alias=MIMAT0000062;Expression=8.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 3 22 8 + . UID=iso-20-1LSKZLVN;Read=AGGTAGTAGGTTGTATAGTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+2;Cigar=20M;Alias=MIMAT0000062;Expression=432.0;expression_OptimiR=432.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 3 22 8 + . UID=iso-21-1LSKZLVNE;Read=AGGTAGTAGGTTGTATAGTTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+2,iso_3p:+1;Cigar=20MT;Alias=MIMAT0000062;Expression=426.0;expression_OptimiR=426.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 3 22 8 + . UID=iso-22-1LSKZLVNO;Read=AGGTAGTAGGTTGTATAGTTTA;Parent=hsa-let-7a-2;Name=hsa-let-7a-5p;Variant=iso_5p:+2,iso_3p:+2;Cigar=20MTA;Alias=MIMAT0000062;Expression=2.0;expression_OptimiR=2.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 3 22 8 + . UID=iso-22-1LSKZLVNQ;Read=AGGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:+2,iso_3p:+2;Cigar=20MTT;Alias=MIMAT0000062;Expression=38.0;expression_OptimiR=38.0;Filter=PASS;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 21 13 + . UID=iso-18-RPV39QZ;Read=GGTAGTAGGTTGTATAGT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_3p:-1;Cigar=18M;Alias=MIMAT0000062;Expression=1.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 21 16 + . UID=iso-21-RPV39Q1OB;Read=GGTAGTAGGTTGTATAGTAAA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_3p:-1,iso_add3p:3;Change=iso_add3p:AAA;Cigar=18MAAA;Alias=MIMAT0000062;Expression=1.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 12 + . UID=iso-19-RPV39QFE;Read=GGTAGTAGGTTGTATAGTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3;Cigar=19M;Alias=MIMAT0000062;Expression=7.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 12 + . UID=iso-20-RPV39Q1Z;Read=GGTAGTAGGTTGTATAGTTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_3p:+1;Cigar=19MT;Alias=MIMAT0000062;Expression=20.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 12 + . UID=iso-21-RPV39Q1ZB;Read=GGTAGTAGGTTGTATAGTTTA;Parent=hsa-let-7a-2;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_3p:+2;Cigar=19MTA;Alias=MIMAT0000062;Expression=102.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 12 + . UID=iso-21-RPV39Q1ZE;Read=GGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7a-1;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_3p:+2;Cigar=19MTT;Alias=MIMAT0000062;Expression=11.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 14 + . UID=iso-21-RPV39Q1XB;Read=GGTAGTAGGTTGTATAGTTAA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_add3p:2;Change=iso_add3p:AA;Cigar=19MAA;Alias=MIMAT0000062;Expression=3227.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 16 + . UID=iso-23-RPV39Q1ZDB;Read=GGTAGTAGGTTGTATAGTTTATA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_add3p:4;Change=iso_add3p:TATA;Cigar=19MTATA;Alias=MIMAT0000062;Expression=9.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 isomiR 4 22 17 + . UID=iso-24-RPV39Q1ZKO;Read=GGTAGTAGGTTGTATAGTTTTTTA;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Variant=iso_5p:+3,iso_add3p:5;Change=iso_add3p:TTTTA;Cigar=19MTTTTA;Alias=MIMAT0000062;Expression=19.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=1;
hsa-let-7a-5p mirbase_21 ref_miRNA 1 22 0 + . UID=iso-22-XKVLRYVPQ;Read=TGAGGTAGTAGGTTGTATAGTT;Parent=hsa-let-7a-1,hsa-let-7a-2,hsa-let-7a-3;Name=hsa-let-7a-5p;Cigar=22M;Alias=MIMAT0000062;Expression=156.0;expression_OptimiR=156.0;Filter=PASS;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 10 + . UID=iso-24-XKVLRYVP26;Read=TGAGGTAGTAGGTTGTATAGTAAA;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:6;Change=iso_add3p:AGTAAA;Cigar=18MAGTAAA;Alias=MIMAT0000064;Expression=1.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 10 + . UID=iso-24-XKVLRYVPKQ;Read=TGAGGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:6;Change=iso_add3p:AGTTTT;Cigar=18MAGTTTT;Alias=MIMAT0000064;Expression=9.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 11 + . UID=iso-25-XKVLRYVPYE;Read=TGAGGTAGTAGGTTGTATAGTTAAT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:7;Change=iso_add3p:AGTTAAT;Cigar=18MAGTTAAT;Alias=MIMAT0000064;Expression=29.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 11 + . UID=iso-25-XKVLRYVPZQ;Read=TGAGGTAGTAGGTTGTATAGTTTAT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:7;Change=iso_add3p:AGTTTAT;Cigar=18MAGTTTAT;Alias=MIMAT0000064;Expression=6.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 11 + . UID=iso-25-XKVLRYVPZZ;Read=TGAGGTAGTAGGTTGTATAGTTTTT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:7;Change=iso_add3p:AGTTTTT;Cigar=18MAGTTTTT;Alias=MIMAT0000064;Expression=19.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 7 + . UID=iso-21-XKVLRYVPE;Read=TGAGGTAGTAGGTTGTATAGT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:3;Change=iso_add3p:AGT;Cigar=18MAGT;Alias=MIMAT0000064;Expression=2.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 8 + . UID=iso-22-XKVLRYVPQ;Read=TGAGGTAGTAGGTTGTATAGTT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:4;Change=iso_add3p:AGTT;Cigar=18MAGTT;Alias=MIMAT0000064;Expression=156.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 9 + . UID=iso-23-XKVLRYVP0O;Read=TGAGGTAGTAGGTTGTATAGTTA;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:5;Change=iso_add3p:AGTTA;Cigar=18MAGTTA;Alias=MIMAT0000064;Expression=111.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 1 18 9 + . UID=iso-23-XKVLRYVP0Q;Read=TGAGGTAGTAGGTTGTATAGTTT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_3p:-4,iso_add3p:5;Change=iso_add3p:AGTTT;Cigar=18MAGTTT;Alias=MIMAT0000064;Expression=29.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 11 + . UID=iso-20-531P7WH3;Read=GAGGTAGTAGGTTGTATAGT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:3;Change=iso_add3p:AGT;Cigar=17MAGT;Alias=MIMAT0000064;Expression=3.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 12 + . UID=iso-21-531P7WH3E;Read=GAGGTAGTAGGTTGTATAGTT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:4;Change=iso_add3p:AGTT;Cigar=17MAGTT;Alias=MIMAT0000064;Expression=15.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 14 + . UID=iso-23-531P7WH30F;Read=GAGGTAGTAGGTTGTATAGTTAA;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:6;Change=iso_add3p:AGTTAA;Cigar=17MAGTTAA;Alias=MIMAT0000064;Expression=273.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 14 + . UID=iso-23-531P7WH30Q;Read=GAGGTAGTAGGTTGTATAGTTTT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:6;Change=iso_add3p:AGTTTT;Cigar=17MAGTTTT;Alias=MIMAT0000064;Expression=23.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 15 + . UID=iso-24-531P7WH327;Read=GAGGTAGTAGGTTGTATAGTTAAT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:7;Change=iso_add3p:AGTTAAT;Cigar=17MAGTTAAT;Alias=MIMAT0000064;Expression=2.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 16 + . UID=iso-25-531P7WH3YN;Read=GAGGTAGTAGGTTGTATAGTTTATT;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:8;Change=iso_add3p:AGTTTATT;Cigar=17MAGTTTATT;Alias=MIMAT0000064;Expression=59.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
hsa-let-7c-5p mirbase_21 isomiR 2 18 17 + . UID=iso-26-531P7WH3ZXB;Read=GAGGTAGTAGGTTGTATAGTTTTTAA;Parent=hsa-let-7c;Name=hsa-let-7c-5p;Variant=iso_5p:+1,iso_3p:-4,iso_add3p:9;Change=iso_add3p:AGTTTTTAA;Cigar=17MAGTTTTTAA;Alias=MIMAT0000064;Expression=50.0;expression_OptimiR=0.0;Filter=REJECT,DISCARDED_SCORING;Hits=2;
mirtop-0.4.23/data/examples/paper/ 0000775 0000000 0000000 00000000000 13547635037 0016765 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/paper/cmd.sh 0000664 0000000 0000000 00000000411 13547635037 0020060 0 ustar 00root root 0000000 0000000 java -jar ~/repos/seqbuster/modules/miraligner/miraligner.jar -sub 1 -trim 3 -add 3 -s hsa -i hsa-let-7a-5p.fa -db ../annotat
e -o hsa-let-7a-5p
mirtop gff --hairpin ../annotate/hairpin.fa --gtf ../annotate/hsa.gff3 --out . --format seqbuster hsa-let-7a-5p.mirna
mirtop-0.4.23/data/examples/paper/hsa-let-7a-5p.fa 0000664 0000000 0000000 00000000043 13547635037 0021456 0 ustar 00root root 0000000 0000000 >example_x1
GAGCTAGTAGGTTGTATAGTAA
mirtop-0.4.23/data/examples/paper/hsa-let-7a-5p.gff 0000664 0000000 0000000 00000000623 13547635037 0021636 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## COLDATA: hsa-let-7a-5p
hsa-let-7a-3 miRBasev21 isomiR 4 25 0 + . Read=GAGCTAGTAGGTTGTATAGTAA; UID=iso-22-5I1P7WH3F; Name=hsa-let-7a-5p; Parent=hsa-let-7a-3; Variant=iso_snv_seed,iso_add3p:2,iso_5p:+1,iso_3p:-1; Cigar=3MC16MAA; Expression=1; Filter=Pass; Hits=1; Changes=iso_5p:t,iso_3p:t,iso_add3p:AA,iso_snv:4CG
mirtop-0.4.23/data/examples/paper/hsa-let-7a-5p.mirna 0000664 0000000 0000000 00000000261 13547635037 0022200 0 ustar 00root root 0000000 0000000 seq name freq mir start end mism add t5 t3 s5 s3 DB precursor ambiguity
GAGCTAGTAGGTTGTATAGTAA example_x1 ample_ hsa-let-7a-5p 5 24 4CG AA t t GAG AGTTTGGG miRNA hsa-let-7a-3 1
mirtop-0.4.23/data/examples/plot/ 0000775 0000000 0000000 00000000000 13547635037 0016634 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/plot/example_count.png 0000664 0000000 0000000 00000117662 13547635037 0022222 0 ustar 00root root 0000000 0000000 PNG
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TGGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTA
mirtop-0.4.23/data/examples/simulation/miRNA.str 0000664 0000000 0000000 00000000104 13547635037 0021535 0 ustar 00root root 0000000 0000000 >hsa-let-7a-1 (-35.60) [hsa-let-7a-5p:6-27] [hsa-let-7a-3p:57-77]
mirtop-0.4.23/data/examples/simulation/reads.fa 0000664 0000000 0000000 00000010674 13547635037 0021460 0 ustar 00root root 0000000 0000000 >hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:11T_add:T_x29
GAGGTAGTAGTTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:null_x108
AGGTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:2T_add:null_x0
GTTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:A_x550
TGAGGTAGTAGGTTGTATAGTA
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null_x508
GGTAGTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:18C_add:null_x198
ATGAGGTAGTAGGTTGTCTAGTT
>hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:null_x4
TGAGGTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:null_x861
ATGAGGTAGTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAA_x0
AGGTAGTAGGTTGTATAGTAAA
>hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAA_x9
GAGGTAGTAGGTTGTATAGTTAA
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:null_x0
TGAGGTAGTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:19A_add:ATT_x158
ATGAGGTAGTAGGTTGTAAAGTTATT
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:null_x59
AGGTAGTAGGTTGTATAAT
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:null_x1
AGGTAGTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:16G_add:ATT_x111
GGTAGTAGGTTGTATGGTATT
>hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TA_x8
TGAGGTAGTAGGTTGTATAGTTTA
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:8C_add:null_x13
TGAGGTACTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:null_x0
GAGGTAGTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TTT_x41
TGAGGTAGTAGGTTGTATAGTTTTT
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:TA_x51
AGGTAGTAGGTTGTATAATTA
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:14G_add:null_x29
GGTAGTAGGTTGTGTAGT
>hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null_x103
ATGAGGTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:null_x37
GAGGTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TAT_x152
TGAGGTAGTAGGTTGTATAGTTAT
>hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:TA_x5
ATGAGGTAGTAGGTTGTATAGTTA
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:A_x239
GGTAGTAGGTTGTATAGTA
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:AT_x713
TGAGGTAGTAGGTTGTATAGTAT
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6G_add:TA_x58
TGAGGGAGTAGGTTGTATAGTTA
>hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:1T_add:TT_x290
TTGAGGTAGTAGGTTGTATAGTTT
>hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AAA_x41
GAGGTAGTAGGTTGTATAGTAAA
>hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:6G_add:ATT_x18
GAGGTGGTAGGTTGTATAGTATT
>hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TTA_x280
GAGGTAGTAGGTTGTATAGTTTTA
>hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:ATT_x32
TGAGGTAGTAGGTTGTATAGTTATT
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:9C_add:null_x6
AGGTAGTACGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:3T_add:TA_x11
ATTAGGTAGTAGGTTGTATAGTTA
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:18C_add:null_x2
GGTAGTAGGTTGTATAGC
>hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:11G_add:null_x8
ATGAGGTAGTGGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:AT_x246
GGTAGTAGGTTGTATAGTTAT
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:4T_add:TT_x616
GGTTGTAGGTTGTATAGTTT
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:10A_add:null_x48
GGTAGTAGGATGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:6A_add:null_x4
GGTAGAAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:T_x16
GGTAGTAGGTTGTATAGTTT
>hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TAT_x543
GAGGTAGTAGGTTGTATAGTTTAT
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TT_x103
TGAGGTAGTAGGTTGTATAGTTT
>hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAT_x15
GAGGTAGTAGGTTGTATAGTTAT
>hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TA_x576
GGTAGTAGGTTGTATAGTTA
>hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:11C_add:null_x8
ATGAGGTAGTCGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TTT_x116
TGAGGTAGTAGGTTGTATAGTTTT
>hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AT_x693
GAGGTAGTAGGTTGTATAGTAT
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TA_x11
TGAGGTAGTAGGTTGTATAGTTA
>hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6A_add:null_x24
TGAGGAAGTAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:10C_add:null_x66
ATGAGGTAGCAGGTTGTATAGT
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:2T_add:T_x20
ATGTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:null_x103
GGTAGTAGGTTGTATAGTT
>hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:TTA_x1001
AGGTAGTAGGTTGTATAGTTTTA
>hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAT_x40
AGGTAGTAGGTTGTATAGTAAT
mirtop-0.4.23/data/examples/simulation/reads.sam 0000664 0000000 0000000 00000020612 13547635037 0021643 0 ustar 00root root 0000000 0000000 @HD VN:1.4 SO:coordinate
@PG ID:razers3 VN:3.3 PN:razers3 CL:-dr 0 -i 80 -rr 90 -f -o reads.sam hairpin.fa reads.fa
@SQ SN:hsa-let-7a-1 LN:80
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:11T_add:T_x29 0 hsa-let-7a-1 7 255 21M * 0 0 GAGGTAGTAGTTTGTATAGTT IIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:10G10
hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:null_x108 0 hsa-let-7a-1 8 255 20M * 0 0 AGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:20
hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:2T_add:null_x0 0 hsa-let-7a-1 9 255 19M * 0 0 GTTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:1G17
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:A_x550 0 hsa-let-7a-1 6 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTA IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:21T
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null_x508 0 hsa-let-7a-1 9 255 18M * 0 0 GGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIII NM:i:0 MD:Z:18
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:18C_add:null_x198 0 hsa-let-7a-1 5 255 23M * 0 0 ATGAGGTAGTAGGTTGTCTAGTT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:17A5
hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:null_x4 0 hsa-let-7a-1 6 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:22
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:null_x861 0 hsa-let-7a-1 5 255 22M * 0 0 ATGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:22
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAA_x0 0 hsa-let-7a-1 8 255 22M1D * 0 0 AGGTAGTAGGTTGTATAGTAAA IIIIIIIIIIIIIIIIIIIIII NM:i:3 MD:Z:19T0T0T^A
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAA_x9 0 hsa-let-7a-1 7 255 23M1D * 0 0 GAGGTAGTAGGTTGTATAGTTAA IIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:21T0T^A
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:null_x0 0 hsa-let-7a-1 6 255 21M * 0 0 TGAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:21
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:19A_add:ATT_x158 0 hsa-let-7a-1 5 255 23M1I2M * 0 0 ATGAGGTAGTAGGTTGTAAAGTTATT IIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:18T6
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:null_x59 0 hsa-let-7a-1 8 255 19M * 0 0 AGGTAGTAGGTTGTATAAT IIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:17G1
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:null_x1 0 hsa-let-7a-1 8 255 19M * 0 0 AGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:16G_add:ATT_x111 0 hsa-let-7a-1 9 255 21M * 0 0 GGTAGTAGGTTGTATGGTATT IIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:15A2T2
hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TA_x8 0 hsa-let-7a-1 6 255 24M1D * 0 0 TGAGGTAGTAGGTTGTATAGTTTA IIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:23T^A
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:8C_add:null_x13 0 hsa-let-7a-1 6 255 21M * 0 0 TGAGGTACTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:7G13
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:null_x0 0 hsa-let-7a-1 7 255 20M * 0 0 GAGGTAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:20
hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TTT_x41 0 hsa-let-7a-1 6 255 25M * 0 0 TGAGGTAGTAGGTTGTATAGTTTTT IIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:24A
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:TA_x51 0 hsa-let-7a-1 8 255 21M * 0 0 AGGTAGTAGGTTGTATAATTA IIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:17G2T
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:14G_add:null_x29 0 hsa-let-7a-1 9 255 18M * 0 0 GGTAGTAGGTTGTGTAGT IIIIIIIIIIIIIIIIII NM:i:1 MD:Z:13A4
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null_x103 0 hsa-let-7a-1 5 255 23M * 0 0 ATGAGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:23
hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:null_x37 0 hsa-let-7a-1 7 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:21
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TAT_x152 0 hsa-let-7a-1 6 255 24M * 0 0 TGAGGTAGTAGGTTGTATAGTTAT IIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:22T1
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:TA_x5 0 hsa-let-7a-1 5 255 24M * 0 0 ATGAGGTAGTAGGTTGTATAGTTA IIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:23T
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:A_x239 0 hsa-let-7a-1 9 255 19M * 0 0 GGTAGTAGGTTGTATAGTA IIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:18T
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:AT_x713 0 hsa-let-7a-1 6 255 23M * 0 0 TGAGGTAGTAGGTTGTATAGTAT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:21T1
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6G_add:TA_x58 0 hsa-let-7a-1 6 255 23M * 0 0 TGAGGGAGTAGGTTGTATAGTTA IIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:5T16T
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:1T_add:TT_x290 0 hsa-let-7a-1 5 255 24M * 0 0 TTGAGGTAGTAGGTTGTATAGTTT IIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:0A23
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AAA_x41 0 hsa-let-7a-1 7 255 23M1D * 0 0 GAGGTAGTAGGTTGTATAGTAAA IIIIIIIIIIIIIIIIIIIIIII NM:i:3 MD:Z:20T0T0T^A
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:6G_add:ATT_x18 0 hsa-let-7a-1 7 255 23M * 0 0 GAGGTGGTAGGTTGTATAGTATT IIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:5A14T2
hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TTA_x280 0 hsa-let-7a-1 7 255 24M * 0 0 GAGGTAGTAGGTTGTATAGTTTTA IIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:24
hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:ATT_x32 0 hsa-let-7a-1 6 255 22M1I2M * 0 0 TGAGGTAGTAGGTTGTATAGTTATT IIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:24
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:9C_add:null_x6 0 hsa-let-7a-1 8 255 19M * 0 0 AGGTAGTACGTTGTATAGT IIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:8G10
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:3T_add:TA_x11 0 hsa-let-7a-1 5 255 24M * 0 0 ATTAGGTAGTAGGTTGTATAGTTA IIIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:2G20T
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:18C_add:null_x2 0 hsa-let-7a-1 9 255 18M * 0 0 GGTAGTAGGTTGTATAGC IIIIIIIIIIIIIIIIII NM:i:1 MD:Z:17T
hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:11G_add:null_x8 0 hsa-let-7a-1 5 255 23M * 0 0 ATGAGGTAGTGGGTTGTATAGTT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:10A12
hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:AT_x246 0 hsa-let-7a-1 9 255 21M * 0 0 GGTAGTAGGTTGTATAGTTAT IIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:19T1
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:4T_add:TT_x616 0 hsa-let-7a-1 9 255 20M * 0 0 GGTTGTAGGTTGTATAGTTT IIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:3A16
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:10A_add:null_x48 0 hsa-let-7a-1 9 255 18M * 0 0 GGTAGTAGGATGTATAGT IIIIIIIIIIIIIIIIII NM:i:1 MD:Z:9T8
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:6A_add:null_x4 0 hsa-let-7a-1 9 255 18M * 0 0 GGTAGAAGGTTGTATAGT IIIIIIIIIIIIIIIIII NM:i:1 MD:Z:5T12
hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:T_x16 0 hsa-let-7a-1 9 255 20M * 0 0 GGTAGTAGGTTGTATAGTTT IIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:20
hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TAT_x543 0 hsa-let-7a-1 7 255 22M1I1M * 0 0 GAGGTAGTAGGTTGTATAGTTTAT IIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:23
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TT_x103 0 hsa-let-7a-1 6 255 23M * 0 0 TGAGGTAGTAGGTTGTATAGTTT IIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:23
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAT_x15 0 hsa-let-7a-1 7 255 23M * 0 0 GAGGTAGTAGGTTGTATAGTTAT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:21T1
hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TA_x576 0 hsa-let-7a-1 9 255 20M * 0 0 GGTAGTAGGTTGTATAGTTA IIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:19T
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:11C_add:null_x8 0 hsa-let-7a-1 5 255 22M * 0 0 ATGAGGTAGTCGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:10A11
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TTT_x116 0 hsa-let-7a-1 6 255 24M * 0 0 TGAGGTAGTAGGTTGTATAGTTTT IIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:24
hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AT_x693 0 hsa-let-7a-1 7 255 22M * 0 0 GAGGTAGTAGGTTGTATAGTAT IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:20T1
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TA_x11 0 hsa-let-7a-1 6 255 23M * 0 0 TGAGGTAGTAGGTTGTATAGTTA IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:22T
hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6A_add:null_x24 0 hsa-let-7a-1 6 255 21M * 0 0 TGAGGAAGTAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:5T15
hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:10C_add:null_x66 0 hsa-let-7a-1 5 255 22M * 0 0 ATGAGGTAGCAGGTTGTATAGT IIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:9T12
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:2T_add:T_x20 0 hsa-let-7a-1 8 255 20M * 0 0 ATGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:1G18
hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:null_x103 0 hsa-let-7a-1 9 255 19M * 0 0 GGTAGTAGGTTGTATAGTT IIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:19
hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:TTA_x1001 0 hsa-let-7a-1 8 255 23M * 0 0 AGGTAGTAGGTTGTATAGTTTTA IIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:23
hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAT_x40 0 hsa-let-7a-1 8 255 22M * 0 0 AGGTAGTAGGTTGTATAGTAAT IIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:19T0T1
mirtop-0.4.23/data/examples/simulation/res/ 0000775 0000000 0000000 00000000000 13547635037 0020633 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/simulation/res/reads.mirna 0000664 0000000 0000000 00000020701 13547635037 0022761 0 ustar 00root root 0000000 0000000 seq name freq chrom start end mism add t5 t3 s5 s3 DB precursor ambiguity Name
ATGAGGTAGTAGGTTGTCTAGTT hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:18C_add:null_x198 198 hsa-let-7a-5p NA NA 17CA 0 A 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.A17C
ATGAGGTAGTAGGTTGTATAGTTA hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:TA_x5 5 hsa-let-7a-5p NA NA 0 A A 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.eA
GAGGTAGTAGGTTGTATAGTTTAT hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TAT_x543 543 hsa-let-7a-5p NA NA 0 AT t T NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.T.eAT
TGAGGAAGTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6A_add:null_x24 24 hsa-let-7a-5p NA NA 5AT 0 0 t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.T5A.t
AGGTAGTAGGTTGTATAAT hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:null_x59 59 hsa-let-7a-5p NA NA 0 AT tg gtt NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.gtt.eAT
GGTAGTAGGTTGTATAGTTA hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TA_x576 576 hsa-let-7a-5p NA NA 0 A tga 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.eA
GGTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:null_x103 103 hsa-let-7a-5p NA NA 0 0 tga 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga
GAGGTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:null_x37 37 hsa-let-7a-5p NA NA 0 0 t 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st
GGTAGTAGGTTGTATAGC hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:18C_add:null_x2 2 hsa-let-7a-5p NA NA 0 C tga tt NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.tt.eC
GGTTGTAGGTTGTATAGTTT hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:4T_add:TT_x616 616 hsa-let-7a-5p NA NA 3TA 0 tga T NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.A3T.T
TTGAGGTAGTAGGTTGTATAGTTT hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:1T_add:TT_x290 290 hsa-let-7a-5p NA NA 0TA 0 T T NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sT.A0T.T
ATGAGGTAGTGGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:11G_add:null_x8 8 hsa-let-7a-5p NA NA 10GA 0 A 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.A10G
GGTAGTAGGTTGTGTAGT hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:14G_add:null_x29 29 hsa-let-7a-5p NA NA 13GA 0 tga t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.A13G.t
ATGAGGTAGTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:null_x861 861 hsa-let-7a-5p NA NA 0 0 A t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.t
TGAGGTAGTAGGTTGTATAGTTTTT hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TTT_x41 41 hsa-let-7a-5p NA NA 0 T 0 TT NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.TT.eT
ATGAGGTAGCAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:10C_add:null_x66 66 hsa-let-7a-5p NA NA 9CT 0 A t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.T9C.t
ATGTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:2T_add:T_x20 20 hsa-let-7a-5p NA NA 1TG 0 tg 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.G1T
TGAGGTAGTAGGTTGTATAGTTAT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TAT_x152 152 hsa-let-7a-5p NA NA 0 AT 0 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.eAT
ATGAGGTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null_x103 103 hsa-let-7a-5p NA NA 0 0 A 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA
TGAGGTAGTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:null_x0 0 hsa-let-7a-5p NA NA 0 0 0 t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.t
GAGGTAGTAGGTTGTATAGTTAT hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAT_x15 15 hsa-let-7a-5p NA NA 0 AT t 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.eAT
GAGGTAGTAGTTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:11T_add:T_x29 29 hsa-let-7a-5p NA NA 10TG 0 t 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.G10T
GGTAGTAGGATGTATAGT hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:10A_add:null_x48 48 hsa-let-7a-5p NA NA 9AT 0 tga t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.T9A.t
GTTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:2T_add:null_x0 0 hsa-let-7a-5p NA NA 1TG 0 tga 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.G1T
AGGTAGTACGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:9C_add:null_x6 6 hsa-let-7a-5p NA NA 8CG 0 tg t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.G8C.t
TGAGGTAGTAGGTTGTATAGTTATT hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:ATT_x32 32 hsa-let-7a-5p NA NA 22A- 0 0 TT NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.-22A.TT
AGGTAGTAGGTTGTATAGTAAA hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAA_x0 0 hsa-let-7a-5p NA NA 19AT AA tg 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.T19A.eAA
GGTAGTAGGTTGTATAGTA hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:A_x239 239 hsa-let-7a-5p NA NA 0 A tga t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.t.eA
AGGTAGTAGGTTGTATAGTTTTA hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:TTA_x1001 1001 hsa-let-7a-5p NA NA 0 0 tg TTA NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.TTA
GAGGTAGTAGGTTGTATAGTAAA hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AAA_x41 41 hsa-let-7a-5p NA NA 20AT AA t 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.T20A.eAA
GGTAGTAGGTTGTATAGTTAT hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:AT_x246 246 hsa-let-7a-5p NA NA 0 AT tga 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.eAT
TGAGGTAGTAGGTTGTATAGTTTA hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TA_x8 8 hsa-let-7a-5p NA NA 0 A 0 T NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.T.eA
AGGTAGTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:null_x1 1 hsa-let-7a-5p NA NA 0 0 tg t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.t
ATGAGGTAGTCGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:11C_add:null_x8 8 hsa-let-7a-5p NA NA 10CA 0 A t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.A10C.t
AGGTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:null_x108 108 hsa-let-7a-5p NA NA 0 0 tg 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg
AGGTAGTAGGTTGTATAGTAAT hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAT_x40 40 hsa-let-7a-5p NA NA 0 AAT tg t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.t.eAAT
TGAGGTAGTAGGTTGTATAGTA hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:A_x550 550 hsa-let-7a-5p NA NA 0 A 0 t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.t.eA
GAGGTAGTAGGTTGTATAGTAT hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AT_x693 693 hsa-let-7a-5p NA NA 0 AT t t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.t.eAT
GAGGTAGTAGGTTGTATAGTTTTA hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TTA_x280 280 hsa-let-7a-5p NA NA 0 0 t TTA NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.TTA
TGAGGTAGTAGGTTGTATAGTAT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:AT_x713 713 hsa-let-7a-5p NA NA 0 AT 0 t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.t.eAT
TGAGGGAGTAGGTTGTATAGTTA hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6G_add:TA_x58 58 hsa-let-7a-5p NA NA 5GT A 0 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.T5G.eA
TGAGGTAGTAGGTTGTATAGTTTT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TTT_x116 116 hsa-let-7a-5p NA NA 0 0 0 TT NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.TT
GAGGTAGTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:null_x0 0 hsa-let-7a-5p NA NA 0 0 t t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.t
GAGGTAGTAGGTTGTATAGTTAA hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAA_x9 9 hsa-let-7a-5p NA NA 0 AA t 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.st.eAA
TGAGGTAGTAGGTTGTATAGTTT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TT_x103 103 hsa-let-7a-5p NA NA 0 0 0 T NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.T
AGGTAGTAGGTTGTATAATTA hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:TA_x51 51 hsa-let-7a-5p NA NA 17AG A tg 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stg.G17A.eA
ATTAGGTAGTAGGTTGTATAGTTA hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:3T_add:TA_x11 11 hsa-let-7a-5p NA NA 2TG A A 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.sA.G2T.eA
GGTAGAAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:6A_add:null_x4 4 hsa-let-7a-5p NA NA 5AT 0 tga t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.T5A.t
GGTAGTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null_x508 508 hsa-let-7a-5p NA NA 0 0 tga t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.t
TGAGGTACTAGGTTGTATAGT hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:8C_add:null_x13 13 hsa-let-7a-5p NA NA 7CG 0 0 t NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.G7C.t
TGAGGTAGTAGGTTGTATAGTTA hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TA_x11 11 hsa-let-7a-5p NA NA 0 A 0 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.eA
TGAGGTAGTAGGTTGTATAGTT hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:null_x4 4 hsa-let-7a-5p NA NA 0 0 0 0 NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.
GGTAGTAGGTTGTATAGTTT hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:T_x16 16 hsa-let-7a-5p NA NA 0 0 tga T NA NA miRNA hsa-let-7a-1 1 hsa-let-7a-5p.stga.T
mirtop-0.4.23/data/examples/simulation/test.gff 0000664 0000000 0000000 00000004105 13547635037 0021505 0 ustar 00root root 0000000 0000000 ## GFF3 adapted for miRNA sequencing data. VERSION 0.0.1
## source-ontology: miRBase1
## COLDATA: sampleX
hsa-let-7a-1 miRBase21 isomiR 4 29 0 + . Read hsa-let-7a-5p.sA.TT.ATGAGGTAGTAGGTTGTATAGTTTT; UID bhJJ5WJ%L2; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_5p:+1,iso_3p:+2; Cigar 25M; Expression 21; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 4 28 0 + . Read hsa-let-7a-5p.sA.G5T.t.eAA.ATGAGTTAGTAGGTTGTATAGTAA; UID bwJJ5WJL; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_snp_seed,iso_add:+2,iso_5p:+1,iso_3p:-1; Cigar 5MT16MAA; Expression 620; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 5 26 0 + . Read hsa-let-7a-5p.t.TGAGGTAGTAGGTTGTATAGT; UID 7AwhRzw; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_3p:-1; Cigar 21M; Expression 0; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 5 28 0 + . Read hsa-let-7a-5p.T.TGAGGTAGTAGGTTGTATAGTTT; UID 7AwhRzwQ1; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_3p:+1; Cigar 23M; Expression 43; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 6 30 0 + . Read hsa-let-7a-5p.st.eAAT.GAGGTAGTAGGTTGTATAGTTAAT; UID 4WWABg5o; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_add:+3,iso_5p:-1; Cigar 21MIAMD; Expression 4; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 6 26 0 + . Read hsa-let-7a-5p.st.A5T.t.GAGGTTGTAGGTTGTATAGT; UID 45WABgW1; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_snp_seed,iso_5p:-1,iso_3p:-1; Cigar 5MT14M; Expression 40; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 6 26 0 + . Read hsa-let-7a-5p.st.t.GAGGTAGTAGGTTGTATAGT; UID 4WWABgW1; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_5p:-1,iso_3p:-1; Cigar 20M; Expression 6; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 7 28 0 + . Read hsa-let-7a-5p.stg.T.AGGTAGTAGGTTGTATAGTTT; UID hJJ5WJ%; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_5p:-2,iso_3p:+1; Cigar 21M; Expression 362; Filter Pass; Hits 1;
hsa-let-7a-1 miRBase21 isomiR 7 27 0 + . Read hsa-let-7a-5p.stg.AGGTAGTAGGTTGTATAGTT; UID hJJ5WJQ1; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_5p:-2; Cigar 20M; Expression 499; Filter Pass; Hits 1;
mirtop-0.4.23/data/examples/spikeins/ 0000775 0000000 0000000 00000000000 13547635037 0017503 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/spikeins/spikeins.fa 0000664 0000000 0000000 00000000043 13547635037 0021635 0 ustar 00root root 0000000 0000000 >spikein-1
ATGATGATGATGATGATGATGAT
mirtop-0.4.23/data/examples/spikeins/spikeins.sam 0000664 0000000 0000000 00000001362 13547635037 0022034 0 ustar 00root root 0000000 0000000 @HD VN:1.4 SO:coordinate
@PG ID:razers3 VN:3.3 PN:razers3 CL:-dr 0 -i 80 -rr 90 -f -o spikeins.sam test_out_spikeins/spikeins_pre.fasta ../../data/examples/spikeins/test-spikeins.fa
@SQ SN:pre-spikein-1 LN:33
spikein-1 0 pre-spikein-1 6 255 23M * 0 0 ATGATGATGATGATGATGATGAT IIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:23
spikein-1-add 0 pre-spikein-1 6 255 25M * 0 0 ATGATGATGATGATGATGATGATAA IIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 MD:Z:23G0G
spikein-1-3p 0 pre-spikein-1 6 255 22M * 0 0 ATGATGATGATGATGATGATGA IIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:22
spikein-1-5p 0 pre-spikein-1 7 255 22M * 0 0 TGATGATGATGATGATGATGAT IIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:22
spikein-1-snp 0 pre-spikein-1 6 255 23M * 0 0 ATGATGATGACGATGATGATGAT IIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:10T12
mirtop-0.4.23/data/examples/spikeins/spikeins_pre.fasta 0000664 0000000 0000000 00000000061 13547635037 0023213 0 ustar 00root root 0000000 0000000 >pre-spikein-1
GGGGGATGATGATGATGATGATGATGATGGGGG
mirtop-0.4.23/data/examples/spikeins/spikeins_pre.gff 0000664 0000000 0000000 00000000327 13547635037 0022664 0 ustar 00root root 0000000 0000000 #microRNAs: spikeins_v1
chrspikein-1 . miRNA_primary_transcript 1 33 . + . Name=pre-spikein-1;ID=pre-spikein-1
chrspikein-1 . miRNA 6 28 . + . Derives_from=pre-spikein-1;Name=spikein-1;ID=spikein-1;
mirtop-0.4.23/data/examples/spikeins/test-spikeins.fa 0000664 0000000 0000000 00000000275 13547635037 0022621 0 ustar 00root root 0000000 0000000 >spikein-1
ATGATGATGATGATGATGATGAT
>spikein-1-add
ATGATGATGATGATGATGATGATAA
>spikein-1-3p
ATGATGATGATGATGATGATGA
>spikein-1-5p
TGATGATGATGATGATGATGAT
>spikein-1-snp
ATGATGATGACGATGATGATGAT
mirtop-0.4.23/data/examples/srnabench/ 0000775 0000000 0000000 00000000000 13547635037 0017621 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/srnabench/microRNAannotation.txt 0000664 0000000 0000000 00000001257 13547635037 0024134 0 ustar 00root root 0000000 0000000 sequence matureName hairpinName isoLabel sequenceVariant readCount RPMlib RPMtotal
ATGAGGTAGTAGGTTGTATAGTTTTT hsa-let-7a-5p hsa-let-7a-1 nta#T|nta#T#1@lv5p|lv5pE|lv5p#1 - 66 11346.054667354307 11346.054667354307
GAGGTAGTAGGTTGTATAGTTTTTAA hsa-let-7a-5p hsa-let-7a-2 lv5p|lv5pT|lv5p#-1@lv3p|lv3pE|lv3p#5 - 50 8595.4959601169 8595.4959601169
ATGAGGTAGTAGGTTGTATAGT hsa-let-7a-5p hsa-let-7a-1 lv5p|lv5pE|lv5p#1@lv3p|lv3pT|lv3p#-1 - 11 1891.0091112257178 1891.0091112257178
TGAGGTAGTAGGTTGTATAGTT hsa-let-7a-5p hsa-let-7a-1$hsa-let-7a-2$hsa-let-7a-3 exact - 156 26817.947395564723 26817.947395564723
ACACACACAAACACACA hsa-miR-8485 hsa-mir-8485 mv|mv - 1 2.940631588852654 0.7665055472006451
mirtop-0.4.23/data/examples/srnabench/reads.annotation 0000664 0000000 0000000 00000001225 13547635037 0023013 0 ustar 00root root 0000000 0000000 GAGGTAGTAGGTTGTATAGTTTTTAA 50 8595.4959601169 mature#sense mature#hsa-let-7a-5p#sense#hsa-let-7a-2,6,31 1
ATGAGGTAGTAGGTTGTATAGTTTTT 66 11346.054667354307 mature#sense mature#hsa-let-7a-5p#sense#hsa-let-7a-1,5,30 1
ATGAGGTAGTAGGTTGTATAGT 11 1891.0091112257178 mature#sense mature#hsa-let-7a-5p#sense#hsa-let-7a-1,5,26 1
TGAGGTAGTAGGTTGTATAGTT 156 26817.947395564723 mature#sense mature#hsa-let-7a-5p#sense#hsa-let-7a-3,4,25$mature#hsa-let-7a-5p#sense#hsa-let-7a-1,6,27$mature#hsa-let-7a-5p#sense#hsa-let-7a-2,5,26 3
ACACACACAAACACACA 1 0.7665055472006451 mature#sense mature#hsa-miR-8485#sense#hsa-mir-8485,68,84$mature#hsa-miR-8485#sense#hsa-mir-8485,70,86 2
mirtop-0.4.23/data/examples/stats/ 0000775 0000000 0000000 00000000000 13547635037 0017014 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/stats/mirtop_stats.txt 0000664 0000000 0000000 00000001541 13547635037 0022306 0 ustar 00root root 0000000 0000000 # mirtop stats version 0.3.7a
,category,sample,counts
0,iso_3p_sum,sampleX,2262.0
1,iso_5p_sum,sampleX,6258.0
2,iso_add_sum,sampleX,5279.0
3,iso_snp_central_offset_sum,sampleX,45.0
4,iso_snp_central_supp_sum,sampleX,12.0
5,iso_snp_seed_sum,sampleX,477.0
6,isomiR_sum,sampleX,6476.0
7,ref_miRNA_sum,sampleX,156.0
0,iso_3p_count,sampleX,31.0
1,iso_5p_count,sampleX,34.0
2,iso_add_count,sampleX,23.0
3,iso_snp_central_offset_count,sampleX,1.0
4,iso_snp_central_supp_count,sampleX,1.0
5,iso_snp_seed_count,sampleX,2.0
6,isomiR_count,sampleX,43.0
7,ref_miRNA_count,sampleX,1.0
0,iso_3p_mean,sampleX,72.9677419355
1,iso_5p_mean,sampleX,184.058823529
2,iso_add_mean,sampleX,229.52173913
3,iso_snp_central_offset_mean,sampleX,45.0
4,iso_snp_central_supp_mean,sampleX,12.0
5,iso_snp_seed_mean,sampleX,238.5
6,isomiR_mean,sampleX,150.604651163
7,ref_miRNA_mean,sampleX,156.0
mirtop-0.4.23/data/examples/synthetic/ 0000775 0000000 0000000 00000000000 13547635037 0017670 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/synthetic/create.sh 0000664 0000000 0000000 00000000156 13547635037 0021471 0 ustar 00root root 0000000 0000000 mirtop gff --hairpin ../annotate/hairpin.fa --gtf ../annotate/hsa.gff3 --format seqbuster let7a-5p.mirna -o .
mirtop-0.4.23/data/examples/synthetic/let7a-5p.fastq 0000664 0000000 0000000 00000000750 13547635037 0022270 0 ustar 00root root 0000000 0000000 >seq_ref_x1
TGAGGTAGTAGGTTGTATAGTT
>seq_iso_3p:t_x1
TGAGGTAGTAGGTTGTATAGT
>seq_iso_3p:tt_x1
TGAGGTAGTAGGTTGTATAG
>seq_iso_3p:T_x1
TGAGGTAGTAGGTTGTATAGTTT
>seq_iso_3p:TT_x1
TGAGGTAGTAGGTTGTATAGTTTT
>seq_iso_add:A_x1
TGAGGTAGTAGGTTGTATAGTTA
>seq_iso_add:AA_x1
TGAGGTAGTAGGTTGTATAGTTAA
>seq_iso_5p:t_x1
GAGGTAGTAGGTTGTATAGTT
>seq_iso_5p:tg_x1
AGGTAGTAGGTTGTATAGTT
>seq_iso_5p:A_x1
ATGAGGTAGTAGGTTGTATAGTT
>seq_iso_5p:GA_x1
GATGAGGTAGTAGGTTGTATAGTT
>seq_iso_snp:11CG_x1
TGAGGTAGTACGTTGTATAGTT mirtop-0.4.23/data/examples/synthetic/let7a-5p.gff 0000664 0000000 0000000 00000004710 13547635037 0021714 0 ustar 00root root 0000000 0000000 ## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add3p:2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add3p:1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
mirtop-0.4.23/data/examples/synthetic/let7a-5p.mirna 0000664 0000000 0000000 00000002535 13547635037 0022263 0 ustar 00root root 0000000 0000000 seq name freq mir start end mism add t5 t3 s5 s3 DB precursor ambiguity
TGAGGTAGTAGGTTGTATAGTTTT seq_iso_3p:TT_x1 1 hsa-let-7a-5p 6 29 0 0 0 TT GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTAGGTTGTATAGTTT seq_iso_3p:T_x1 1 hsa-let-7a-5p 6 28 0 0 0 T GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTAGGTTGTATAGT seq_iso_3p:t_x1 1 hsa-let-7a-5p 6 26 0 0 0 t GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTAGGTTGTATAG seq_iso_3p:tt_x1 1 hsa-let-7a-5p 6 25 0 0 0 tt GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
ATGAGGTAGTAGGTTGTATAGTT seq_iso_5p:A_x1 1 hsa-let-7a-5p 5 27 0 0 A 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
GATGAGGTAGTAGGTTGTATAGTT seq_iso_5p:GA_x1 1 hsa-let-7a-5p 4 27 0 0 GA 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
GAGGTAGTAGGTTGTATAGTT seq_iso_5p:t_x1 1 hsa-let-7a-5p 7 27 0 0 t 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
AGGTAGTAGGTTGTATAGTT seq_iso_5p:tg_x1 1 hsa-let-7a-5p 8 27 0 0 tg 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTAGGTTGTATAGTTAA seq_iso_add:AA_x1 1 hsa-let-7a-5p 6 27 0 AA 0 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTAGGTTGTATAGTTA seq_iso_add:A_x1 1 hsa-let-7a-5p 6 27 0 A 0 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTACGTTGTATAGTT seq_iso_snp:11CG_x1 1 hsa-let-7a-5p 6 27 11CG 0 0 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
TGAGGTAGTAGGTTGTATAGTT seq_ref_x1 1 hsa-let-7a-5p 6 27 0 0 0 0 GGGATGAG AGTTTTAG miRNA hsa-let-7a-1 1
mirtop-0.4.23/data/examples/versions/ 0000775 0000000 0000000 00000000000 13547635037 0017526 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/examples/versions/version1.0.gff 0000664 0000000 0000000 00000002036 13547635037 0022117 0 ustar 00root root 0000000 0000000 ## GFF3 adapted for miRNA sequencing data. VERSION 1.0
## source-ontology: miRBasev21
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=seq_iso_5p:GA_x1; UID=F4WWABg5; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1; Changes=iso_5p:AT,iso_3p:0,iso_add:0,iso_snp:0
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=seq_iso_5p:A_x1; UID=bhJJ5WJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1; Changes=iso_5p:T,iso_3p:0,iso_add:0,iso_snp:0
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=seq_iso_snp:11CG_x1; UID=7AwdRzwL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1; Changes=iso_5p:0,iso_3p:0,iso_add:0,iso_snp:11CG
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=seq_iso_add:AA_x1; UID=7AwhRzwL; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1; Changes=iso_5p:0,iso_3p:0,iso_add:AA,iso_snp:0
mirtop-0.4.23/data/merge/ 0000775 0000000 0000000 00000000000 13547635037 0015137 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/data/merge/samples1.sam 0000664 0000000 0000000 00000001371 13547635037 0017370 0 ustar 00root root 0000000 0000000 @HD VN:1.4 SO:coordinate
@PG ID:razers3 VN:3.3 PN:razers3 CL:-dr 0 -i 80 -rr 90 -f -o /n/scratch2/hsph_bioinformatic_core/lp113/mirtop/example-merged/work2/bcbiotx/tmplRFN4e/SRR5756178.bam /n/app/bcbio/dev/genomes/Hsapiens/hg19/srnaseq/hairpin.fa /n/scratch2/hsph_bioinformatic_core/lp113/mirtop/example-merged/work2/trimmed/SRR5756178/SRR5756178.clean.trimming.fastq
@SQ SN:hsa-let-7a-1 LN:80
@SQ SN:hsa-let-7a-2 LN:72
@SQ SN:hsa-let-7a-3 LN:74
seq_1010_x33 0 hsa-let-7a-1 6 255 19M * 0 0 TGAGGTAGTAGGTTGTATA @@?CEDDDGFFGEHHFFGF NM:i:0 MD:Z:19
seq_1156_x2 0 hsa-let-7a-1 6 255 22M * 0 0 TGAGGTAGTAGGTTGGATAGTT <<7<@6==7=:@6?5,5/2.4? NM:i:1 MD:Z:15T6
seq_1711_x4 0 hsa-let-7a-1 5 255 1D22M * 0 0 AGAGGTAGTAGGTTGTATAGTT 04`_.
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mirtop-0.4.23/docs/conf.py 0000664 0000000 0000000 00000013615 13547635037 0015364 0 ustar 00root root 0000000 0000000 # -*- coding: utf-8 -*-
#
# mirtop documentation build configuration file, created by
# sphinx-quickstart on Tue Nov 14 15:51:17 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
source_suffix = ['.rst', '.md']
# source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'mirtop'
copyright = u'2017, Lorena Pantano, Thomas Desvignes, Karen EIlbeck, Ioannis Vlachos, Bastian Fromm, Marc K. Halushka, Michael Hackenberg, Gianvito Urgese'
author = u'Lorena Pantano, Thomas Desvignes, Karen EIlbeck, Ioannis Vlachos, Bastian Fromm, Marc K. Halushka, Michael Hackenberg, Gianvito Urgese'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = u'0.3'
# The full version, including alpha/beta/rc tags.
release = u'0.3.12a'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'alabaster'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
html_theme_options = {
'description': "API to work with GFF3 sRNA-data files",
'github_user': 'miRTop',
'github_repo': 'mirtop',
'github_banner': True,
'travis_button': True,
'fixed_sidebar': False,
'github_button': True,
'travis_button': True,
'sidebar_collapse': True,
'codecov_button': True
}
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# This is required for the alabaster theme
# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
html_sidebars = {
'**': [
'about.html',
'navigation.html',
'searchbox.html',
'relations.html', # needs 'show_related': True theme option to display
'searchbox.html',
]
}
# -- Options for HTMLHelp output ------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'mirtopdoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'mirtop.tex', u'mirtop Documentation',
u'Lorena Pantano, Thomas Desvignes, Karen EIlbeck, Ioannis Vlachos, Bastian Fromm, Marc K. Halushka, Michael Hackenberg, Gianvito Urgese', 'manual'),
]
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'mirtop', u'mirtop Documentation',
[author], 1)
]
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'mirtop', u'mirtop Documentation',
author, 'mirtop', 'API to work with the mirGFF3 format to unify miRNA/isomiR annotation.',
'Miscellaneous'),
]
from recommonmark.parser import CommonMarkParser
source_parsers = {
'.md': CommonMarkParser,
}
source_suffix = ['.rst', '.md']
mirtop-0.4.23/docs/how_to_contribute.md 0000664 0000000 0000000 00000006452 13547635037 0020145 0 ustar 00root root 0000000 0000000 # Examples of contributions
## How to add a new sub-command
**You need first to clone and install the tool in [develop mode](installation.html)**
Let's say that you want to add a new operation to `mirtop`, for instance, similar to the `stats` command to work with sGFF3 files. Assume a `test` function for this exmaple to just read the file and print `Hello GFF3.`
* Create the folder inside `mirtop/test`. The create to empty files named:
* `test.py`
* `__init__.py`
* Modify the `test.py` file with this content:
```
from mirtop.gff.body import read_gff_line
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def test(args):
for fn in args.files:
_test(fn)
logger.info("Hello GFF3: %s" % fn)
def _test(fn):
logger.debug("I am going to read this file: %s" % fn)
for line in fn:
read_gff_line(line)
```
* Choose a sub_command name, in this case: `test`.
* Add the arguments function at the end of this file: https://github.com/miRTop/mirtop/blob/dev/mirtop/libs/parse.py, using a naming following `add_subparser_test`.
```
def add_subparser_test(subparsers):
parser = subparsers.add_parser("test", help="test function")
parser.add_argument("files", nargs="*", help="GFF/GTF files.")
parser = _add_debug_option(parser)
return parser
```
* Add the function name to `parse_cl` function, at the end of the `sub_cmds` array.
```
sub_cmds = {"gff": add_subparser_gff,
"stats": add_subparser_stats,
"compare": add_subparser_compare,
"target": add_subparser_target,
"simulator": add_subparser_simulator,
"counts": add_subparser_counts,
"export": add_subparser_export,
"test": add_subparser_test
}
```
* To get the function re-directed from the command line when you use the sub_cmd name, add a line to the `command_line.py` file, adding another `else` statement:
```
elif "test" in kwargs:
logger.info("Run test.")
test(kwargs["args"])
```
* The function you use to link to the operation added need to be imported at the beginning. Let's say that the `test` function is at `mirtop/test/test.py`:
```
from mirtop.test import test
```
Try the new operation:
```
mirtop test data/examples/correct_file.gff
```
## Add a unit test
## for the internal function
Add to the end of `test/test_functions.py`, but inside `class FunctionsTest(unittest.TestCase):` this code:
```
@attr(fn_test=True)
def test_function_test(self):
from mirtop import test
test._test("data/examples/gff/correct_file.gff")
```
## for the sub-command
Add to the end of `test/test_function.py`, but inside `class AutomatedAnalysisTest(unittest.TestCase):` this code:
```
@attr(cmd_test=True)
def test_srnaseq_annotation_bam(self):
"""Run test analysis
"""
with make_workdir():
clcode = ["mirtop",
"test",
"../../data/examples/gff/correct_file.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
```
## test the unit
**nose is needed: pip install nose**
Run the function test from the top parent folder:
```
./run_test.sh fn_test
```
Run the command test from the top parent folder:
```
./run_test.sh cmd_test
```
mirtop-0.4.23/docs/index.rst 0000664 0000000 0000000 00000000723 13547635037 0015722 0 ustar 00root root 0000000 0000000 .. mirtop documentation master file, created by
sphinx-quickstart on Tue Nov 14 15:51:17 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to mirtop's documentation!
==================================
.. toctree::
:maxdepth: 2
:caption: Contents:
competition.rst
installation.md
quick_start.md
output.md
code_structure.md
how_to_contribute.md
code.rst
mirtop-0.4.23/docs/installation.md 0000664 0000000 0000000 00000001344 13547635037 0017104 0 ustar 00root root 0000000 0000000 # Installation
## bioconda
`conda install mirtop -c bioconda`
## pypi
`pip install mirtop`
## update to develop version from pip
```
pip install --upgrade --no-deps git+https://github.com/miRTop/mirtop.git#egg=mirtop
```
## install develop version
Thes best solution is to install conda to get an independent enviroment.
```
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
export PATH=$PATH:~/mirtop_env
conda install -c bioconda bioconda bedtools samtools pip nose pysam pandas dateutil pyyaml pybedtools biopython setuptools
git clone http://github.com/miRTop/mirtop
cd mirtop
git fetch origin dev
git checkout dev
python setup.py develop
``` mirtop-0.4.23/docs/issue_template.md 0000664 0000000 0000000 00000000242 13547635037 0017422 0 ustar 00root root 0000000 0000000 ### Expected behavior and actual behavior.
### Steps to reproduce the problem.
### Specifications like the version of the project, operating system, or hardware.
mirtop-0.4.23/docs/make.bat 0000664 0000000 0000000 00000001452 13547635037 0015466 0 ustar 00root root 0000000 0000000 @ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=.
set BUILDDIR=_build
set SPHINXPROJ=mirtop
if "%1" == "" goto help
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
goto end
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
:end
popd
mirtop-0.4.23/docs/output.md 0000664 0000000 0000000 00000003367 13547635037 0015752 0 ustar 00root root 0000000 0000000 # Output
## GFF command
The `mirtop gff` generates the GFF3 adapter format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/incubator/blob/master/format/definition.md).
## Stats command
The `mirtop stats` generates a table with different statistics for each type of isomiRs:
* total counts
* average counts
* total sequences
It generates as well a JSON file with the same information to be integrated easily with QC tools like [MultiQC](https://multiqc.info/).
## Compare command
The `mirtop compare` generates a tabular file with information about the difference and similarities. The first file in the command line will be considered the reference and the following files will be compared to the reference. Each line of the output has the following information for each file:
* sample
* idu
* seq
* tag: `E` if not in reference, `D` detected in both, `M` missing in target file
* same_mirna: if the sequence map to the same miRNA in the reference and target file
* one column for each isomiR type with the following tags: `FP` (variation not in reference), `TP` (variation in both), `FN` (variation not in target file)
## Counts command
The `mirtop counts` generates a tabular file with the following columns:
* unique identifier
* read sequence
* miRNA name
* Variant attribute from GFF3 column
* One column for each isomiR type showing the exact variation
* One column for each sample with the counts for that sequence
## Export command
The `mirtop export` generates different files from a mirGFF3 file:
* [isomiRs](https://bioconductor.org/packages/release/bioc/html/isomiRs.html) compatible files
* [FASTA files](https://en.wikipedia.org/wiki/FASTA_format)
* [VCF files](https://samtools.github.io/hts-specs/VCFv4.2.pdf) mirtop-0.4.23/docs/quick_start.md 0000664 0000000 0000000 00000006465 13547635037 0016745 0 ustar 00root root 0000000 0000000 # Quick Start
## Importer
### From Bam files to GFF3
```
git clone mirtop
cd mirtop/data
```
You can use the example data. Here the reads have been mapped to the precursor sequences.
```
mirtop gff -sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam
```
### From `seqbuster::miraligner` files to GFF3
miRNA annotation generated from [miraligner](https://github.com/lpantano/seqbuster) tool:
```
mirtop gff --format seqbuster --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out examples/seqbuster/reads.mirna
```
### From `sRNAbench` files to GFF3
miRNA annotation generated from [sRNAbench](http://bioinfo2.ugr.es:8080/ceUGR/srnabench/) tool:
```
mirtop gff --format sranbench -sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out srnabench examples/srnabench
```
### From `PROST!` files to GFF3
miRNA annotation generated from [PROST!]() tool. Export isomiRs tab from excel file to a tabular text format file.
```
mirtop gff --format prost -sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out examples/prost/prost.example.txt
```
### From `isomiR-SEA` files to GFF3
miRNA annotation generated from [isomiR-SEA]() tool.
```
mirtop validate examples/gff/correct_file.gff
```
## Operations
### Validator
To validate your mirGFF3 file and make sure if follows the current format:
```
mirtop gff --format isomirsea -sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out examples/isomir-sea/tagMir-all.gff
```
### Get statistics from GFF
Get number of isomiRs and miRNAs annotated in the GFF file by isomiR category.
```
cd mirtop/data
mirtop stats -o test_out example/gff/correct_file.gff
```
### Compare GFF file with reference
Compare the sequences from two or more GFF files. The first one will be used as the reference data.
```
cd mirtop/data
mirtop compare -o test_out example/gff/correct_file.gff example/gff/alternative.gff
```
### Updates mirGFF3
Updates older versions with the most current one.
```
cd mirtop/data
mirtop update -o test_out_mirs examples/versions/version1.0.gff
```
## Export
### Export file to isomiRs format
To be compatible with [isomiRs](https://bioconductor.org/packages/release/bioc/html/isomiRs.html) bioconductor package use:
```
cd mirtop/data
mirtop export -o test_out_mirs --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 examples/gff correct_file.gff
```
### Export file to FASTA format
```
cd mirtop/data
mirtop export -o test_out_mirs --format fasta -d -vd --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 examples/gff/correct_file.gff
```
### Export file to VCF format
```
cd mirtop/data
mirtop export -o test_out_mirs --format vcf --hairpin examples/annotate/hairpin.fa --gtf examples/a
nnotate/hsa.gff3 examples/gff/correct_file.gff
```
### Get count file
This file it is useful to load into R as a matrix. It contains the minimal information about each sequence and the count data in columns for each samples.
```
cd mirtop/data
mirtop counts -o test_out_mirs --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 examples/synthetic/let7a-5p.gtf
```
mirtop-0.4.23/mirtop/ 0000775 0000000 0000000 00000000000 13547635037 0014441 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/__init__.py 0000664 0000000 0000000 00000000074 13547635037 0016553 0 ustar 00root root 0000000 0000000 from mirtop.libs import config
__version__ = config.version mirtop-0.4.23/mirtop/bam/ 0000775 0000000 0000000 00000000000 13547635037 0015200 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/bam/__init__.py 0000664 0000000 0000000 00000000000 13547635037 0017277 0 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/bam/bam.py 0000664 0000000 0000000 00000036152 13547635037 0016320 0 ustar 00root root 0000000 0000000 """ Read bam files"""
from __future__ import print_function
# from memory_profiler import profile
import os.path as op
import os
import pysam
from collections import defaultdict
import pybedtools
from mirtop.libs import do
from mirtop.libs.utils import file_exists
import mirtop.libs.logger as mylog
from mirtop.mirna.realign import isomir, hits, reverse_complement
from mirtop.mirna.mapper import get_primary_transcript, guess_database
from mirtop.bam import filter
from mirtop.gff import body
from mirtop.mirna.annotate import annotate
from mirtop.libs import sql
logger = mylog.getLogger(__name__)
# fp = open('memory_profiler.log', 'w+')
# @profile(stream=fp)
def read_bam(bam_fn, args, clean=True):
"""
Read bam file and perform realignment of hits
Args:
*bam_fn*: a BAM file with alignments to the precursor
*precursors*: dict with keys being precursor names and values
being sequences. Come from mirtop.mirna.fasta.read_precursor().
*clean*: Use mirtop.filter.clean_hits() to remove lower score hits.
Returns:
*reads (dict)*:
keys are read_id and values are *mirtop.realign.hits*
"""
bam_fn = _sam_to_bam(bam_fn)
bam_fn = _bam_sort(bam_fn)
reads = defaultdict(hits)
if args.genomic:
logger.warning("This is under development and variants can be unexact.")
bed_fn = os.path.join(args.out, os.path.basename(bam_fn) + ".bed")
logger.info("Making bed file.")
_bed(bam_fn, bed_fn)
logger.info("Intersecting bed file.")
intersect_fn = intersect(bed_fn, args.gtf)
# logger.info("Analyzing hits.")
# reads = _read_lifted_bam(intersect_fn, reads, args, clean)
logger.info("Loading database.")
conn = _read_lifted_bam_alpha(intersect_fn, bam_fn, args)
rows = sql.select_all_reads(conn)
logger.info("Analyzing database.")
precursors = args.precursors
database = guess_database(args)
reads = _read_lifted_lines(rows, precursors, database)
conn.close()
else:
reads = _read_original_bam(bam_fn, reads, args, clean)
logger.info("Done.")
return reads
# @profile(stream=fp)
def low_memory_bam(bam_fn, sample, out_handle, args):
if args.genomic:
raise ValueError("low-memory option is not compatible with genomic coordinates.")
precursors = args.precursors
bam_fn = _sam_to_bam(bam_fn)
bam_fn = _bam_sort(bam_fn)
mode = "r" if bam_fn.endswith("sam") else "rb"
handle = pysam.Samfile(bam_fn, mode)
lines = []
current = None
for line in handle:
if not current or current == line.query_name:
lines.append(line)
current = line.query_name
else:
reads = _read_lines(lines, precursors, handle, args)
ann = annotate(reads, args.matures, args.precursors, quiet=True)
gff_lines = body.create(ann, args.database, sample, args, quiet=True)
body.write_body_on_handle(gff_lines, out_handle)
current = line.query_name
lines = []
lines.append(line)
reads = _read_lines(lines, precursors, handle, args)
ann = annotate(reads, args.matures, args.precursors, quiet=True)
gff_lines = body.create(ann, args.database, sample, args, quiet=True)
body.write_body_on_handle(gff_lines, out_handle)
def low_memory_genomic_bam(bam_fn, sample, out_handle, args):
logger.info("Reading BAM file in low memory mode.")
logger.warning("This is under development and variants can be unexact.")
precursors = args.precursors
bam_fn = _sam_to_bam(bam_fn)
bam_fn = _bam_sort(bam_fn)
database = guess_database(args)
bed_fn = os.path.join(args.out, os.path.basename(bam_fn) + ".bed")
logger.info("Making bed file.")
_bed(bam_fn, bed_fn)
logger.info("Intersecting bed file.")
intersect_fn = intersect(bed_fn, args.gtf)
logger.info("Loading database.")
# TODO this'll return conn_reads and conn_counts
conn = _read_lifted_bam_alpha(intersect_fn, bam_fn, args)
rows = sql.select_all_reads(conn)
lines = []
current = None
logger.info("Analyzing database.")
for row in rows:
if not current or current == row[0]:
lines.append(row)
current = row[0]
else:
# TODO counts of sequence = conn_counts.query UID
# it could be counts only same location UID+chrom+start, or counts all UID
reads = _read_lifted_lines(lines, precursors, database)
ann = annotate(reads, args.matures, args.precursors, quiet=True)
gff_lines = body.create(ann, args.database, sample, args, quiet=True)
body.write_body_on_handle(gff_lines, out_handle)
current = row[0]
lines = []
lines.append(row)
reads = _read_lifted_lines(lines, precursors, database)
ann = annotate(reads, args.matures, args.precursors, quiet=True)
gff_lines = body.create(ann, args.database, sample, args, quiet=True)
body.write_body_on_handle(gff_lines, out_handle)
conn.close()
logger.info("Done")
def _analyze_line(line, reads, precursors, handle, args):
if line.reference_id < 0:
logger.debug("READ::Sequence not mapped: %s" % line.reference_id)
return reads
if not line.cigarstring:
logger.debug("READ::Sequence malformed: %s" % line)
return reads
query_name = line.query_name
if query_name not in reads and not line.query_sequence:
return reads
sequence = line.query_sequence if not line.is_reverse else reverse_complement(line.query_sequence)
logger.debug(("READ::Read name:{0} and Read sequence:{1}").format(line.query_name, sequence))
if line.query_sequence and line.query_sequence.find("N") > -1:
return reads
if query_name not in reads:
reads[query_name].set_sequence(sequence)
reads[query_name].counts = _get_freq(query_name)
# TODO if args.quant set to 0
# TODO if args.quant increase by 1
if line.is_reverse and not args.genomic:
logger.debug("READ::Sequence is reverse: %s" % line.query_name)
return reads
chrom = handle.getrname(line.reference_id)
start = line.reference_start
cigar = line.cigartuples
# if line.cigarstring.find("I") > -1:
# indels_skip += 1
iso = isomir()
iso.align = line
iso.set_pos(start, len(reads[query_name].sequence))
logger.debug("READ::From BAM start %s end %s at chrom %s" % (iso.start, iso.end, chrom))
if len(precursors[chrom].replace("N","")) + 3 < start + len(reads[query_name].sequence):
logger.debug("READ::%s start + %s sequence size are bigger than"
" size precursor %s" % (
line.reference_id,
len(reads[query_name].sequence),
len(precursors[chrom])))
return reads
iso.subs, iso.add, iso.cigar = filter.tune(
reads[query_name].sequence, precursors[chrom],
start, cigar)
logger.debug("READ::After tune start %s end %s" % (iso.start, iso.end))
logger.debug("READ::iso add %s iso subs %s" % (iso.add, iso.subs))
reads[query_name].set_precursor(chrom, iso)
return reads
def _read_lines(lines, precursors, handle, args, clean=True):
reads = defaultdict(hits)
for line in lines:
reads = _analyze_line(line, reads, precursors, handle, args)
if clean:
reads = filter.clean_hits(reads)
return reads
def _read_lifted_bam_alpha(bed_fn, bam_fn, args):
database = guess_database(args)
conn = sql.create_connection()
key = "name" if args.keep_name else "sequence"
sql.create_reads_table(conn, key)
# TODO create counts table sequence and autoincrement or from read
cur = conn.cursor()
counts = 0
seen = set()
for line in bed_fn:
fields = _parse_intersect(line, database, bed=True)
# TODO add sequence to count table args.quant on/off name=UID or name=UID+chrom+pos
if fields:
hit = ".".join(fields[:3])
if hit not in seen:
counts += 1
sql.insert_row_in_reads_table(cur, fields)
seen.add(hit)
# if counts == 1000:
# counts = 0
del(seen)
logger.info("Read %s lines that intersected with miRNAs." % counts)
conn.commit()
# TODO this'll return conn_reads and conn_counts
return conn
def _read_original_bam(bam_fn, reads, args, clean):
mode = "r" if bam_fn.endswith("sam") else "rb"
handle = pysam.Samfile(bam_fn, mode)
indels_skip = 0
precursors = args.precursors
for line in handle:
reads = _analyze_line(line, reads, precursors, handle, args)
logger.info("Hits: %s" % len(reads))
logger.info("Hits with indels %s" % indels_skip)
if clean:
reads = filter.clean_hits(reads)
logger.info("Hits after clean: %s" % len(reads))
return reads
def _parse_intersect(line, database, bed=False):
"Parse bedtools intersect between bam_bed file and gtf from database"
start_idx = 9 if bed else 15
end_idx = 10 if bed else 16
attr_idx = 14 if bed else 20
if str(line).find(get_primary_transcript(database)) < 0: # only working with mirbase
return None
query_name = line[3]
sequence = line[4]
chrom = line[attr_idx].strip().split("Name=")[-1]
start = line[1]
end = line[2]
strand = line[5]
if not start:
return None
if strand == "+":
start = int(start) - int(line[start_idx]) + 1
else:
start = int(line[end_idx]) - int(end)
return (query_name, sequence, chrom, start)
def _analyze_lifted_line(line, reads, precursors, database):
query_name = line[0]
sequence = line[1]
logger.debug(("READ::line name:{0}").format(line))
if sequence and sequence.find("N") > -1:
return reads
if query_name not in reads:
reads[query_name].set_sequence(sequence)
reads[query_name].counts = _get_freq(query_name)
reads[query_name].sequence = sequence
chrom = line[2]
start = line[3]
iso = isomir()
iso.align = line
iso.set_pos(start, len(reads[query_name].sequence))
logger.debug("READ::From BAM start %s end %s at chrom %s" % (iso.start, iso.end, chrom))
if len(precursors[chrom]) < start + len(reads[query_name].sequence):
logger.debug("READ::%s start + %s sequence size are bigger than"
" size precursor %s" % (
chrom,
len(reads[query_name].sequence),
len(precursors[chrom])))
return reads
iso.subs, iso.add, iso.cigar = filter.tune(
reads[query_name].sequence, precursors[chrom],
start, None)
logger.debug("READ::After tune start %s end %s" % (iso.start, iso.end))
logger.debug("READ::iso add %s iso subs %s" % (iso.add, iso.subs))
reads[query_name].set_precursor(chrom, iso)
return reads
def _read_lifted_lines(lines, precursors, database, clean=True):
reads = defaultdict(hits)
for line in lines:
reads = _analyze_lifted_line(line, reads, precursors, database)
if clean:
reads = filter.clean_hits(reads)
return reads
def _read_lifted_bam(handle, reads, args, clean):
indels_skip = 0
precursors = args.precursors
database = guess_database(args)
for line in handle:
rows = _parse_intersect(line, database, bed=True)
reads = _analyze_lifted_line(rows, reads, precursors, database)
logger.info("Hits: %s" % len(reads))
logger.info("Hits with indels %s" % indels_skip)
if clean:
reads = filter.clean_hits(reads)
logger.info("Hits after clean: %s" % len(reads))
return reads
def _sam_to_bam(bam_fn):
if not bam_fn.endswith("bam"):
bam_out = "%s.bam" % os.path.splitext(bam_fn)[0]
cmd = "samtools view -Sbh {bam_fn} -o {bam_out}"
do.run(cmd.format(**locals()))
return bam_out
return bam_fn
def _bam_sort(bam_fn):
bam_sort_by_n = op.splitext(bam_fn)[0] + "_sort.bam"
if not file_exists(bam_sort_by_n):
do.run(("samtools sort -n -o {bam_sort_by_n} {bam_fn}").format(
**locals()))
return bam_sort_by_n
def _get_freq(name):
"""
Check if name read contains counts (_xNumber)
"""
try:
counts = int(name.split("_x")[1])
except:
return 0
return counts
def _bed(bam_fn, bed_fn):
mode = "r" if bam_fn.endswith("sam") else "rb"
handle = pysam.Samfile(bam_fn, mode)
current = None
if os.path.exists(bed_fn):
return bed_fn
with open(bed_fn, 'w') as outh:
for line in handle:
if line.reference_id < 0:
logger.debug("READ::Sequence not mapped: %s" % line.reference_id)
continue
if not line.cigarstring:
logger.debug("READ::Sequence malformed: %s" % line)
continue
query_name = line.query_name
if (not current or query_name!=current) and not line.query_sequence:
continue
if not current or query_name!=current:
sequence = line.query_sequence if not line.is_reverse else reverse_complement(line.query_sequence)
logger.debug(("READ::Read name:{0} and Read sequence:{1}").format(line.query_name, sequence))
if line.query_sequence and line.query_sequence.find("N") > -1:
continue
chrom = handle.getrname(line.reference_id)
start = line.reference_start
end = start + len(sequence) - 1
current = query_name
strand = "+" if not line.is_reverse else "-"
bed_line = "\t".join(list(map(str, [chrom, start, end, query_name, sequence, strand])))
outh.write(bed_line + '\n')
def intersect(bam, gtf):
bampy = pybedtools.BedTool(bam)
gtfpy = pybedtools.BedTool(gtf)
return bampy.intersect(gtfpy, wo=True, bed=True, s=True)
# deprecated from now on
def _read_quick_lines(lines):
reads = defaultdict(hits)
for line in lines:
_analyze_quick_line(line, reads)
return reads
def _analyze_quick_line(line, reads):
if line.reference_id < 0:
logger.debug("READ::Sequence not mapped: %s" % line.reference_id)
return reads
if not line.cigarstring:
logger.debug("READ::Sequence malformed: %s" % line)
return reads
query_name = line.query_name
if query_name not in reads and not line.query_sequence:
return reads
sequence = line.query_sequence if not line.is_reverse else reverse_complement(line.query_sequence)
logger.debug(("READ::Read name:{0} and Read sequence:{1}").format(line.query_name, sequence))
if line.query_sequence and line.query_sequence.find("N") > -1:
return reads
if query_name not in reads:
reads[query_name].set_sequence(sequence)
reads[query_name].counts = _get_freq(query_name)
return reads
def _read_quick_bam(bam_fn, reads):
mode = "r" if bam_fn.endswith("sam") else "rb"
handle = pysam.Samfile(bam_fn, mode)
for line in handle:
reads = _analyze_quick_line(line, reads)
return reads
mirtop-0.4.23/mirtop/bam/filter.py 0000664 0000000 0000000 00000005645 13547635037 0017051 0 ustar 00root root 0000000 0000000 from collections import defaultdict
from mirtop.mirna.realign import hits, cigar_correction, make_cigar, align
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def tune(seq, precursor, start, cigar):
"""
The actual fn that will realign the sequence to find the nt changes
at 5', 3' sequence and nt variations.
Args:
*seq (str)*: sequence of the read.
*precursor (str)*: sequence of the precursor.
*start (int)*: start position of sequence on the precursor, +1.
*cigar (str)*: similar to SAM CIGAR attribute.
Returns:
*list* with:
subs (list): substitutions
add (list): nt added to the end
cigar (str): updated cigar
"""
end = len(seq)
if start < 0:
end = end + start
start = 0
if cigar:
seq, mature = cigar_correction(cigar, seq, precursor[start:])
else:
seq, mature, score, p, size = align(seq, precursor[start:start + end])
cigar = make_cigar(seq, mature)
if seq.startswith("-"):
seq = seq[1:]
if seq.endswith("-"):
seq = seq[:-1]
logger.debug("TUNE:: %s %s %s" % (cigar, seq, mature))
error = set()
for pos in range(0, len(seq)):
if seq[pos] != mature[pos]:
error.add(pos)
subs, add = [], []
prob = 0
add_position = []
for e in range(len(seq) - 1, len(seq) - 6, -1):
if e in error:
prob = 1
if prob == 1:
add.append(seq[e])
add_position.append(e)
if e not in error and prob == 0 and seq[e] in ["A", "T"]:
add.append(seq[e])
add_position.append(e)
continue
if e not in error:
if add:
add.pop()
add_position.pop()
if prob == 0:
add = []
add_position = []
break
for e in error:
if e not in add_position:
subs.append([e, seq[e], mature[e]])
logger.debug("TUNE:: %s %s" % (subs, add))
return subs, "".join(add), make_cigar(seq, mature)
def clean_hits(reads):
"""
Select only best matches from a list of hits from the same read.
Args:
*reads*: dictionary as:
>>> {'read_id': mirtop.realign.hits, ...}
Returns:
*reads*: same than input but with best hits only.
"""
new_reads = defaultdict(hits)
for r in reads:
world = {}
sc = 0
for p in reads[r].precursors:
world[p] = reads[r].precursors[p].get_score(len(reads[r].sequence))
if sc < world[p]:
sc = world[p]
new_reads[r] = reads[r]
for p in world:
logger.debug("CLEAN::score %s %s %s" % (r, p, world[p]))
if sc != world[p]:
logger.debug("CLEAN::remove %s %s %s" % (r, p, world[p]))
new_reads[r].remove_precursor(p)
return new_reads
mirtop-0.4.23/mirtop/command_line.py 0000664 0000000 0000000 00000003652 13547635037 0017446 0 ustar 00root root 0000000 0000000 """Main functions to simulates reads"""
import sys
from mirtop.libs.logger import initialize_logger
from mirtop.libs.parse import parse_cl
from mirtop.libs.simulator import simulate
from mirtop.gff import reader
from mirtop.gff.stats import stats
from mirtop.gff.compare import compare
from mirtop.gff.convert import convert_gff_counts
from mirtop.exporter import export
from mirtop.gff import validator
from mirtop.libs import spikeins
from mirtop.gff import update
import mirtop.libs.logger as mylog
import time
def main(**kwargs):
kwargs = parse_cl(sys.argv[1:])
initialize_logger(kwargs['args'].out, kwargs['args'].debug,
kwargs['args'].print_debug)
logger = mylog.getLogger(__name__)
start = time.time()
#logger.warning("This is devel-live changes")
if "gff" in kwargs:
logger.info("Run annotation")
reader(kwargs["args"])
elif "stats" in kwargs:
logger.info("Run stats.")
stats(kwargs["args"])
elif "compare" in kwargs:
logger.info("Run compare.")
compare(kwargs["args"])
elif "simulator" in kwargs:
logger.info("Run simulation")
simulate(kwargs["args"])
elif "counts" in kwargs:
logger.info("Run convert of GFF to TSV containing expression")
convert_gff_counts(kwargs["args"])
elif "export" in kwargs:
logger.info("Run export of GFF into other format.")
export(kwargs["args"])
elif "validator" in kwargs:
logger.info("Run validator.")
validator.check_multiple(kwargs["args"])
elif "query" in kwargs:
logger.info("Not yet ready: This will allow queries to GFF files.")
elif "spikein" in kwargs:
logger.info("Run spike-in tools")
spikeins.convert(kwargs["args"])
elif "update" in kwargs:
logger.info("Run update tools")
update.convert(kwargs["args"])
logger.info('It took %.3f minutes' % ((time.time()-start)/60))
mirtop-0.4.23/mirtop/exporter/ 0000775 0000000 0000000 00000000000 13547635037 0016311 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/exporter/__init__.py 0000664 0000000 0000000 00000000561 13547635037 0020424 0 ustar 00root root 0000000 0000000 from mirtop.exporter import seqbuster, isomirs, fasta, vcf
def export(args):
"""
GFF3 to others formats
"""
if args.format == "seqbuster":
seqbuster.convert(args)
if args.format == "isomir":
isomirs.convert(args)
elif args.format == "fasta":
fasta.convert(args)
elif args.format == "vcf":
vcf.convert(args)
mirtop-0.4.23/mirtop/exporter/fasta.py 0000664 0000000 0000000 00000002111 13547635037 0017754 0 ustar 00root root 0000000 0000000 """ Read GFF files and output FASTA format"""
from __future__ import print_function
import os
import sys
import mirtop.libs.logger as mylog
from mirtop.gff.classgff import feature
from mirtop.mirna.realign import read_id
logger = mylog.getLogger(__name__)
def convert(args):
"""
Main function to convert from GFF3 to FASTA format.
Args:
*args*: supported options for this sub-command.
See *mirtop.libs.parse.add_subparser_export()*.
"""
for fn in args.files:
logger.info("Reading %s" % fn)
_process(fn, args.out)
def _process(fn, out_dir):
if out_dir:
out_fasta = os.path.join(out_dir, "%s.fasta" %
os.path.splitext(os.path.basename(fn))[0])
outh = sys.stdout if not out_dir else open(out_fasta, 'w')
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
gff = feature(line)
attr = gff.attributes
read = read_id(attr["UID"])
print((">{0}\n{1}").format(attr["UID"], read), file=outh)
mirtop-0.4.23/mirtop/exporter/isomirs.py 0000664 0000000 0000000 00000010553 13547635037 0020354 0 ustar 00root root 0000000 0000000 """ Read GFF files and output isomiRs compatible format"""
from __future__ import print_function
import os
import mirtop.libs.logger as mylog
from mirtop.mirna import fasta, mapper
from mirtop.gff.classgff import feature
from mirtop.gff.header import read_samples
from mirtop.mirna.realign import get_mature_sequence, align_from_variants
from mirtop.mirna.realign import read_id, variant_to_5p, \
variant_to_3p, variant_to_add
from mirtop.gff.body import variant_with_nt
logger = mylog.getLogger(__name__)
def convert(args):
"""
Main function to convert from GFF3 to isomiRs Bioc Package.
Reads a GFF file to produces output file containing Expression counts
Args:
*args(namedtuple)*: arguments parsed from command line with
*mirtop.libs.parse.add_subparser_counts()*.
Returns:
*file (file)*: with columns like:
UID miRNA Variant Sample1 Sample2 ... Sample N
"""
logger.info("INFO Writing TSV file to directory %s", args.out)
for gff in args.files:
logger.info("INFO Reading GFF file %s", gff)
_convert_file(gff, args)
def _convert_file(gff, args):
sep = "\t"
precursors = fasta.read_precursor(args.hairpin, args.sps)
matures = mapper.read_gtf_to_precursor(args.gtf)
variant_header = sep.join(['mism', 'add', 't5', 't3'])
gff_file = open(gff, 'r')
out_file = os.path.join(args.out, "%s_rawData.tsv" % os.path.splitext(os.path.basename(gff))[0])
missing_parent = 0
missing_mirna = 0
unvalid_uid = 0
with open(out_file, 'w') as outh:
for samples_line in gff_file:
if samples_line.startswith("## COLDATA:"):
samples = sep.join(samples_line.strip().split("COLDATA:")[1].strip().split(","))
header = sep.join(['seq', 'mir',
variant_header, samples])
print(header, file=outh)
break
for mirna_line in gff_file:
gff = feature(mirna_line)
attr = gff.attributes
UID = attr["UID"]
Read = attr["Read"]
mirna = attr["Name"]
parent = attr["Parent"]
variant = attr["Variant"]
try:
Read = read_id(UID)
except KeyError:
unvalid_uid += 1
continue
expression = sep.join(attr["Expression"].strip().split(","))
cols_variants = sep.join(_expand(variant))
logger.debug("COUNTS::Read:%s" % Read)
logger.debug("COUNTS::EXTRA:%s" % variant)
if parent not in precursors:
missing_parent += 1
continue
if mirna not in matures[parent]:
missing_mirna += 1
continue
extra = variant_with_nt(mirna_line, precursors, matures)
if extra == "Invalid":
continue
logger.debug("COUNTS::EXTRA:%s" % extra)
cols_variants = sep.join(_expand(extra, True))
summary = sep.join([Read, mirna,
cols_variants, expression])
logger.debug(summary)
print(summary, file=outh)
gff_file.close()
logger.info("Missing Parents in hairpin file: %s" % missing_parent)
logger.info("Missing MiRNAs in GFF file: %s" % missing_mirna)
logger.info("Non valid UID: %s" % unvalid_uid)
logger.info("Output file is at %s" % out_file)
def _expand(variant, nts=False):
"""Expand Variant field into list for iso_5p, iso_3p, iso_add3p, iso_snv"""
list_variant = []
isomir = {}
snp_var = []
for v in variant.split(","):
if v.find(":") > 0:
isomir[v.split(":")[0]] = v.split(":")[1]
elif v.find("snv") > 0:
snp_var.append(1)
if nts:
if "iso_snv" in isomir:
list_variant.append(isomir["iso_snv"])
else:
list_variant.append(0)
else:
snp = sum(snp_var)
list_variant.append(snp)
if "iso_add3p" in isomir:
list_variant.append(isomir["iso_add3p"])
else:
list_variant.append(0)
if "iso_5p" in isomir:
list_variant.append(isomir["iso_5p"])
else:
list_variant.append(0)
if "iso_3p" in isomir:
list_variant.append(isomir["iso_3p"])
else:
list_variant.append(0)
return list(map(str, list_variant))
mirtop-0.4.23/mirtop/exporter/seqbuster.py 0000664 0000000 0000000 00000006314 13547635037 0020704 0 ustar 00root root 0000000 0000000 """ Read GFF files and output isomiRs compatible format"""
from __future__ import print_function
import os
import mirtop.libs.logger as mylog
from mirtop.mirna import fasta, mapper
from mirtop.gff.classgff import feature
from mirtop.gff.header import read_samples
from mirtop.mirna.realign import get_mature_sequence, align_from_variants
from mirtop.mirna.realign import read_id, variant_to_5p, \
variant_to_3p, variant_to_add
logger = mylog.getLogger(__name__)
def convert(args):
"""
Main function to convert from GFF3 to isomiRs Bioc Package.
Args:
*args*: supported options for this sub-command.
See *mirtop.libs.parse.add_subparser_export()*.
"""
precursors = fasta.read_precursor(args.hairpin, args.sps)
matures = mapper.read_gtf_to_precursor(args.gtf)
for fn in args.files:
logger.info("Reading %s" % fn)
_read_file(fn, precursors, matures, args.out)
def _read_file(fn, precursors, matures, out_dir):
samples = read_samples(fn)
for sample in samples:
with open(os.path.join(out_dir, "%s.mirna" % sample), 'w') as outh:
print("\t".join(
["seq", "name", "freq", "mir", "start", "end",
"mism", "add", "t5", "t3", "s5", "s3", "DB",
"precursor", "ambiguity"]), file=outh)
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
gff = feature(line)
cols = gff.columns
attr = gff.attributes
read = read_id(attr["UID"])
t5 = variant_to_5p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
t3 = variant_to_3p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
add = variant_to_add(read,
attr["Variant"])
mature_sequence = get_mature_sequence(
precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]])
mm = align_from_variants(read,
mature_sequence,
attr["Variant"])
if len(mm) > 1:
continue
elif len(mm) == 1:
mm = "".join(list(map(str, mm[0])))
else:
mm = "0"
hit = attr["Hits"] if "Hits" in attr else "1"
logger.debug("exporter::isomir::decode %s" % [attr["Variant"],
t5, t3, add, mm])
# Error if attr["Read"] doesn't exist
# print(cols)
line = [read, attr["Read"], "0", attr["Name"],
cols['source'], cols['type'],
mm, add, t5, t3, "NA", "NA", "miRNA", attr["Parent"], hit]
for sample, counts in zip(samples, attr["Expression"].split(",")):
with open(os.path.join(out_dir, "%s.mirna" % sample),
'a') as outh:
line[2] = counts
print("\t".join(line), file=outh)
mirtop-0.4.23/mirtop/exporter/vcf.py 0000664 0000000 0000000 00000032355 13547635037 0017451 0 ustar 00root root 0000000 0000000 from __future__ import print_function
import datetime
import sys
import os.path as op
import six
from mirtop.mirna.fasta import read_precursor
from mirtop.mirna.mapper import read_gtf_to_precursor, read_gtf_to_mirna
from mirtop.gff.body import read_gff_line
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def convert(args):
"""
Main function to convert from GFF3 to VCF.
Args:
*args*: supported options for this sub-command.
See *mirtop.libs.parse.add_subparser_export()*.
"""
for fn in args.files:
out_file = op.join(args.out, "%s.vcf" % op.splitext(op.basename(fn))[0])
logger.info("Reading %s" % fn)
create_vcf(fn, args.hairpin, args.gtf, out_file)
logger.info("VCF generated %s" % out_file)
def cigar_2_key(cigar, readseq, refseq, pos, var5p, var3p, parent_ini_pos, parent_end_pos, hairpin):
"""
Args:
'cigar(str)': CIGAR standard of a compressed alignment representation, this CIGAR omits the '1' integer.
'readseq(str)': the read sequence
'refseq(str)': the reference sequence
'pos(str)': the start current position
'var5p(int)': extra nucleotides not in the reference miRNA (5p strand)
'var3p(int)': extra nucleotides not in the reference miRNA (3p strand)
'parent_ini_pos(int)': the start position of the parent miRNA
'parent_end_pos(int)': the last position of the parent miRNA
'hairpin(str)': the string of the hairpin for all the miRNA
Returns:
'key_pos(str list)': a list with the positions of the variants.
'key_var(str list)': a list with the variant keys found.
'ref(str)': reference base(s).
'alt(str)': altered base(s).
"""
key_pos = []
key_var = []
ref = []
alt = []
n_Mpar = "0"
n_M = 0
n_NM = 0
n_D = 0
n_I = 0
# Obtaining the part of the hairpin outside of its parent region (previous)
if var5p < 0:
previous_pos = hairpin[parent_ini_pos + var5p:parent_ini_pos]
refseq = previous_pos + refseq
else:
refseq = refseq[var5p:]
# Obtaining the part of the hairpin outside of its parent region (posterior)
if var3p >= 0:
posterior_pos = hairpin[parent_end_pos+1:parent_end_pos+var3p+1]
refseq = refseq + posterior_pos
else:
refseq = refseq[:var3p]
# Calculating the type of variant and its ref/alt positions.
logger.debug("VCF::precursor::read %s" % refseq)
logger.debug("VCF::CIGAR::read %s" % cigar)
for i in range(len(cigar)):
if cigar[i].isdigit():
n_Mpar = n_Mpar + (cigar[i])
elif cigar[i] in ["A", "T", "C", "G"]:
pos_rel_ref = n_M + n_D + n_NM + 1
key_pos.append(pos + pos_rel_ref - 1)
key_var.append(cigar[i])
ref.append(refseq[pos_rel_ref - 1])
alt.append(cigar[i])
n_NM += 1
elif cigar[i] == "D":
if i == 0:
print("Unexpected error: 'D' in first Cigar pos")
elif cigar[i-1] == "D":
ref[-1] = ref[-1] + refseq[n_M + n_NM + n_D] # Adds new del in the REF column
key_var[-1] = "D" + str(int(key_var[-1][1:]) + 1) # Adds '1' to the number of Dels in succession
n_D += 1
else:
pos_rel_ref = n_M + n_NM + n_D
key_pos.append(pos + pos_rel_ref)
ref.append(refseq[pos_rel_ref-1:pos_rel_ref+1])
alt.append(refseq[pos_rel_ref-1])
key_var.append("D1")
n_D += 1
elif cigar[i] == "I":
if i == 0:
print("Unexpected error: 'I' in first Cigar pos")
elif cigar[i-1] == "I":
alt[-1] = alt[-1] + readseq[n_M + n_NM + n_I] # Adds the new Insert in the ALT column
key_var[-1] = key_var[-1] + 'I' + readseq[n_M + n_NM + n_I] # Adds new Ins in the Key
n_I += 1
else:
pos_rel_read = n_M + n_NM + n_I
pos_rel_ref = n_M + n_NM + n_D
key_pos.append(pos + pos_rel_ref)
alt.append(readseq[pos_rel_read-1:pos_rel_read+1])
ref.append(refseq[pos_rel_ref-1])
key_var.append("I" + alt[-1][-1])
n_I += 1
elif cigar[i] == "M":
if (i == 0) | (not cigar[i - 1].isdigit()):
n_M = n_M + 1
else:
n_M = n_M + int(n_Mpar)
n_Mpar = "0"
else:
print("Unexpected error: %s, index: %s" % (cigar[i], i))
return(key_pos, key_var, ref, alt)
def create_vcf(mirgff3, precursor, gtf, vcffile):
"""
Args:
'mirgff3(str)': File with mirGFF3 format that will be converted
'precursor(str)': Fasta format sequences of all miRNA hairpins
'gtf(str)': Genome coordinates
'vcffile': name of the file to be saved
Returns:
Nothing is returned, instead, a VCF file is generated
"""
#Check if the input files exist:
try:
gff3_file = open(mirgff3, "r", encoding="utf-8") if six.PY3 else open(mirgff3, "r")
except IOError:
print ("Can't read the file", end=mirgff3)
sys.exit()
with gff3_file:
data = gff3_file.read()
if six.PY2:
data = data.decode("utf-8-sig").encode("utf-8")
gff3_data = data.split("\n")
vcf_file = open(vcffile, "w")
ver = "v4.3" # Current VCF version formatting
vcf_file.write("##fileformat=VCF%s\n" % ver)
date = datetime.datetime.now().strftime("%Y%m%d")
vcf_file.write("##fileDate=%s\n" % date)
source = "\n".join(s for s in gff3_data if "## source-ontology: " in s)[20:]
line = 0
sample_names = []
while gff3_data[line][:2] == "##":
if gff3_data[line][:19] == "## source-ontology:":
source = gff3_data[line][20:]
elif gff3_data[line][:11] == "## COLDATA:":
sample_names = gff3_data[line][12:].split(",")
line += 1
vcf_file.write("##source=%s\n" % source)
vcf_file.write('##INFO=\n")
vcf_file.write('##FORMAT=\n')
vcf_file.write('##FORMAT=\n')
vcf_file.write('##FORMAT=\n')
vcf_file.write('##FORMAT=\n')
header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
# Adds Header
for s in range(len(sample_names)):
header = header + "\t" + sample_names[s]
vcf_file.write(header)
all_dict = dict() # initializing an empty dictionary where all info will be added
key_list = [] # Initializing a list which will contain all the keys of the dictionary
mirna_dict = dict() # initializing an empty dictionary where mirna info will be put
n_SNP = 0
n_noSNP = 0
no_var = 0
hairpins = read_precursor(precursor)
gff3 = read_gtf_to_precursor(gtf)
gtf_dic = read_gtf_to_mirna(gtf)
for line in range(0, len(gff3_data)):
if not gff3_data[line]:
continue
if gff3_data[line][1] == "#":
continue
else: # Parsing the gff3 mirna lecture:
gff_fields = read_gff_line(gff3_data[line])
gtf_name = gff_fields['attrb']['Name']
gtf_parent = gff_fields['attrb']['Parent']
if gtf_parent not in gff3:
continue
if gtf_name not in gff3[gtf_parent]:
continue
parent_ini_pos = gff3[gtf_parent][gtf_name][0]
parent_end_pos = gff3[gtf_parent][gtf_name][1]
ref_seq = (hairpins[gtf_parent][parent_ini_pos:parent_end_pos+1])
vcf_chrom = gtf_dic[gtf_name][gtf_parent][0]
vcf_pos = int(gff_fields['start']) + int(gtf_dic[gtf_name][gtf_parent][1])
hairpin = hairpins[gtf_parent]
variants = gff_fields['attrb']['Variant'].split(",")
logger.debug("VCF::Variant::%s" % variants)
# Obtaining the iso_3p, iso_add3p and iso_5p values:
var3p = [s for s in variants if 'iso_3p' in s]
if len(var3p):
var3p = int(var3p[0][7:]) # Position of iso_3p value
else:
var3p = 0
var_add3p = [s for s in variants if 'iso_add3p' in s]
if len(var_add3p):
var_add3p = int(var_add3p[0][10:]) # Position of iso_add3p value
else:
var_add3p = 0
var3p = var3p + var_add3p
logger.debug("VCF::VAR_3p::%s" % var3p)
var5p = [s for s in variants if 'iso_5p' in s]
if len(var5p):
var5p = int(var5p[0][7:]) # Position of iso_5p value
else:
var5p = 0 #
logger.debug("VCF::VAR_5p::%s" % var5p)
cigar = gff_fields['attrb']["Cigar"]
# Obtaining all the variants from the cigar:
if 1:
(key_pos, key_var, vcf_ref, vcf_alt) = cigar_2_key(cigar, gff_fields['attrb']['Read'], ref_seq, vcf_pos,
var5p, var3p, parent_ini_pos, parent_end_pos, hairpin)
# Adding the variants to a dictionary and calculating all the fields of a vcf file format:
if len(key_var) > 0:
for s in range(len(key_var)):
key_dict = vcf_chrom + '-' + str(key_pos[s]) + '-' + str(key_var[s])
raw_counts = gff_fields['attrb']['Expression']
raw_counts = [int(i) for i in raw_counts.split(',')]
nozero_counts = [int(i > 0) for i in raw_counts] # counts for every sample if expr != 0.
if gtf_name in mirna_dict: # Adding expression values to same mirnas
mirna_dict[gtf_name]['Z'] = [sum(x) for x in zip(mirna_dict[gtf_name]['Z'], raw_counts)]
else:
mirna_dict[gtf_name] = {}
mirna_dict[gtf_name]["Z"] = raw_counts
if key_dict in all_dict:
if all_dict[key_dict]["Type"] in ["A", "C", "T", "G"]:
all_dict[key_dict]['X'] = [sum(x) for x in zip(all_dict[key_dict]['X'], nozero_counts)]
all_dict[key_dict]['Y'] = [sum(x) for x in zip(all_dict[key_dict]['Y'], raw_counts)]
else:
key_list.append(key_dict)
all_dict[key_dict] = {}
all_dict[key_dict]["Chrom"] = vcf_chrom
all_dict[key_dict]["Position"] = key_pos[s]
all_dict[key_dict]["mirna"] = gtf_name
all_dict[key_dict]["Type"] = key_var[s]
if key_var[s][0] in ["A", "C", "T", "G"]:
n_SNP += 1
all_dict[key_dict]["SNP"] = True
all_dict[key_dict]["ID"] = gff_fields['attrb']['Name'] + '-SNP' + str(n_SNP)
all_dict[key_dict]['X'] = nozero_counts
all_dict[key_dict]['Y'] = raw_counts
else:
n_noSNP += 1
all_dict[key_dict]["SNP"] = False
all_dict[key_dict]["ID"] = gff_fields['attrb']['Name'] + '-nonSNP' + str(n_noSNP)
all_dict[key_dict]["Ref"] = vcf_ref[s]
all_dict[key_dict]["Alt"] = vcf_alt[s]
all_dict[key_dict]["Qual"] = "."
all_dict[key_dict]["Filter"] = gff_fields['attrb']['Filter']
all_dict[key_dict]["Info"] = "NS=" + str(len(sample_names))
else:
no_var += 1
# Writing the VCF file:
for s in key_list:
variant_line = ("\n%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %
(all_dict[s]["Chrom"], all_dict[s]["Position"], all_dict[s]["ID"],
all_dict[s]["Ref"], all_dict[s]["Alt"], all_dict[s]["Qual"],
all_dict[s]["Filter"], all_dict[s]["Info"]))
if all_dict[s]["Type"] in ["A", "T", "C", "G"]:
format_col = "TRC:TSC:TMC:GT"
variant_line = variant_line + "\t" + format_col
samples = ""
for n in range(len(sample_names)):
X = all_dict[s]["X"][n]
Y = all_dict[s]["Y"][n]
Z = mirna_dict[all_dict[s]["mirna"]]["Z"][n]
# Calculating the genotype:
if Y == 0:
GT = "0|0"
elif Z == Y:
GT = "1|1"
else:
GT = "1|0"
samples = samples + "\t" + str(X) + ":" + str(Y) + ":" + str(Z) + ":" + GT
variant_line = variant_line + samples
else:
format_col = ""
variant_line = variant_line + format_col
vcf_file.write(variant_line)
vcf_file.close()
mirtop-0.4.23/mirtop/gff/ 0000775 0000000 0000000 00000000000 13547635037 0015203 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/gff/__init__.py 0000664 0000000 0000000 00000007511 13547635037 0017320 0 ustar 00root root 0000000 0000000 """mirGFF3 proxy converter"""
from __future__ import print_function
import os.path as op
from mirtop.mirna import fasta, mapper
from mirtop.bam.bam import read_bam
from mirtop.importer import seqbuster, srnabench, prost, isomirsea, manatee, optimir
from mirtop.mirna.annotate import annotate
from mirtop.gff import body, header, merge, read
from mirtop.mirna.mapper import read_gtf_to_mirna
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def reader(args):
"""
Realign BAM hits to miRBAse to get better accuracy and annotation
"""
if args.low_memory:
read.reader(args)
return None
samples = []
database = mapper.guess_database(args)
args.database = database
precursors = fasta.read_precursor(args.hairpin, args.sps)
args.precursors = precursors
matures = mapper.read_gtf_to_precursor(args.gtf)
args.matures = matures
# TODO check numbers of miRNA and precursors read
# TODO print message if numbers mismatch
out_dts = dict()
if args.keep_name and len(args.files) > 1:
logger.warning("--keep-name when running multiple samples\n"
"can generate wrong results if the\n"
"name read is different across sample\n"
"for the same sequence.")
for fn in args.files:
fn = op.normpath(fn)
if args.format != "gff":
sample = op.splitext(op.basename(fn))[0]
samples.append(sample)
fn_out = op.join(args.out, sample + ".%s" % args.out_format)
if args.format == "BAM":
reads = _read_bam(fn, args)
elif args.format == "seqbuster":
reads = seqbuster.read_file(fn, args)
elif args.format == "srnabench":
out_dts[fn] = srnabench.read_file(fn, args)
elif args.format == "prost":
reads = prost.read_file(fn, precursors, database, args.gtf)
elif args.format == "isomirsea":
out_dts[fn] = isomirsea.read_file(fn, args)
elif args.format == "manatee":
out_dts[fn] = manatee.read_file(fn, database, args)
elif args.format == "optimir":
out_dts[fn] = optimir.read_file(fn, args)
elif args.format == "gff":
samples.extend(header.read_samples(fn))
out_dts[fn] = body.read(fn, args)
continue
if args.format not in ["isomirsea", "srnabench", "manatee", 'optimir']:
ann = annotate(reads, matures, precursors)
out_dts[fn] = body.create(ann, database, sample, args)
h = header.create([sample], database, header.make_tools(args.format))
_write(out_dts[fn], h, fn_out, args)
# merge all reads for all samples into one dict
if args.low_memory:
return None
merged = merge.merge(out_dts, samples)
fn_merged_out = op.join(args.out, "mirtop.%s" % args.out_format)
_write(merged, header.create(samples, database, header.make_tools([args.format])), fn_merged_out, args)
def _write(lines, header, fn, args = None):
out_handle = open(fn, 'w')
print(header, file=out_handle)
mapper = read_gtf_to_mirna(args.gtf)
for m in lines:
for s in sorted(lines[m].keys()):
for hit in lines[m][s]:
# TODO: convert to genomic if args.out_genomic
if args and args.out_genomic:
lifted = body.lift_to_genome(hit[4], mapper)
print(lifted, file=out_handle)
else:
print(hit[4], file=out_handle)
out_handle.close()
def _read_bam(bam_fn, precursors):
if bam_fn.endswith("bam") or bam_fn.endswith("sam"):
logger.info("Reading %s" % bam_fn)
reads = read_bam(bam_fn, precursors)
else:
raise ValueError("Format not recognized."
" Only working with BAM/SAM files.")
return reads
mirtop-0.4.23/mirtop/gff/body.py 0000664 0000000 0000000 00000033302 13547635037 0016513 0 ustar 00root root 0000000 0000000 """GFF reader and creator helpers"""
from __future__ import print_function
from collections import defaultdict, OrderedDict
from mirtop.mirna.realign import get_mature_sequence, align_from_variants, \
read_id, variant_to_5p, variant_to_3p, variant_to_add, \
is_sequence, make_id
from mirtop.gff.header import read_samples
from mirtop.gff.classgff import feature
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def read(fn, args):
"""Read GTF/GFF file and load into annotate, chrom counts, sample, line"""
samples = read_samples(fn)
lines = defaultdict(dict)
sep = " " if args.out_format == "gtf" else "="
corrupted_uid = 0
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
line = paste_columns(feature(line), sep=sep)
gff = feature(line)
cols = gff.columns
attr = gff.attributes
if attr['UID'] and not read_id(attr['UID']):
corrupted_uid += 1
continue
if 'UID' not in attr:
msg = "UID not found."
if 'Read' not in attr:
if not is_sequence(attr['Read']):
msg = msg + " Sequence not valid in Read attribute."
else:
attr['UID'] = make_id(attr['Read'])
if 'sequence' not in attr:
msg = msg + " Sequence not found in sequence attribute."
if not is_sequence(attr['sequence']):
msg = msg + " Sequence not valid in sequence attribute."
else:
attr['UID'] = make_id(attr['Read'])
if 'UID' not in attr:
logger.warning("Line is not a valid GFF3 line: %s" %
line.strip())
logger.warning(msg)
if cols['start'] not in lines[cols['chrom']]:
lines[cols['chrom']][cols['start']] = []
uid = "%s-%s-%s" % (attr['UID'],
attr['Variant'],
attr['Name'])
if args.keep_name:
uid = "%s-%s" % (uid, attr['Read'])
lines[cols['chrom']][cols['start']].append(
[uid,
cols['chrom'],
attr['Expression'].strip().split(","),
samples,
line.strip()])
logger.info("Lines skipped due to corrupted UID: %s" % corrupted_uid)
return lines
def write_body_on_handle(lines, out_handle):
for m in lines:
for s in sorted(lines[m].keys()):
for hit in lines[m][s]:
print(hit[4], file=out_handle)
def create(reads, database, sample, args, quiet=False):
"""Read https://github.com/miRTop/mirtop/issues/9"""
sep = " " if args.out_format == "gtf" else "="
seen = set()
lines = defaultdict(defaultdict)
seen_ann = {}
filter_precursor = 0
filter_score = 0
n_hits = 0
n_reads = 0
n_seen = 0
if args.add_extra:
precursors = args.precursors
matures = args.matures
for (r, read) in reads.items():
hits = set()
[hits.add(mature.mirna) for mature in read.precursors.values()
if mature.mirna]
hits = len(hits)
if len(read.precursors) > 0:
n_reads += 1
for (ps, iso) in read.precursors.items():
p = list(ps)[0]
if not iso.mirna:
filter_precursor += 1
continue
if (r, iso.mirna) not in seen:
seen.add((r, iso.mirna))
chrom = p
seq = reads[r].sequence
seq_name = seq if not args.keep_name else r
if iso.get_score(len(seq)) < 1:
filter_score += 1
continue
if iso.subs:
iso.subs = [] if "N" in iso.subs[0] else iso.subs
idseq = reads[r].idseq
source = "ref_miRNA" if not iso.is_iso() else "isomiR"
strand = iso.strand
start, end = iso.start, iso.end
score = iso.map_score
mirName = iso.mirna
preName = p
Variant = iso.formatGFF()
Cigar = iso.cigar
counts = read.counts
Filter = iso.filter
annotation = "%s.%s.%s" % (chrom, idseq, seq_name)
# TODO: This need to be moved to use the feature class
# It needs a dict with all variable in keys
fields = {'seq_name': seq_name, 'idseq': idseq,
'name': mirName, 'parent': preName,
'variant': Variant, 'cigar': Cigar,
'counts': counts, 'filter': Filter,
'hits': hits, 'chrom': chrom,
'start': start, 'end': end,
'database': database, 'source': source,
'score': score, 'strand': strand}
line = feature(fields).line
logger.debug("GFF::%s" % line)
if args.add_extra:
extra = variant_with_nt(line, precursors, matures)
line = "%s Changes %s;" % (line, extra)
if annotation in seen_ann and seq.find("N") < 0 and (
seen_ann[annotation].split("\t")[0].find("N") < 0):
logger.warning(
"Same isomir %s from different sequence:"
" \n%s and \n%s" % (annotation, line,
seen_ann[annotation]))
seen_ann[annotation] = line
logger.debug("GFF::external %s" % iso.external)
if start not in lines[chrom]:
lines[chrom][start] = []
lines[chrom][start].append([annotation, chrom,
counts, sample, line])
logger.debug("GFF::%s" % line)
n_hits += 1
else:
n_seen += 1
if not quiet:
logger.info("GFF miRNAs: %s" % len(lines))
logger.info("GFF hits %s by %s reads" % (n_hits, n_reads))
logger.info("Filtered by being duplicated: %s" % n_seen)
logger.info("Filtered by being outside miRNA positions:"
" %s" % filter_precursor)
logger.info("Filtered by being low score: %s" % filter_score)
return lines
def lift_to_genome(line, mapper):
"""
Function to get a class of type feature from classgff.py
and map the precursors coordinates to the genomic coordinates
Args:
*line(str)*: string GFF line.
*mapper(dict)*: dict with mirna-precursor-genomic coordinas from
mirna.mapper.read_gtf_to_mirna function.
Returns:
*(line)*: string with GFF line with updated chr, star, end, strand
"""
features = feature(line)
features.attributes["Variant"]
chr, start, end, strand, id = mapper[features.attributes["Name"]][features.attributes["Parent"]]
logger.debug("LIFT2GENOME:: %s of %s found in %s(%s) " % (features.attributes["Name"],
features.attributes["Parent"],
chr, strand))
nstart = start
nend = end
variants = read_variant(features.attributes["Variant"])
logger.debug("LIFT2GENOME:: variants %s " % (features.attributes["Variant"]))
if 'iso_5p' in variants:
if strand == "+":
nstart = start + variants['iso_5p']
else:
nend = end - variants['iso_5p']
if 'iso_3p' in variants:
if strand == "+":
nend = end + variants['iso_3p']
else:
nstart = start - variants['iso_3p']
if 'iso_add3p' in variants:
if strand == "+":
nend = nend + variants['iso_add3p']
else:
nstart = nstart - variants['iso_add3p']
logger.debug("LIFT2GENOME:: start %s to %s | end %s to %s " % (start, nstart, end, nend))
features.columns['chrom'] = chr
features.columns['start'] = str(start)
features.columns['end'] = str(end)
features.columns['strand'] = strand
return features.paste_columns()
def create_line(read, name, database, args):
sep = " " if args.out_format == "gtf" else "="
if args.add_extra:
precursors = args.precursors
matures = args.matures
for (ps, iso) in read.precursors.items():
p = list(ps)[0]
if not iso.mirna:
continue
chrom = p
seq = read.sequence
seq_name = seq if not args.keep_name else name
if iso.get_score(len(seq)) < 1:
continue
if iso.subs:
iso.subs = [] if "N" in iso.subs[0] else iso.subs
idseq = read.idseq
source = "ref_miRNA" if not iso.is_iso() else "isomiR"
strand = iso.strand
start, end = iso.start, iso.end
score = iso.map_score
mirName = iso.mirna
preName = p
Variant = iso.formatGFF()
Cigar = iso.cigar
counts = read.counts
Filter = iso.filter
annotation = "%s.%s.%s" % (chrom, idseq, seq_name)
# This get correctly formated with paste_columns below
attrb = ("Read {seq_name};UID {idseq};Name {mirName};"
"Parent {preName};"
"Variant {Variant};Cigar {Cigar};"
"Expression {counts};"
"Filter {Filter};").format(**locals())
line = ("{chrom}\t{database}\t{source}\t{start}\t{end}"
"\t{score}\t{strand}\t.\t{attrb}").format(**locals())
logger.debug("GFF::%s" % line)
if args.add_extra:
extra = variant_with_nt(line, precursors, matures)
line = "%s Changes %s;" % (line, extra)
line = feature(line).paste_columns(sep)
return line
def guess_format(line):
return "=" if line.find("Name=") > -1 else " "
def paste_columns(line, sep=" "):
"""
Create GFF/GTF line from read_gff_line
"""
cols = line.columns
attr = line.attributes
attr_paste = "; ".join(
"%s%s%s" % (a, sep, attr[a]) for a in attr)
return "\t".join([cols['chrom'], cols['source'], cols['type'],
cols['start'], cols['end'], cols['score'],
cols['strand'], cols['ext'], attr_paste])
def read_variant(attrb, sep=" "):
"""
Read string in variants attribute.
Args:
*attrb(str)*: string in Variant attribute.
Returns:
*(gff_dict)*: dictionary with:
>>> {'iso_3p': -3, ...}
"""
gff_dict = OrderedDict()
logger.debug("variant: %s" % attrb)
for gff_item in attrb.strip().split(","):
item_pair = gff_item.strip().split(":")
if len(item_pair) > 1:
gff_dict[item_pair[0].strip()] = int(item_pair[1].strip())
else:
gff_dict[item_pair[0].strip()] = True
logger.debug("VARIANTS::Keys found: %s" % gff_dict.keys())
logger.debug("VARIANTS::Values found: %s" % gff_dict.values())
return gff_dict
def read_attributes(gff_line, sep=" "):
gff_line = gff_line.strip().split("\t")[8]
gff_dict = OrderedDict()
for gff_item in gff_line.strip().split(";"):
item_pair = gff_item.strip().split(sep)
if len(item_pair) > 1:
gff_dict[item_pair[0].strip()] = item_pair[1].strip()
return gff_dict
def read_gff_line(line):
"""
Read GFF/GTF line and return dictionary with fields
"""
if line.startswith("#"):
return line
cols = line.strip().split("\t")
sep = guess_format(line)
if len(cols) != 9:
raise ValueError("Line has less than 9 elements: %s" % line)
fields = {'chrom': cols[0],
'source': cols[1],
'type': cols[2],
'start': cols[3],
'end': cols[4],
'score': cols[5],
'strand': cols[6],
'ext': cols[7],
'attrb': read_attributes(line, sep)}
return fields
def variant_with_nt(line, precursors, matures):
"""
Return nucleotides changes for each variant type
using Variant attribute, precursor sequences and
mature position.
"""
gff = feature(line)
attr = gff.attributes
read = read_id(attr["UID"])
attr["Parent"] = attr["Parent"].split(",")[0]
if attr["Parent"] not in matures:
logger.warning("Parent miRNA not found in database %s" % attr["Parent"])
return ""
if attr["Name"] not in matures[attr["Parent"]]:
logger.warning("miRNA not found in database %s" % attr["Name"])
return ""
logger.debug("GFF::BODY::precursors %s" % precursors[attr["Parent"]])
logger.debug("GFF:BODY::mature %s" % matures[attr["Parent"]][attr["Name"]])
t5 = variant_to_5p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
t3 = variant_to_3p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
add = variant_to_add(read,
attr["Variant"])
mature_sequence = get_mature_sequence(
precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
nt=8)
logger.debug("GFF::BODY::mature_sequence %s" % mature_sequence)
mm = align_from_variants(read,
mature_sequence,
attr["Variant"])
if mm == "Invalid":
return mm
if len(mm) > 0:
mm = "".join(["".join([str(v) for v in m]) for m in mm])
else:
mm = "0"
return "iso_5p:%s,iso_3p:%s,iso_add3p:%s,iso_snv:%s" % (t5, t3, add, mm)
mirtop-0.4.23/mirtop/gff/check.py 0000664 0000000 0000000 00000000000 13547635037 0016620 0 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/gff/classgff.py 0000664 0000000 0000000 00000005616 13547635037 0017355 0 ustar 00root root 0000000 0000000 from mirtop.gff import gff_versions
from collections import OrderedDict
class feature:
""""Class with alignment information."""
def __init__(self, line, sep="="):
# if isinstance(line, basestring) # str in python 3
if isinstance(line, dict):
line = self.create_line(line, sep)
self.line = line
self.attributes = {}
self.columns = {}
self.read_gff_line()
self.reserved_attributes = gff_versions.ATTRv['1.1']
def guess_format(self):
return "=" if self.line.find("Name=") > -1 else " "
def create_line(self, fields, sep):
"""
Create GFF/GTF line from dictionary with fields
"""
# TODO: need unit test. Check all exists.
fields["attrb"] = ("Read {seq_name}; UID {idseq}; Name {name};"
"Parent {parent}; "
"Variant {variant}; Cigar {cigar};"
"Expression {counts}; "
"Filter {filter}; Hits {hits};").format(**fields)
line = ("{chrom}\t{database}\t{source}\t{start}\t{end}"
"\t{score}\t{strand}\t.\t{attrb}").format(**fields)
return line
def paste_columns(self, sep=None):
"""
Create GFF/GTF line from read_gff_line
"""
sep = self.guess_format()
attributes = "%s;" % "; ".join(
"%s%s%s" % (a, sep, self.attributes[a]) for a in self.attributes)
return "\t".join([self.columns['chrom'], self.columns['source'],
self.columns['type'],
self.columns['start'], self.columns['end'],
self.columns['score'],
self.columns['strand'], self.columns['ext'],
attributes])
def read_attributes(self, gff_attrb, sep=" "):
"""
Read GFF/GTF attributes and return dictionary with fields
"""
sep = self.guess_format()
gff_dict = OrderedDict()
for gff_item in gff_attrb.split(";"):
item_pair = gff_item.strip().split(sep)
if len(item_pair) > 1:
gff_dict[item_pair[0].strip()] = item_pair[1].strip()
self.attributes = gff_dict
def read_gff_line(self):
"""
Read GFF/GTF line and return dictionary with fields
"""
line = self.line
if line.startswith("#"):
return line
cols = line.strip().split("\t")
if len(cols) != 9:
raise ValueError("Line has less than 9 elements: %s" % line)
self.read_attributes(cols[8])
fields = {'chrom': cols[0],
'source': cols[1],
'type': cols[2],
'start': cols[3],
'end': cols[4],
'score': cols[5],
'strand': cols[6],
'ext': cols[7]}
self.columns = fields
mirtop-0.4.23/mirtop/gff/compare.py 0000664 0000000 0000000 00000011263 13547635037 0017206 0 ustar 00root root 0000000 0000000 """
Compare multiple GFF files to a reference
"""
from __future__ import print_function
import os
from mirtop.gff.classgff import feature
from mirtop.mirna.realign import read_id
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def compare(args):
"""
From a list of GFF files produce comparison with a reference set.
Args:
*args(namedtuple)*: arguments parsed from command line with
*mirtop.libs.parse.add_subparser_compare()*.
First file will be considered the reference set.
Returns:
*(out_file)*: comparison of the GFF files with the reference.
"""
result = dict()
reference = read_reference(args.files[0])
for fn in args.files[1:]:
if not os.path.exists(fn):
raise IOError("%s doesn't exist" % fn)
result[os.path.basename(fn)] = _compare_to_reference(fn, reference)
if args.out != "tmp_mirtop":
fn_out = os.path.join(args.out, "summary.txt")
with open(fn_out, 'w') as outh:
for fn in result:
print("sample\tidu\tseq\ttag\tsame_mirna\t%s" % "\t".join(result[fn][0][3].keys()), file=outh)
for line in result[fn]:
read = read_id(line[0])
acc = "\t".join([line[3][v] for v in line[3]])
print("%s\t%s\t%s\t%s\t%s\t%s" % (fn, line[0], read, line[1], line[2], acc), file=outh)
def read_reference(fn):
"""Read GFF into UID:Variant
Args:
*fn (str)*: GFF file.
Returns:
*srna (dict)*: dict with >>> {'UID': 'iso_snp:-2,...'}
"""
srna = dict()
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
gff = feature(line)
attr = gff.attributes
srna[attr['UID']] = [_simplify(attr['Variant']), attr]
return srna
def _compare_to_reference(fn, reference):
same = 0
diff = list()
extra = list()
miss = list()
results = list()
seen = 0
seen_reference = set()
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
gff = feature(line)
attr = gff.attributes
if attr['UID'] in reference:
mirna = "Y" if attr['Name'] == reference[attr['UID']][1]['Name'] else attr['Name']
accuracy = _accuracy(_simplify(attr['Variant']), reference[attr['UID']][0])
results.append([attr['UID'], "D", mirna, accuracy])
if _simplify(attr['Variant']) == reference[attr['UID']][0]:
same += 1
else:
diff.append("%s | reference: %s" % (line.strip(), reference[attr['UID']][1]))
seen += 1
seen_reference.add(attr['UID'])
else:
extra.append("%s | extra" % line.strip())
results.append([attr['UID'], "E", attr['Name'], _accuracy(_simplify(attr['Variant']), "")])
for uid in reference:
if uid not in seen_reference:
results.append([uid, "M", "N", _accuracy("", reference[uid][0])])
miss.append("| miss %s" % reference[uid][1])
logger.info("Number of sequences found in reference: %s" % seen)
logger.info("Number of sequences matches reference: %s" % same)
logger.info("Number of sequences different than reference: %s" % len(diff))
logger.info("Number of sequences extra sequences: %s" % len(extra))
logger.info("Number of sequences missed sequences: %s" % len(miss))
return results
def _simplify(variant):
simple = [v.split(":")[0] for v in variant.split(",")]
return ",".join(simple)
def _get_samples(fn):
with open(fn) as inh:
for line in inh:
if line.startswith("## COLDATA"):
return line.strip().split(": ")[1].strip().split(",")
raise ValueError("%s doesn't contain COLDATA header." % fn)
def _accuracy(target, reference):
"""Compare each isomir label in Variant field
and return a list with values whether:
FP: no in reference
FN: no in target
TP: same values
"""
logger.debug("COMPARE::ACCURACY::values %s vs %s" % (target, reference))
accuracy = dict()
types = ["iso_5p", "iso_3p", "iso_add3p", "iso_snv",
"iso_snv_seed", "iso_snv_central",
"iso_snv_central_supp", "iso_snv_central_offset"]
for t in types:
if t in reference:
accuracy[t] = "TP" if t in target else "FN"
else:
accuracy[t] = "TN" if t not in target else "FP"
logger.debug("COMPARE::ACCURACY::%s" % accuracy.keys())
logger.debug("COMPARE::ACCURACY::%s" % accuracy.values())
return accuracy
mirtop-0.4.23/mirtop/gff/convert.py 0000664 0000000 0000000 00000010570 13547635037 0017240 0 ustar 00root root 0000000 0000000 """Convert GFF file into count matrix"""
from __future__ import print_function
import os.path as op
from mirtop.mirna import fasta, mapper
from mirtop.mirna.realign import read_id
from mirtop.gff.classgff import feature
from mirtop.gff.body import variant_with_nt
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def convert_gff_counts(args):
""" Reads a GFF file to produces output file containing Expression counts
Args:
*args(namedtuple)*: arguments parsed from command line with
*mirtop.libs.parse.add_subparser_counts()*.
Returns:
*file (file)*: with columns like:
UID miRNA Variant Sample1 Sample2 ... Sample N
"""
sep = "\t"
variant_header = sep.join(['iso_5p', 'iso_3p',
'iso_add3p', 'iso_snp'])
if args.add_extra:
precursors = fasta.read_precursor(args.hairpin, args.sps)
matures = mapper.read_gtf_to_precursor(args.gtf)
variant_header = sep.join([variant_header,
'iso_5p_nt', 'iso_3p_nt',
'iso_add3p_nt', 'iso_snp_nt'])
logger.info("INFO Reading GFF file %s", args.gff)
logger.info("INFO Writing TSV file to directory %s", args.out)
gff_file = open(args.gff, 'r')
out_file = op.join(args.out, "%s.tsv" % op.splitext(op.basename(args.gff))[0])
missing_parent = 0
missing_mirna = 0
unvalid_uid = 0
with open(out_file, 'w') as outh:
for samples_line in gff_file:
if samples_line.startswith("## COLDATA:"):
samples = sep.join(samples_line.strip().split("COLDATA:")[1].strip().split(","))
header = sep.join(['UID', 'Read', 'miRNA', 'Variant',
variant_header, samples])
print(header, file=outh)
break
for mirna_line in gff_file:
gff = feature(mirna_line)
attr = gff.attributes
UID = attr["UID"]
Read = attr["Read"]
mirna = attr["Name"]
parent = attr["Parent"]
variant = attr["Variant"]
try:
read_id(UID)
except KeyError:
unvalid_uid += 1
continue
expression = sep.join(attr["Expression"].strip().split(","))
cols_variants = sep.join(_expand(variant))
logger.debug("COUNTS::Read:%s" % Read)
logger.debug("COUNTS::EXTRA:%s" % variant)
if args.add_extra:
if parent not in precursors:
missing_parent += 1
continue
if mirna not in matures[parent]:
missing_mirna += 1
continue
extra = variant_with_nt(mirna_line, precursors, matures)
if extra == "Invalid":
continue
logger.debug("COUNTS::EXTRA:%s" % extra)
cols_variants = sep.join([cols_variants] + _expand(extra, True))
summary = sep.join([UID, Read, mirna, variant,
cols_variants, expression])
logger.debug(summary)
print(summary, file=outh)
gff_file.close()
logger.info("Missing Parents in hairpin file: %s" % missing_parent)
logger.info("Missing MiRNAs in GFF file: %s" % missing_mirna)
logger.info("Non valid UID: %s" % unvalid_uid)
logger.info("Output file is at %s" % out_file)
def _expand(variant, nts=False):
"""Expand Variant field into list for iso_5p, iso_3p, iso_add3p, iso_snv"""
list_variant = []
isomir = {}
snp_var = []
for v in variant.split(","):
if v.find(":") > 0:
isomir[v.split(":")[0]] = v.split(":")[1]
elif v.find("snv") > 0:
snp_var.append(1)
if "iso_5p" in isomir:
list_variant.append(isomir["iso_5p"])
else:
list_variant.append(0)
if "iso_3p" in isomir:
list_variant.append(isomir["iso_3p"])
else:
list_variant.append(0)
if "iso_add3p" in isomir:
list_variant.append(isomir["iso_add3p"])
else:
list_variant.append(0)
if nts:
if "iso_snv" in isomir:
list_variant.append(isomir["iso_snv"])
else:
list_variant.append(0)
else:
snp = sum(snp_var)
list_variant.append(snp)
return list(map(str, list_variant))
mirtop-0.4.23/mirtop/gff/gff_versions.py 0000664 0000000 0000000 00000002422 13547635037 0020247 0 ustar 00root root 0000000 0000000 current = "1.2"
GFFv = {'1.0': ["iso_5p", "iso_3p", "iso_add", "iso_snp_seed",
"iso_snp_central_offset", "iso_snp_central",
"iso_snp_central_supp", "iso_snp", "NA"],
'1.1': ["iso_5p", "iso_3p", "iso_add3p", "iso_snv_seed",
"iso_snv_central_offset", "iso_snv_central",
"iso_snv_central_supp", "iso_snv", "NA"],
'1.2': ["iso_5p", "iso_3p", "iso_add3p", "iso_snv_seed",
"iso_snv_central_offset", "iso_snv_central",
"iso_snv_central_supp", "iso_snv", "NA"]}
ATTRv = {'1.0': set(('IDU', 'Name', 'Alias', 'Parent',
'Read', 'Variant', 'Changes',
'Cigar', 'Hits', 'Genomic',
'Expression', 'Filter', 'Cigar',
'Seed_fam')),
'1.1': set(('IDU', 'Name', 'Alias', 'Parent',
'Read', 'Variant', 'Changes',
'Cigar', 'Hits', 'Genomic',
'Expression', 'Filter', 'Cigar',
'Seed_fam')),
'1.2': set(('IDU', 'Name', 'Alias', 'Parent',
'Read', 'Variant', 'Changes',
'Cigar', 'Hits', 'Genomic',
'Expression', 'Filter', 'Cigar',
'Seed_fam'))}
mirtop-0.4.23/mirtop/gff/header.py 0000664 0000000 0000000 00000004311 13547635037 0017004 0 ustar 00root root 0000000 0000000 """Helpers to define the header fo the GFF file"""
from mirtop.gff import gff_versions as version
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def create(samples, database, custom, filter=None):
"""Create header for GFF file.
Args:
*samples (list)*: character list with names for samples
*database (str)*: name of the database.
*custom (str)*: extra lines.
*filter (list)*: character list with filter definition.
Returns:
*header (str)*: header string.
"""
header = ""
header += get_gff_version()
header += _get_database(database)
header += custom
header += _get_samples(samples)
return header
def get_gff_version():
return ("## mirGFF3. VERSION"
" %s\n" % version.current)
def make_tools(tools):
return("## TOOLS: %s\n" % ",".join(tools))
def _get_samples(samples):
return "## COLDATA: %s" % ",".join(samples)
def _get_database(database):
if database.lower().find("mirbase") > -1:
so = "doi:10.25504/fairsharing.hmgte8"
elif database.lower().find("mirgenedb") > -1:
so = "http://mirgenedb.org"
else:
so = "Custom."
return ("## source-ontology: %s %s\n" % (database, so))
def _filter(filters):
if not filters:
return "## FILTER: PASS\n"
return "## FILTER: %s" % ";\n".join(filters)
def read_version(fn):
"""Extract mirGFF3 version"""
with open(fn) as inh:
for line in inh:
if line.find("VERSION") > -1:
return line.split("VERSION")[1].strip()
if not line.startswith("#"):
ValueError("Version not found in the header."
"A valid file should have a line like this:"
"## mirGFF3. VERSION X.X")
def read_samples(fn):
"""Read samples from the header of a GFF file.
Args:
*fn(str)*: GFF file to read.
Returns:
*(list)*: character list with sample names.
"""
with open(fn) as inh:
for line in inh:
if line.startswith("## COLDATA"):
return line.strip().split(": ")[1].strip().split(",")
raise ValueError("%s doesn't contain COLDATA header." % fn)
mirtop-0.4.23/mirtop/gff/merge.py 0000664 0000000 0000000 00000005423 13547635037 0016660 0 ustar 00root root 0000000 0000000 from collections import defaultdict
from mirtop.gff.body import paste_columns, guess_format
import mirtop.libs.logger as mylog
from mirtop.gff.classgff import feature
logger = mylog.getLogger(__name__)
def merge(dts, samples):
"""
For dictionary with sample as keys and values as lines
merge them into one GFF file.
Args:
*dts(dict)*: dictionary as >>> {'file': {'mirna': {start: gff_list}}}.
gff_list has the format as defined in *mirtop.gff.body.read()*.
*samples(list)*: character list with sample names.
Returns:
*merged_lines (nested dicts)*:gff_list has the format as defined in *mirtop.gff.body.read()*.
"""
logger.debug("MERGE::SAMPLES::given %s" % samples)
all_data = defaultdict(dict)
all_lines = defaultdict(list)
merged_lines = defaultdict(dict)
for fn in dts:
for m in dts[fn]:
for s in dts[fn][m]:
for hit in dts[fn][m][s]:
idu = hit[0]
logger.debug("MERGE::SAMPLES::counts %s" % [hit[3], hit[2]])
formatted_counts = _format_samples_counts(hit[3], hit[2])
logger.debug("MERGE::SAMPLES::fixed %s" % formatted_counts)
for sample in formatted_counts:
all_data[idu][sample] = formatted_counts[sample] # get the expression of the sample from line
all_lines[idu] = hit[4] # get the line
for idu in all_data:
line = all_lines[idu]
expression = _convert_to_string(all_data[idu], samples)
if _start(line) not in merged_lines[_chrom(line)]:
merged_lines[_chrom(line)][_start(line)] = []
merged_lines[_chrom(line)][_start(line)].append([idu, "", "", "",
_fix(line, expression)])
return merged_lines
def _format_samples_counts(samples, expression):
"""Return a dictionary of samples counts"""
if isinstance(samples, list):
if len(samples) != len(expression):
raise ValueError("samples %s has different length than expression %s" % (samples,
expression))
else:
samples = [samples]
expression = [expression]
return dict(zip(samples, expression))
def _fix(line, expression):
# Need to fix Read attribute since not usefull when multiple sample in a line.
gff = feature(line)
attr = gff.attributes
attr['Expression'] = expression
return paste_columns(gff, guess_format(line))
def _convert_to_string(d, s):
v = [str(d[ss]) if ss in d else "0" for ss in s]
return "%s" % ",".join(v)
def _chrom(string):
return string.split("\t")[0]
def _start(string):
return string.split("\t")[3]
mirtop-0.4.23/mirtop/gff/query.py 0000664 0000000 0000000 00000000000 13547635037 0016710 0 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/gff/read.py 0000664 0000000 0000000 00000003571 13547635037 0016476 0 ustar 00root root 0000000 0000000 """mirGFF3 proxy converter"""
from __future__ import print_function
import os.path as op
from mirtop.mirna import fasta, mapper
from mirtop.bam.bam import low_memory_bam, low_memory_genomic_bam
from mirtop.importer import seqbuster
from mirtop.gff import header
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def reader(args):
"""
Realign BAM hits to miRBase to get better accuracy and annotation
"""
samples = []
database = mapper.guess_database(args)
args.database = database
precursors = fasta.read_precursor(args.hairpin, args.sps)
args.precursors = precursors
matures = mapper.read_gtf_to_precursor(args.gtf)
args.matures = matures
# TODO check numbers of miRNA and precursors read
# TODO print message if numbers mismatch
if args.keep_name and len(args.files) > 1:
logger.warning("--keep-name when running multiple samples\n"
"can generate wrong results if the\n"
"name read is different across sample\n"
"for the same sequence.")
for fn in args.files:
fn = op.normpath(fn)
if args.format != "gff":
sample = op.splitext(op.basename(fn))[0]
samples.append(sample)
fn_out = op.join(args.out, sample + ".%s" % args.out_format)
h = header.create([sample], args.database, "")
out_handle = open(fn_out, 'w')
print(h, file=out_handle)
if args.format == "BAM":
if args.genomic:
low_memory_genomic_bam(fn, sample, out_handle, args)
else:
low_memory_bam(fn, sample, out_handle, args)
elif args.format == "seqbuster":
seqbuster.read_file_low_memory(fn, sample, args, out_handle)
else:
raise ValueError("%s not supported for low memory" % args.format)
out_handle.close()
mirtop-0.4.23/mirtop/gff/stats.py 0000664 0000000 0000000 00000010324 13547635037 0016713 0 ustar 00root root 0000000 0000000 """
Produce stats from GFF3 format
"""
from __future__ import print_function
import os
import pandas as pd
import json
import re
from collections import defaultdict
from mirtop.gff.classgff import feature
from mirtop import version
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def stats(args):
"""
From a list of GFF files produce general isomiRs stats.
Args:
*args (namedtupled)*: arguments parsed from command line with
*mirtop.libs.parse.add_subparser_stats()*.
Returns:
*(stdout) or (out_file)*: GFF general stats.
"""
v = version.__version__
message_info = ("# mirtop stats version {v}").format(**locals())
out = list()
for fn in args.files:
if not os.path.exists(fn):
raise IOError("%s doesn't exist" % fn)
logger.info("Reading: %s" % fn)
out.append(_calc_stats(fn))
df_final = pd.concat(out)
_dump_log(df_final, version, os.path.join(args.out, "mirtop_stats.log"))
outfn = os.path.join(args.out, "mirtop_stats.txt")
if args.out != "tmp_mirtop":
with open(outfn, 'w') as outh:
print(message_info, file=outh)
df_final.to_csv(outh)
logger.info("Stats saved at %s" % outfn)
else:
print(message_info)
print(df_final)
def _get_samples(fn):
with open(fn) as inh:
for line in inh:
if line.startswith("## COLDATA"):
return line.strip().split(": ")[1].strip().split(",")
raise ValueError("%s doesn't contain COLDATA header." % fn)
def _calc_stats(fn):
"""
Read files and parse into categories
"""
samples = _get_samples(fn)
lines = []
seen = set()
ok = re.compile('pass', re.IGNORECASE)
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
gff = feature(line)
cols = gff.columns
attr = gff.attributes
logger.debug("## STATS: attribute %s" % attr)
if not ok.match(attr['Filter']):
continue
if "-".join([attr['UID'], attr['Variant'], attr['Name']]) in seen:
continue
seen.add("-".join([attr['UID'], attr['Variant'], attr['Name']]))
lines.extend(_classify(cols['type'], attr, samples))
df = _summary(lines)
return df
def _classify(srna_type, attr, samples):
"""
Parse the line and return one
line for each category and sample.
"""
# iso_5p, iso_3p, iso_add ...
# FILTER :: exact/isomiR_type
lines = []
counts = dict(zip(samples, attr['Expression'].split(",")))
for s in counts:
if int(counts[s]) > 0:
lines.append([srna_type, s, counts[s]])
if attr['Variant'].find("iso") == -1:
continue
for v in attr['Variant'].split(","):
if int(counts[s]) > 0:
lines.append([v.split(":")[0], s, counts[s]])
return lines
def _summary(lines):
"""
Summarize long table according to thresholds
"""
# summarize > 0, > 5, >10, >50, >100 and bind rows
labels = ["category", "sample", "counts"]
df = pd.DataFrame.from_records(lines, columns=labels)
df.counts = df.counts.astype(int)
df_sum = df.groupby(['category', 'sample'], as_index=False).sum()
df_sum['category'] = ["%s_sum" % r for r in df_sum['category']]
df_count = df.groupby(['category', 'sample'], as_index=False).count()
df_count['category'] = ["%s_count" % r for r in df_count['category']]
df_mean = df.groupby(['category', 'sample'], as_index=False).mean()
df_mean['category'] = ["%s_mean" % r for r in df_mean['category']]
df = pd.concat([df_sum, df_count, df_mean])
return df
def _dump_log(df, version, out_file):
"""Function to dump the table into a json log file."""
json_dict = defaultdict(dict)
for index, row in df.iterrows():
json_dict[row['sample']][row['category']] = row['counts']
log = {'meta': {'tool': 'mirtop',
'version': 'v%s' % version.__version__,
'homepage': version.__url__},
'metrics': json_dict}
logger.debug(log)
if out_file:
with open(out_file, 'w') as outh:
json.dump(log, outh)
mirtop-0.4.23/mirtop/gff/update.py 0000664 0000000 0000000 00000004627 13547635037 0017050 0 ustar 00root root 0000000 0000000 """Update gff3 files to newest version"""
from __future__ import print_function
import sys
import os
from mirtop.gff.classgff import feature
from mirtop.gff.header import read_version, get_gff_version
from mirtop.mirna.keys import *
from mirtop.mirna.realign import make_id
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def convert(args):
"""
Update previous GFF3 versions.
Args:
*args (namedtupled)*: arguments parsed from command line with
*mirtop.libs.parse.add_subparser_update()*.
Returns:
*(out_file)*: most updated GFF3 file.
"""
for fn in args.files:
out_fn = os.path.join(args.out, os.path.basename(fn))
update_file(fn, out_fn)
def read_uid_10(idu):
seq = ""
for i in idu:
if i == "1" or i == "2":
return seq[:-int(i)]
else:
if i not in CODE2NT:
logger.error("UID is not valid (%s)" % idu)
return False
seq += CODE2NT[i]
return seq
def to10to11(gff_line):
gff_line = gff_line.replace("_snp", "_snv")
gff_line = gff_line.replace("_add", "_add3p")
features = feature(gff_line)
if "iso_5p" in features.attributes["Variant"]:
variants = features.attributes["Variant"].split(",")
iso_5p = [v.split(":") for v in variants if v.startswith("iso_5p")]
iso_5p = -1 * int(iso_5p[0][1])
if iso_5p > 0:
iso_5p = "+%s" % iso_5p
variants = ["iso_5p:%s" % iso_5p if v.startswith("iso_5p") else v for v in variants]
features.attributes["Variant"] = ",".join(variants)
features.attributes["UID"] = make_id(read_uid_10(features.attributes["UID"]))
return features.paste_columns()
def update_file(gff_file, new_gff_file):
"""Update file from file version to current version"""
versions = ["1.0"]
functions = [to10to11]
version = read_version(gff_file)
init = versions.index(version)
outh = sys.stdout if not new_gff_file else open(new_gff_file, 'w')
with open(gff_file) as inh:
for line in inh:
if line.find("VERSION") > -1:
print(get_gff_version(), file=outh)
continue
if line.startswith("##"):
print(line.strip(), file=outh)
continue
for updates in range(init, len(functions)):
print(functions[updates](line), file=outh)
mirtop-0.4.23/mirtop/gff/validator.py 0000664 0000000 0000000 00000010411 13547635037 0017537 0 ustar 00root root 0000000 0000000 from mirtop.gff.classgff import feature
import mirtop.libs.logger as mylog
from mirtop.gff import gff_versions as version
from mirtop.mirna.realign import read_id
logger = mylog.getLogger(__name__)
def _check_header(header):
""" Check that header has the minimum mandatory fields
"""
# Check mandatory fields present:
num_samples = 0
matching = []
mandatory_fields = ["source-ontology", "COLDATA", "VERSION", "TOOLS"]
for field in mandatory_fields:
match = ([s for s in header if field in s])
if len(match) != 0:
matching.append(match)
all_present = len(matching) == len(mandatory_fields)
if all_present:
for line in header:
if line.startswith("## COLDATA"):
samples = line.strip().split(": ")[1].strip().split(",")
num_samples = len(samples)
return [all_present, num_samples]
def _check_line(line, num, num_samples):
""" Check file for minimum
"""
gff = feature(line)
fields = gff.columns
attr = gff.attributes
errors = 0
# Check seqID
if not fields['chrom']:
logger.error('MISSING seqID in line %s' % (num))
errors += 1
# Check source
source = (fields['source']).lower()
valid_source = False
valid_sources = ["mirBase", "mirgeneDB"]
if (any(s.lower() in source for s in valid_sources)):
valid_source = True
if valid_source is False:
logger.warning('NOT STANDARD SOURCE in line %s' % (num))
# Check type
type = fields['type']
source = (fields['source']).lower()
valid_type = False
if type in ["ref_miRNA", "isomiR"]:
valid_type = True
if valid_type is False:
logger.error('INCORRECT TYPE in line %s' % (num))
errors += 1
# Check start/end
if not fields['start']:
logger.error('MISSING START value in line %s' % (num))
errors += 1
if not fields['end']:
logger.error('MISSING END value in line %s' % (num))
errors += 1
# Check strand
if str(fields['strand']) not in ["+", "-"]:
logger.error('INCORRECT STRAND in line %s' % (num))
errors += 1
# Check UID
if 'UID' not in attr:
logger.error('UID not found in line %s' % (num))
errors += 1
else:
if not read_id(attr['UID']):
logger.error('UID is not in a correct format in line %s. '
'Use mirtop gff to fix this or open an issue.' % num)
errors += 1
# Check attribute-variant
variant = (attr['Variant']).lower()
valid_variant = False
valid_variants = version.GFFv[version.current]
if (any(s.lower() in variant for s in valid_variants)):
valid_variant = True
if valid_variant is False:
logger.error('INCORRECT VARIANT type in line %s' % (num))
errors += 1
# Check attribute-expression
expression = attr['Expression'].strip().split(",")
expression = list(filter(None, expression))
if len(expression) != num_samples:
logger.error('INCORRECT number of EXPRESSION VALUES \
in line %s' % (num))
errors += 1
return errors
def _check_file(file):
"""
"""
errors = 0
# Get header to check.
header = []
with open(file) as ch:
for line in ch:
if line.startswith("##"):
header.append(line)
else:
break
all_present, num_samples = _check_header(header)
if all_present is False:
logger.warning("%s doesn't contain all \
the mandatory fields for the header." % file)
errors += 1
logger.info("HEADER CHECKED")
# Check lines
with open(file) as ch:
for num, line in enumerate(ch, 1):
if line.startswith("##"):
next
else:
errors += _check_line(line, num, num_samples)
return errors
def check_multiple(args):
"""
Check GFF3 format.
Args:
*args (namedtupled)*: arguments parsed from command line with
*mirtop.libs.parse.add_subparser_validator()*.
Returns:
*(std_out)*: warnings or errors of the files showing issues with the format.
"""
for file in args.files:
_check_file(file)
logger.info('%s checked' % file)
mirtop-0.4.23/mirtop/importer/ 0000775 0000000 0000000 00000000000 13547635037 0016302 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/importer/__init__.py 0000664 0000000 0000000 00000000000 13547635037 0020401 0 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/importer/isomirsea.py 0000664 0000000 0000000 00000016514 13547635037 0020656 0 ustar 00root root 0000000 0000000 """ Read isomiR GFF files"""
import os
from collections import defaultdict, Counter
import mirtop.libs.logger as mylog
from mirtop.mirna import mapper
from mirtop.mirna.realign import expand_cigar, make_id
from mirtop.gff.body import paste_columns, read_attributes
from mirtop.gff.body import variant_with_nt
from mirtop.gff.classgff import feature
logger = mylog.getLogger(__name__)
def header(fn):
"""
Custom header for isomiR-SEA importer.
Args:
*fn (str)*: file name with isomiR-SEA GFF output
Returns:
*(str)*: isomiR-SEA header string.
"""
h = ""
return h
def read_file(fn, args):
"""
Read isomiR-SEA file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with isomiR-SEA output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
database = args.database
gtf = args.gtf
sep = " " if args.out_format == "gtf" else "="
map_mir = mapper.read_gtf_to_mirna(gtf)
reads = defaultdict(dict)
reads_in = 0
sample = os.path.splitext(os.path.basename(fn))[0]
hits = _get_hits(fn)
logger.debug("ISOMIRSEA::SAMPLE::%s" % sample)
with open(fn) as handle:
for line in handle:
cols = line.strip().split("\t")
attr = read_attributes(line, "=")
query_name = attr['TS']
query_sequence = attr['TS'].replace("U", "T")
start = int(cols[3])
end = int(cols[4])
isomirseq_iso = attr['ISO']
if query_name not in reads and query_sequence == None:
continue
if query_sequence and query_sequence.find("N") > -1:
continue
counts = attr["TC"]
chrom = cols[0]
# logger.debug("SEQBUSTER:: cigar {cigar}".format(**locals()))
cigar = attr['CI'].replace("U", "T")
idu = make_id(query_sequence)
isoformat = cigar2variants(cigar, query_sequence, attr['ISO'])
logger.debug("\nISOMIRSEA::NEW::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" idu: {idu}\n"
" start: {start}\n"
" cigar: {cigar}\n"
" iso: {isoformat}\n"
" variant: {isoformat}".format(**locals()))
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
strand = "+"
database = cols[1]
mirName = attr['MIN'].split()[0]
preName = attr['PIN'].split()[0]
score = "."
Filter = attr['FILTER']
isotag = attr['ISO']
tchrom, tstart = _genomic2transcript(map_mir[mirName],
chrom, start)
start = start if not tstart else tstart
chrom = chrom if not tstart else tchrom
end = start + len(query_sequence)
hit = hits[idu]
fields = {'seq_name': query_sequence, 'idseq': idu,
'name': mirName, 'parent': preName,
'variant': isoformat, 'cigar': cigar,
'counts': counts, 'filter': Filter,
'hits': hit, 'chrom': chrom,
'start': start, 'end': end,
'database': database, 'source': source,
'score': score, 'strand': strand}
# TODO: convert to genomic if args.out_genomic
line = feature(fields).line
if args.add_extra:
extra = variant_with_nt(line, args.precursors, args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(feature(line), sep=sep)
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
reads_in += 1
reads[chrom][start].append([idu, chrom, counts, sample, line])
logger.info("Hits: %s" % reads_in)
return reads
def _get_hits(fn):
hits = Counter()
with open(fn) as handle:
for line in handle:
attr = read_attributes(line, "=")
query_sequence = attr['TS'].replace("U", "T")
if query_sequence and query_sequence.find("N") > -1:
continue
idu = make_id(query_sequence)
hits[idu] += 1
return hits
def cigar2variants(cigar, sequence, tag):
"""From cigar to Variants in GFF format"""
pos = 0
iso5p = 0
logger.debug("\nISOMIRSEA:: expanded: %s" % expand_cigar(cigar))
for l in expand_cigar(cigar):
if l == "I":
iso5p -= 1
elif l == "D":
iso5p += 1
else:
break
iso3p = 0
for l in reversed(expand_cigar(cigar)):
if l == "I":
iso3p += 1
elif l == "D":
iso3p -= 1
else:
break
isosnp = []
for l in expand_cigar(cigar):
if l in ['A', 'T', 'C', 'G' ]:
isosnp.append([pos, sequence[pos], l])
if l in ['D']:
continue
pos += 1
iso5p = "iso_5p:%s" % _fix(iso5p) if iso5p else ""
if tag[-1] == "T" or iso3p < 0:
iso3p = "iso_3p:%s" % _fix(iso3p) if iso3p else ""
else:
iso3p = "iso_add3p:%s" % iso3p if iso3p else ""
variant = ""
for iso in [iso5p, iso3p, _define_snp(isosnp)]:
if iso:
variant += "%s," % iso
variant = "NA;" if not variant else variant
return variant[:-1]
def _define_snp(subs):
value = ""
logger.debug("\nISOMIRSEA:: subs %s" % subs)
for sub in subs:
if sub:
if sub[0] > 1 and sub[0] < 8:
value += "iso_snv_seed,"
elif sub[0] == 8:
value += "iso_snv_central_offset,"
elif sub[0] > 8 and sub[0] < 13:
value += "iso_snv_central,"
elif sub[0] > 12 and sub[0] < 18:
value += "iso_snv_central_supp,"
else:
value += "iso_snv,"
return value[:-1]
def _fix(n):
if n > 0:
return "+%s" % n
return n
def _genomic2transcript(code, chrom, pos):
for ref in code:
if _is_chrom(chrom, code[ref][0]):
if _is_inside(pos, code[ref][1:3]):
return [ref, _transcript(pos, code[ref][1:4])]
return [None, None]
def _is_chrom(chrom, annotated):
logger.debug("TRANSCRIPT::CHROM::read position %s and db position %s" % (chrom, annotated))
if chrom == annotated:
return True
if chrom == annotated.replace("chr", ""):
return True
return False
def _is_inside(pos, annotated):
logger.debug("TRANSCRIPT::INSIDE::read position %s and db position %s" % (pos, annotated))
if pos > annotated[0] and pos < annotated[1]:
return True
return False
def _transcript(pos, annotated):
logger.debug("TRANSCRIPT::TRANSCRIPT::read position %s and db position %s" % (pos, annotated))
if annotated[2] == "+":
return pos - annotated[0]
elif annotated[2] == "-":
return annotated[1] - pos
raise ValueError("Strand information is incorrect %s" % annotated[3])
mirtop-0.4.23/mirtop/importer/manatee.py 0000664 0000000 0000000 00000013044 13547635037 0020270 0 ustar 00root root 0000000 0000000 """ Read Manatee files"""
from __future__ import print_function
from collections import defaultdict
import os
import mirtop.libs.logger as mylog
from mirtop.bam.bam import intersect
from mirtop.bam import filter
from mirtop.mirna.mapper import get_primary_transcript, guess_database
from mirtop.mirna.realign import isomir, reverse_complement, make_id, hits
from mirtop.gff.body import paste_columns, variant_with_nt
# from mirtop.mirna import mapper
from mirtop.gff.classgff import feature
from mirtop.gff import body
from mirtop.mirna.annotate import annotate
logger = mylog.getLogger(__name__)
def read_file(fn, database, args):
"""
Read Manatee file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with Manatee output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
reads = defaultdict(dict)
sample = os.path.splitext(os.path.basename(fn))[0]
precursors = args.precursors
bed_fn = os.path.join(args.out, os.path.basename(fn) + ".bed")
sep = " " if args.out_format == "gtf" else "="
seen = set()
with open(fn, 'r') as handle:
if not os.path.exists(bed_fn):
_bed(handle, bed_fn)
intersect_fn = intersect(bed_fn, args.gtf)
for line in intersect_fn:
data = _analyze_line(line, precursors, database, sample, sep, args)
if data:
start = data["start"]
chrom = data["chrom"]
key = "%s:%s" % (data['mirna'], data["name"])
if start not in reads[chrom]:
reads[chrom][start] = []
if key not in seen:
seen.add(key)
reads[chrom][start].append(data["line"])
return reads
def _analyze_line(line, precursors, database, sample, sep, args):
start_idx = 10
end_idx = 11
attr_idx = 15
query_name = line[3]
sequence = line[4]
if str(line).find(get_primary_transcript(guess_database(args))) < 0: # only working with mirbase
return None
logger.debug(("READ::line name:{0}").format(line))
if sequence and sequence.find("N") > -1:
return None
chrom = line[attr_idx].strip().split("Name=")[-1]
start = line[1]
end = line[2]
strand = line[5]
counts = float(line[6])
Filter = "Pass"
reads = dict()
if not start:
return None
if strand == "+":
start = int(start) - int(line[start_idx]) + 1
else:
start = int(line[end_idx]) - int(end)
iso = isomir()
iso.align = line
iso.set_pos(start, len(sequence))
logger.debug("READ::From BAM start %s end %s at chrom %s" % (iso.start, iso.end, chrom))
if len(precursors[chrom]) < start + len(sequence):
logger.debug("READ::%s start + %s sequence size are bigger than"
" size precursor %s" % (
chrom,
len(sequence),
len(precursors[chrom])))
iso.subs, iso.add, iso.cigar = filter.tune(
sequence, precursors[chrom],
start, None)
logger.debug("READ::After tune start %s end %s" % (iso.start, iso.end))
logger.debug("READ::iso add %s iso subs %s" % (iso.add, iso.subs))
idu = make_id(sequence)
reads[query_name] = hits()
reads[query_name].set_sequence(sequence)
reads[query_name].counts = counts
reads[query_name].sequence = sequence
reads[query_name].set_precursor(chrom, iso)
reads = annotate(reads, args.matures, args.precursors, quiet=True)
gff_line = body.create(reads, args.database, sample, args, quiet=True)
if start not in gff_line[chrom]:
return None
line = gff_line[chrom][start][0][4]
logger.debug("READ::line:%s" % line)
if args.add_extra:
extra = variant_with_nt(line, args.precursors,
args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(feature(line), sep=sep)
return {'chrom': chrom,
'start': start,
'name': query_name,
'mirna': reads[query_name].precursors[chrom].mirna,
'line': [idu, chrom, counts, sample, line]}
def _bed(handle, bed_fn):
with open(bed_fn, 'w') as outh:
for line in handle:
if line.startswith("@"):
continue
cols = line.strip().split()
if cols[2]=="*":
logger.debug("READ::Sequence not mapped: %s" % cols[0])
continue
query_name = cols[0]
query_sequence = cols[9]
counts = cols[14]
start = int(cols[3])
strand = "-" if cols[1] == "16" else "+"
chrom = cols[2]
# if there no hits
# if the sequence always matching the read, assuming YES now
# if not current or query_name!=current:
query_sequence = query_sequence if not strand=="-" else reverse_complement(query_sequence)
# logger.debug(("READ::Read name:{0} and Read sequence:{1}").format(line.query_name, sequence))
if query_sequence and query_sequence.find("N") > -1:
continue
end = start + len(query_sequence) - 1
bed_line = "\t".join(list(map(str, [chrom, start, end, query_name,
query_sequence, strand, counts])))
outh.write(bed_line + '\n')
mirtop-0.4.23/mirtop/importer/optimir.py 0000664 0000000 0000000 00000004341 13547635037 0020341 0 ustar 00root root 0000000 0000000 """ Read isomiR GFF files from optimir tool"""
from collections import defaultdict
import mirtop.libs.logger as mylog
from mirtop.gff.header import read_samples
from mirtop.gff.body import paste_columns
from mirtop.gff.body import variant_with_nt
from mirtop.gff.classgff import feature
logger = mylog.getLogger(__name__)
def read_file(fn, args):
"""
Read OptimiR file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with isomiR-SEA output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
database = args.database
gtf = args.gtf
sep = " " if args.out_format == "gtf" else "="
sample = read_samples(fn)
reads = defaultdict(dict)
logger.debug("OPTIMIR::SAMPLE::%s" % sample)
with open(fn) as handle:
for line in handle:
gff = feature(line)
fixed_line = line
if gff.columns:
if "Variant" not in gff.attributes:
gff.attributes["Variant"] = "NA"
logger.debug("OPTIMIR::Chrom update from %s to %s" % (gff.columns["chrom"], gff.attributes["Parent"]))
gff.columns["chrom"] = gff.attributes["Parent"].split(",")[0]
fixed_line = gff.paste_columns(sep=sep)
if args.add_extra:
extra = variant_with_nt(fixed_line, args.precursors, args.matures)
fixed_line = "%s Changes %s;" % (fixed_line, extra)
fixed_line = paste_columns(feature(fixed_line), sep=sep)
counts = gff.attributes["Expression"].split(",")
chrom = gff.columns["chrom"]
start = gff.columns["start"]
if start not in reads[chrom]:
reads[chrom][start] = []
reads[chrom][start].append([gff.attributes["UID"],
gff.columns["chrom"],
counts,
sample, fixed_line])
return reads
mirtop-0.4.23/mirtop/importer/prost.py 0000664 0000000 0000000 00000012661 13547635037 0020031 0 ustar 00root root 0000000 0000000 """ Read prost! files"""
import os
from collections import defaultdict
from mirtop.mirna import mapper
import mirtop.libs.logger as mylog
from mirtop.mirna.realign import isomir, hits, get_mature_sequence, align
from mirtop.bam import filter
logger = mylog.getLogger(__name__)
def header():
"""
Custom header for PROST! importer.
Returns:
*(str)*: PROST! header string.
"""
return ""
def read_file(fn, hairpins, database, mirna_gtf):
"""
Read PROST! file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with PROST output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads*: dictionary where keys are read_id and values are *mirtop.realign.hits*
"""
reads = defaultdict(hits)
sample = os.path.splitext(os.path.basename(fn))[0]
genomics = mapper.read_gtf_to_mirna(mirna_gtf)
matures = mapper.read_gtf_to_precursor(mirna_gtf)
non_mirna = 0
non_chromosome_mirna = 0
outside_mirna = 0
lines_read = 0
ann, ann_type = _group_seqs_by_ann(fn)
with open(fn) as handle:
handle.readline()
for line in handle:
lines_read += 1
cols = line.strip().split("\t")
query_name = cols[0]
query_sequence = cols[0]
if not ann[query_sequence]:
non_mirna += 1
continue
miRNA = ann_type[ann[query_sequence]][1]
preNames = ann_type[ann[query_sequence]][0]
if query_name not in reads and not query_sequence:
continue
if query_sequence and query_sequence.find("N") > -1:
continue
reads[query_name].set_sequence(query_sequence)
reads[query_name].counts = cols[9]
for preName in preNames.split(","):
if preName in reads[query_name].precursors:
continue
if preName not in hairpins:
non_chromosome_mirna += 1
continue
reference_start = _align_to_mature(query_sequence, hairpins[preName], matures[preName][miRNA])
logger.debug("\nPROST!::NEW::query: {query_sequence}\n"
" precursor {preName}\n"
" name: {query_name}\n"
" reference_start: {reference_start}\n"
" mirna: {miRNA}".format(**locals()))
iso = isomir()
iso.align = line
iso.set_pos(reference_start, len(reads[query_name].sequence))
logger.debug("PROST!:: start %s end %s" % (iso.start, iso.end))
if len(hairpins[preName]) < reference_start + len(reads[query_name].sequence):
continue
iso.subs, iso.add, iso.cigar = filter.tune(
reads[query_name].sequence,
hairpins[preName],
reference_start, None)
logger.debug("PROST!::After tune start %s end %s" % (
iso.start, iso.end))
if len(iso.subs) < 2:
reads[query_name].set_precursor(preName, iso)
logger.info("Lines loaded: %s" % lines_read)
logger.info("Skipped lines because non miRNA in line: %s" % non_mirna)
logger.info("Skipped lines because non chromosome in GTF:"
" %s" % non_chromosome_mirna)
logger.info("Skipped lines because outside precursor: %s" % outside_mirna)
logger.info("Hits: %s" % len(reads))
return reads
def _group_seqs_by_ann(fn):
"""Read file once to group sequences to same miRNA sequence"""
ann = dict()
ann_type = defaultdict(list)
with open(fn) as inh:
inh.readline()
for line in inh:
cols = line.strip().split("\t")
ann[cols[0]] = cols[4]
mirna = cols[11] if cols[11] else cols[13]
hairpin = cols[15]
if not cols[4] in ann_type:
ann_type[cols[4]] = ["", ""]
if mirna:
ann_type[cols[4]][1] = mirna
if hairpin:
ann_type[cols[4]][0] = hairpin
return [ann, ann_type]
def _align_to_mature(seq, hairpin, mature):
"""Get alignment between seq and mature"""
mirna = get_mature_sequence(hairpin, mature)
hit = align(seq, mirna)
start = hit[0][:8].count("-") - 4 + int(mature[0])
logger.debug("PROST::align:sequence to mature %s" % hit[0])
logger.debug("PROST::align:start: %s -> %s" % (mature[0], start))
return start
def _cigar_to_variants(seq, mature, cigar):
"""From mature based cigar get variants"""
return None
def _make_variant(cols):
logger.debug("PROST::variant: %s" % cols)
variant = []
if cols[0] != "0":
variant.append("iso_5p:%s" % -1 * int(cols[0]))
if cols[1] != "0":
variant.append("iso_3p:%s" % cols[1])
if cols[2] != "0":
variant.append("iso_add3p:%s" % int(cols[2]))
if cols[3] == "True":
variant.append("iso_snv_seed")
if cols[4] == "True":
variant.append("iso_snv_central_offset")
if cols[5] == "True":
variant.append("iso_snv_central")
if cols[6] == "True":
variant.append("iso_snv_supp")
if cols[7] == "True":
variant.append("iso_snv")
if not variant:
return "NA"
return ",".join(variant)
mirtop-0.4.23/mirtop/importer/seqbuster.py 0000664 0000000 0000000 00000007437 13547635037 0020704 0 ustar 00root root 0000000 0000000 """ Read seqbuster files"""
from collections import defaultdict
import mirtop.libs.logger as mylog
from mirtop.mirna.realign import isomir, hits
from mirtop.bam import filter
from mirtop.gff import body
from mirtop.mirna.annotate import annotate
logger = mylog.getLogger(__name__)
def header():
"""
Custom header for seqbuster importer.
Returns:
*(str)*: seqbuster header string.
"""
h = ("## CMD: seqbuster: http://seqcluster.readthedocs.io/mirna_annotation.html#mirna-isomir-annotation-with-java\n"
"# iso_snp are not filtered yet. Use isomiRs R pacakge to correct for error sequencing\n")
return h
def read_file(fn, args):
"""
Read seqbuster file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with seqbuster output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads*: dictionary where keys are read_id and values are *mirtop.realign.hits*
"""
precursors = args.precursors
reads = defaultdict(hits)
col_fix = 0
with open(fn) as handle:
header = handle.readline()
if header.find("freq") < 0:
col_fix = 1
for line in handle:
reads.update(_read_line(line, col_fix, precursors))
logger.info("Hits: %s" % len(reads))
return reads
def read_file_low_memory(fn, sample, args, out_handle):
precursors = args.precursors
reads = defaultdict(hits)
col_fix = 0
with open(fn) as handle:
header = handle.readline()
if header.find("freq") < 0:
col_fix = 1
for line in handle:
reads = _read_line(line, col_fix, precursors)
ann = annotate(reads, args.matures, args.precursors, quiet=True)
gff_lines = body.create(ann, args.database, sample, args, quiet=True)
body.write_body_on_handle(gff_lines, out_handle)
def _read_line(line, col_fix, precursors):
reads = defaultdict(hits)
cols = line.strip().split("\t")
query_name = cols[1]
query_sequence = cols[0]
reference_start = int(cols[4-col_fix]) - 1
seqbuster_iso = ":".join(cols[6-col_fix:10-col_fix])
if query_sequence and query_sequence.find("N") > -1:
return reads
if query_name not in reads:
reads[query_name].set_sequence(query_sequence)
reads[query_name].counts = _get_freq(query_name)
chrom = cols[13-col_fix]
logger.debug("\nSEQBUSTER::NEW::query: {query_sequence}\n"
" precursor: {chrom}\n"
" name: {query_name}\n"
" start: {reference_start}\n"
" iso: {seqbuster_iso}".format(**locals()))
# logger.debug("SEQBUSTER:: cigar {cigar}".format(**locals()))
iso = isomir()
iso.align = line
iso.set_pos(reference_start, len(reads[query_name].sequence))
logger.debug("\nSEQBUSTER:: start %s end %s" % (iso.start, iso.end))
if len(precursors[chrom]) < reference_start + len(reads[query_name].sequence):
logger.debug("\nSEQBUSTER::len precursor" % len(precursors[chrom]))
return reads
iso.subs, iso.add, iso.cigar = filter.tune(reads[query_name].sequence,
precursors[chrom],
reference_start, None)
logger.debug("\nSEQBUSTER::After tune start %s end %s" % (iso.start, iso.end))
if len(iso.subs) < 6:
logger.debug("\nSEQBUSTER::iso.subs %s - length %s" % (iso.subs, len(iso.subs)))
reads[query_name].set_precursor(chrom, iso)
return reads
def _get_freq(name):
"""
Check if name read contains counts (_xNumber)
"""
try:
counts = int(name.split("_x")[1])
except:
return 0
return counts
mirtop-0.4.23/mirtop/importer/srnabench.py 0000664 0000000 0000000 00000020227 13547635037 0020622 0 ustar 00root root 0000000 0000000 """ Read sRNAbench files"""
import os
from collections import defaultdict
import mirtop.libs.logger as mylog
from mirtop.gff.body import paste_columns, variant_with_nt
from mirtop.mirna.realign import make_cigar, make_id
from mirtop.gff.classgff import feature
logger = mylog.getLogger(__name__)
def read_file(folder, args):
"""
Read sRNAbench file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with sRNAbench output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
reads_anno = os.path.join(folder, "reads.annotation")
reads_iso = os.path.join(folder, "microRNAannotation.txt")
sep = " " if args.out_format == "gtf" else "="
sample = os.path.basename(folder)
database = args.database
precursors = args.precursors
matures = args.matures
n_out = 0
n_in = 0
n_ns = 0
n_notassign = 0
n_notindb = 0
reads = defaultdict(dict)
seen = set()
source_iso = _read_iso(reads_iso)
logger.info("Reads with isomiR information %s" % len(source_iso))
with open(reads_anno) as handle:
for sequence in handle:
cols = sequence.strip().split("\t")
query_name = cols[0]
query_sequence = cols[0]
if query_name not in reads and not query_sequence:
continue
if query_sequence and query_sequence.find("N") > -1:
n_ns += 1
continue
if cols[3].find("mature") == -1:
n_in += 1
continue
counts = int(cols[1])
hits = len(set([mirna.split("#")[1] for mirna in cols[4].split("$")]))
for nhit in cols[4].split("$"):
logger.debug("SRNABENCH::line hit: %s" % nhit)
hit_info = nhit.split("#")
pos_info = hit_info[3].split(",")
start = int(pos_info[1]) - 1
end = start + len(query_sequence) # int(pos_info[2]) - 1
chrom = pos_info[0]
mirName = hit_info[1]
if chrom not in precursors or chrom not in matures:
n_notindb += 1
if mirName not in matures[chrom]:
n_notindb += 1
if (query_sequence, mirName) in seen:
continue
seen.add((query_sequence, mirName))
if (query_sequence, mirName) not in source_iso:
continue
isoformat = source_iso[(query_sequence, mirName)]
if isoformat == "mv":
n_notassign += 1
continue
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
logger.debug("SRNABENCH::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" start: {start}\n"
" external: {isoformat}\n"
" hit: {hits}".format(**locals()))
logger.debug("SRNABENCH:: start %s end %s" % (start, end))
if len(precursors[chrom]) < start + len(query_sequence):
n_out += 1
continue
Filter = "Pass"
cigar = make_cigar(query_sequence,
precursors[chrom][start:end])
preName = chrom
score = "."
strand = "+"
idu = make_id(query_sequence)
# attrb = ("Read {query_sequence}; UID {idu}; Name {mirName};"
# " Parent {preName}; Variant {isoformat};"
# " Cigar {cigar}; Expression {counts};"
# " Filter {Filter}; Hits {hits};").format(**locals())
# line = ("{chrom}\t{database}\t{source}\t{start}\t{end}\t"
# "{score}\t{strand}\t.\t{attrb}").format(**locals())
fields = {'seq_name': query_sequence, 'idseq': idu,
'name': mirName, 'parent': preName,
'variant': isoformat, 'cigar': cigar,
'counts': counts, 'filter': Filter,
'hits': hits, 'chrom': chrom,
'start': start, 'end': end,
'database': database, 'source': source,
'score': score, 'strand': strand}
# TODO: convert to genomic if args.out_genomic
line = feature(fields).line
if args.add_extra:
extra = variant_with_nt(line, args.precursors,
args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(feature(line), sep=sep)
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
n_in += 1
reads[chrom][start].append([idu, chrom, counts,
sample, line])
logger.info("Loaded %s reads with %s hits" % (len(reads), n_in))
logger.info("Reads without precursor information: %s" % n_notindb)
logger.info("Reads with MV as variant definition,"
" not supported by GFF: %s" % n_notassign)
logger.info("Hit Filtered by having > 3 changes: %s" % n_out)
return reads
def _read_iso(fn):
"""
Read definitions of isomiRs by srnabench
"""
iso = dict()
with open(fn) as inh:
inh.readline()
for line in inh:
cols = line.strip().split("\t")
label = cols[3].split("$")
mirnas = cols[1].split("$")
if len(mirnas) == 1 and len(label) > 1:
label = [cols[3].split("$")[0]]
if len(mirnas) != len(label):
label = label * (len(mirnas) - len(label))
anno = dict(zip(mirnas, label))
logger.debug("TRANSLATE::%s with %s" % (mirnas, label))
for m in anno:
iso[(cols[0], m)] = _translate(anno[m], cols[4])
logger.debug("TRANSLATE::code %s" % iso[(cols[0], m)])
return iso
def _translate(isomirs, description):
# TODO: make unit test for this
iso = []
labels = isomirs.split("@")
logger.debug("TRANSLATE::label:%s" % isomirs)
for label in labels:
logger.debug("TRANSLATE::label:%s" % label)
if label == "exact":
return "NA"
if label.find("mv") > -1:
return "mv"
number_nts = label.split("|")[-1].split("#")[-1]
if number_nts.find("-") < 0:
number_nts = "+%s" % number_nts
if label.find("lv3p") > -1:
iso.append("iso_3p:%s" % number_nts)
if label.find("lv5p") > -1:
if number_nts.startswith("+"):
number_nts = number_nts.replace("+", "-")
else:
number_nts = number_nts.replace("-", "+")
iso.append("iso_5p:%s" % number_nts)
if label.find("nta") > -1:
number_nts = label.split("|")[1].split("#")[-1]
if number_nts.find("-") < 0:
number_nts = "%s" % number_nts
iso.append("iso_add3p:%s" % number_nts)
if label.find("NucVar") > -1:
for nt in description.split(","):
logger.debug("TRANSLATE::change:%s" % description)
if nt == "-" or nt == "NA":
return "notsure"
iso.extend(_iso_snp(int(nt.split(":")[0])))
logger.debug("TRANSLATE::iso:%s" % iso)
return ",".join(iso)
def _iso_snp(pos):
iso = []
if pos > 1 and pos < 8:
iso.append("iso_snv_seed")
elif pos == 8:
iso.append("iso_snv_central_offset")
elif pos > 8 and pos < 13:
iso.append("iso_snv_central")
elif pos > 12 and pos < 18:
iso.append("iso_snv_central_supp")
else:
iso.append("iso_snv")
return iso
mirtop-0.4.23/mirtop/install.py 0000664 0000000 0000000 00000002031 13547635037 0016455 0 ustar 00root root 0000000 0000000 """
Some commands to install common databases like mirbase and some human/mouse annotation
"""
import os.path as op
import subprocess
try:
import bcbio
except:
print("Probably this will fail, you need bcbio-nextgen for many installation functions.")
pass
REMOTES = {
"requirements": "https://raw.github.com/lpantano/seqcluster/master/requirements.txt",
"gitrepo": "https://github.com/lpantano/seqcluster.git",
"gitrepo-bcbio": "https://github.com/chapmanb/bcbio-nextgen.git"
}
def _get_miraligner():
try:
tool = bcbio.pipeline.config_utils.get_program("miraligner", {}, "cmd")
except ImportError:
tool = None
pass
if not tool:
url = "https://github.com/lpantano/seqbuster/raw/master/modules/miraligner/miraligner.jar"
subprocess.check_call(["wget", "-O", "miraligner.jar", "--no-check-certificate", url])
tool = "java -jar {opts} %s" % op.abspath("miraligner.jar")
else:
tool = "%s {opts}" % tool
return tool
mirtop-0.4.23/mirtop/libs/ 0000775 0000000 0000000 00000000000 13547635037 0015372 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/libs/__init__.py 0000664 0000000 0000000 00000000000 13547635037 0017471 0 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/libs/config.py 0000664 0000000 0000000 00000000120 13547635037 0017202 0 ustar 00root root 0000000 0000000 import pkg_resources
version = pkg_resources.get_distribution("mirtop").version mirtop-0.4.23/mirtop/libs/do.py 0000664 0000000 0000000 00000006140 13547635037 0016347 0 ustar 00root root 0000000 0000000 """Centralize running of external commands, providing logging and tracking. Integrated from bcbio package with some changes.
"""
import collections
import os
import subprocess
import logging
import six
logger = logging.getLogger("run")
def run(cmd, data=None, checks=None, region=None, log_error=True,
log_stdout=False):
"""Run the provided command, logging details and checking for errors.
"""
try:
logger.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, six.string_types) else cmd)
_do_run(cmd, checks, log_stdout)
except:
if log_error:
logger.info("error at command")
raise
def find_bash():
"""Find bash full path
"""
for test_bash in [find_cmd("bash"), "/bin/bash", "/usr/bin/bash", "/usr/local/bin/bash"]:
if test_bash and os.path.exists(test_bash):
return test_bash
raise IOError("Could not find bash in any standard location. Needed for unix pipes")
def find_cmd(cmd):
"""Find comand in session
"""
try:
return subprocess.check_output(["which", cmd]).strip()
except subprocess.CalledProcessError:
return None
def _normalize_cmd_args(cmd):
"""Normalize subprocess arguments to handle list commands, string and pipes.
Piped commands set pipefail and require use of bash to help with debugging
intermediate errors.
"""
if isinstance(cmd, six.string_types):
# check for standard or anonymous named pipes
if cmd.find(" | ") > 0 or cmd.find(">(") or cmd.find("<("):
return "set -o pipefail; " + cmd, True, find_bash()
else:
return cmd, True, None
else:
return [str(x) for x in cmd], False, None
def _do_run(cmd, checks, log_stdout=False):
"""Perform running and check results, raising errors for issues.
"""
cmd, shell_arg, executable_arg = _normalize_cmd_args(cmd)
s = subprocess.Popen(cmd, shell=shell_arg, executable=executable_arg,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, close_fds=True)
debug_stdout = collections.deque(maxlen=100)
while 1:
line = s.stdout.readline()
if line:
debug_stdout.append(line)
if log_stdout:
logger.debug(line.rstrip())
else:
logger.debug(line.rstrip())
exitcode = s.poll()
if exitcode is not None:
for line in s.stdout:
debug_stdout.append(line)
if exitcode is not None and exitcode != 0:
error_msg = " ".join(cmd) if not isinstance(cmd, six.string_types) else cmd
error_msg += "\n"
error_msg += "".join(debug_stdout)
s.communicate()
s.stdout.close()
raise subprocess.CalledProcessError(exitcode, error_msg)
else:
break
s.communicate()
s.stdout.close()
# Check for problems not identified by shell return codes
if checks:
for check in checks:
if not check():
raise IOError("External command failed")
mirtop-0.4.23/mirtop/libs/fastq.py 0000664 0000000 0000000 00000003054 13547635037 0017064 0 ustar 00root root 0000000 0000000 """Helpers to work with fastq files"""
import os
from itertools import product
import gzip
def open_fastq(in_file):
""" open a fastq file, using gzip if it is gzipped
(from bcbio package)
Args:
*in_file(str)*: file name.
Returns:
*(File)*: file handler.
"""
_, ext = os.path.splitext(in_file)
if ext == ".gz":
return gzip.open(in_file, 'rb')
if ext in [".fastq", ".fq", ".fasta", ".fa"]:
return open(in_file, 'r')
return ValueError("File needs to be fastq|fasta|fq|fa [.gz]")
def is_fastq(in_file):
"""Check whether file is fastq accepting
txt, fq and fastq extensions understanding
compression with gzip: .gzip and .gz
(copy from bcbio)
Args:
*in_file(str)*: file name.
Returns:
*(boolean)*: Yes or Not.
"""
fastq_ends = [".txt", ".fq", ".fastq"]
zip_ends = [".gzip", ".gz"]
base, first_ext = os.path.splitext(in_file)
second_ext = os.path.splitext(base)[1]
if first_ext in fastq_ends:
return True
elif (second_ext, first_ext) in product(fastq_ends, zip_ends):
return True
else:
return False
def splitext_plus(fn):
"""Split on file extensions, allowing for zipped extensions.
(copy from bcbio)
Args:
*fn(str)*: file name.
Returns:
*base, ext(str, str)*: basename and extesion.
"""
base, ext = os.path.splitext(fn)
if ext in [".gz", ".bz2", ".zip"]:
base, ext2 = os.path.splitext(base)
ext = ext2 + ext
return base, ext
mirtop-0.4.23/mirtop/libs/logger.py 0000664 0000000 0000000 00000005151 13547635037 0017225 0 ustar 00root root 0000000 0000000 import logging
try:
from colorlog import ColoredFormatter
except:
pass
import os
def getLogger(name):
return logging.getLogger(__name__)
def set_format(frmt, frmt_col=None, datefmt=None):
if frmt_col:
try:
formatter = ColoredFormatter(frmt_col, datefmt=datefmt)
return formatter
except:
pass
formatter = logging.Formatter(frmt)
return formatter
def initialize_logger(output_dir, debug=False, level=False):
NOTE = 15
COLOR_FORMAT = "%(log_color)s%(asctime)s%(levelname)s-%(name)s(%(lineno)d)%(reset)s: %(message)s"
COLOR_FORMAT_INFO = "%(log_color)s%(asctime)s %(levelname)s%(reset)s: %(message)s"
DATE_FRT = '%m/%d/%Y %I:%M:%S'
FORMAT = "%(asctime)s %(levelname)s-%(name)s(%(lineno)d): %(message)s"
FORMAT_INFO = "%(asctime)s %(levelname)s %(message)s"
logging.addLevelName(NOTE, "NOTE")
if not os.path.exists(output_dir):
os.mkdir(output_dir)
output_dir = os.path.join(output_dir, "log")
if not os.path.exists(output_dir):
os.mkdir(output_dir)
def note(self, message, *args, **kws):
self.log(NOTE, message, *args, **kws)
logging.Logger.note = note
numeric_level = getattr(logging, "DEBUG", None)
if not debug:
numeric_level = getattr(logging, "INFO", None)
logger = logging.getLogger()
logger.setLevel(numeric_level)
# create console handler and set level to info
handler = logging.StreamHandler()
handler.setLevel(logging.INFO)
if level:
handler.setLevel(logging.DEBUG)
formatter = logging.Formatter(fmt=FORMAT_INFO, datefmt=DATE_FRT)
handler.setFormatter(formatter)
logger.addHandler(handler)
# create error file handler and set level to error
handler = logging.FileHandler(os.path.join(output_dir, "error.log"),
"w", encoding=None, delay="true")
handler.setLevel(logging.ERROR)
formatter = logging.Formatter(fmt=FORMAT, datefmt=DATE_FRT)
handler.setFormatter(formatter)
logger.addHandler(handler)
# create debug file handler and set level to debug
handler = logging.FileHandler(os.path.join(output_dir, "run.log"), "w")
handler.setLevel(numeric_level)
formatter = logging.Formatter(FORMAT, datefmt=DATE_FRT)
handler.setFormatter(formatter)
logger.addHandler(handler)
# create debug file handler and set level to debug
handler = logging.FileHandler(os.path.join(output_dir, "trace.log"), "w")
handler.setLevel(NOTE)
formatter = logging.Formatter("%(levelname)s - %(message)s")
handler.setFormatter(formatter)
logger.addHandler(handler)
mirtop-0.4.23/mirtop/libs/parse.py 0000664 0000000 0000000 00000020717 13547635037 0017065 0 ustar 00root root 0000000 0000000 from __future__ import print_function
import argparse
import sys
from mirtop import __version__
def parse_cl(in_args):
"""Function to parse the subcommands arguments.
"""
sub_cmds = {"gff": _add_subparser_gff,
"stats": _add_subparser_stats,
"compare": _add_subparser_compare,
"target": _add_subparser_target,
"simulator": _add_subparser_simulator,
"counts": _add_subparser_counts,
"export": _add_subparser_export,
"validate": _add_subparser_validator,
"spikein": _add_subparser_spikein,
"update": _add_subparser_update
}
parser = argparse.ArgumentParser(description="small RNA analysis")
parser.add_argument("--version", action="store_true",help="show version.")
sub_cmd = None
if len(in_args) > 0 and in_args[0] in sub_cmds:
print(in_args)
subparsers = parser.add_subparsers(help="mirtop supplemental commands")
sub_cmds[in_args[0]](subparsers)
sub_cmd = in_args[0]
elif (len(in_args) > 0):
args = parser.parse_args()
if args.version:
print("mirtop %s" % __version__)
sys.exit(0)
else:
print("use %s" % sub_cmds.keys())
print("mirtop %s" % __version__)
sys.exit(0)
args = parser.parse_args()
if "files" in args:
if not args.files:
print("use %s -h to see help." % in_args[0])
print("mirtop %s" % __version__)
sys.exit(1)
assert sub_cmd is not None
kwargs = {"args": args, sub_cmd: True}
return kwargs
def _add_debug_option(parser):
parser.add_argument("-d", "--debug", action="store_true",
dest="debug", help="max verbosity mode", default=False)
parser.add_argument("-vd", "--print_debug", action="store_true",
help="print debug messages on terminal", default=False)
return parser
def _add_subparser_stats(subparsers):
parser = subparsers.add_parser("stats", help="show general stats for each sample.")
parser.add_argument("files", nargs="*", help="GFF/GTF files.")
parser.add_argument("-o", "--out", dest="out", default="tmp_mirtop",
help="folder of output files")
parser = _add_debug_option(parser)
return parser
def _add_subparser_compare(subparsers):
parser = subparsers.add_parser("compare", help="Compare two GFF files.")
parser.add_argument("files", nargs="*", help="Files to compare."
"First will be used as reference.")
parser.add_argument("-o", "--out", dest="out", default="tmp_mirtop",
help="folder of output files")
parser = _add_debug_option(parser)
return parser
def _add_subparser_gff(subparsers):
parser = subparsers.add_parser("gff", help="realign miRNA BAM file")
parser.add_argument("files", nargs="*", help="Bam files.")
parser.add_argument("-o", "--out", dest="out", required=1,
help="dir of output files")
parser.add_argument("--sps",
help="species")
parser.add_argument("--keep-name", action="store_true",
default=False,
help="Use sequence name in the Attribute column.")
parser.add_argument("--hairpin", help="hairpin.fa")
parser.add_argument("--gtf",
help="GFF file with precursor and mature position to genome.")
parser.add_argument("--format", help="Input format, default BAM file.",
choices=['BAM', 'seqbuster', 'srnabench',
'prost', 'isomirsea', 'optimir',
'manatee', 'gff'], default="BAM")
parser.add_argument("--out-format", help="Supported formats: gff3 or gtf",
choices=["gff", "gft"], default="gff")
parser.add_argument("--add-extra", help="Add extra attributes to gff",
action="store_true")
parser.add_argument("--database", help="Custom database name",
default=None)
parser.add_argument("--genomic", action="store_true", default=False,
help="BAM file is mapped against genome.")
parser.add_argument("--out-genomic", action="store_true", default=False,
help="output in genomic coordinates.")
parser.add_argument("--low-memory", action="store_true", default=False,
help="Read File by chunks. Only supported for BAM files.")
parser = _add_debug_option(parser)
return parser
def _add_subparser_export(subparsers):
parser = subparsers.add_parser("export", help="export GFF into other format")
parser.add_argument("files", nargs="*", help="GFF files.")
parser.add_argument("-o", "--out", dest="out", required=1,
help="dir of output files")
parser.add_argument("--sps",
help="species")
parser.add_argument("--hairpin", help="hairpin.fa")
parser.add_argument("--gtf", help="gtf file with precursor and mature position to genome.")
parser.add_argument("--format", help="Output format",
choices=['seqbuster', 'fasta', 'vcf', 'isomir'], default="isomir")
parser = _add_debug_option(parser)
return parser
def _add_subparser_target(subparsers):
parser = subparsers.add_parser("target", help="Annotate miRNA targets.")
parser.add_argument("--input", required=1,
help="list of miRNAs in 1 column format")
parser.add_argument("--sps", required=1,
help="species")
parser.add_argument("-o", "--out", dest="out", required=1,
help="dir of output files")
parser.add_argument("--annotation", required=1,
help="Folder with tarets annotation. If bcbio installed would be the srnaseq ffolder")
parser = _add_debug_option(parser)
return parser
def _add_subparser_simulator(subparsers):
parser = subparsers.add_parser("simulator", help="simulate small RNAfrom fasta/bed file")
parser.add_argument("--bed",
help="bed file with position of precursors <=200 nt")
parser.add_argument("--fasta", help="fasta with precursors.")
parser.add_argument("-o", "--out", dest="out", required=1,
help="dir of output files")
parser.add_argument("-r", "--reference", dest="ref",
help="reference fasta file with index"),
parser = _add_debug_option(parser)
return parser
def _add_subparser_counts(subparsers):
parser = subparsers.add_parser("counts", help="extract expression counts for each sample for mirna/variants")
parser.add_argument("--gff",
help="/path/to/GFF/file/file.gff", required = 1)
parser.add_argument("-o", "--out",
required=True,
help="/path/to/output/directory")
parser.add_argument("--add-extra", help="Add extra attributes to gff", action="store_true")
parser.add_argument("--hairpin", help="hairpin.fa")
parser.add_argument("--gtf", help="gtf/gff file with precursor and mature position to genome.")
parser.add_argument("--sps",
help="species")
parser = _add_debug_option(parser)
return parser
def _add_subparser_validator(subparsers):
parser = subparsers.add_parser("validate", help="validate if the file has the correct format")
parser.add_argument("files", nargs="*", help="GFF files")
parser.add_argument("-o", "--out", dest="out", default="tmp_mirtop",
help="folder of output files")
parser = _add_debug_option(parser)
return parser
def _add_subparser_spikein(subparsers):
parser = subparsers.add_parser("spikein",
help="Work with spike-ins.")
parser.add_argument("file", help="FASTA file with spikeins.")
parser.add_argument("-o", "--out", dest="out",
help="folder of output files")
parser = _add_debug_option(parser)
return parser
def _add_subparser_update(subparsers):
parser = subparsers.add_parser("update",
help="update GFF to current format version.")
parser.add_argument("files", nargs="*", help="GFF/GTF files.")
parser.add_argument("-o", "--out", dest="out", default="tmp_mirtop",
help="folder of output files")
parser = _add_debug_option(parser)
return parser
mirtop-0.4.23/mirtop/libs/read.py 0000664 0000000 0000000 00000000451 13547635037 0016657 0 ustar 00root root 0000000 0000000 """functions for explore tool"""
from __future__ import print_function
from mirtop.libs.do import run
def get_fasta(bed_file, ref, out_fa):
"""Run bedtools to get fasta from bed file"""
cmd = "bedtools getfasta -s -fi {ref} -bed {bed_file} -fo {out_fa}"
run(cmd.format(**locals()))
mirtop-0.4.23/mirtop/libs/simulator.py 0000664 0000000 0000000 00000006563 13547635037 0017775 0 ustar 00root root 0000000 0000000 """simulate cluster over the genome"""
from __future__ import print_function
import random
from mirtop.libs.read import get_fasta
def simulate(args):
"""Main function that manage simulation of small RNAs
"""
reads = dict()
if args.fasta:
name = None
seq = ""
with open(args.fasta) as in_handle:
for line in in_handle:
if line.startswith(">"):
if name:
reads.update(_generate_reads(seq, name))
seq = ""
name = line[1:-1]
else:
seq += line.strip()
reads.update(_generate_reads(seq, name))
if reads:
_write_reads(reads, args.out)
def _generate_reads(seq, name):
"""Main function that create reads from precursors"""
reads = dict()
if len(seq) < 150 and len(seq) > 70:
reads.update(_mature(seq[:40], 0, name))
reads.update(_mature(seq[-40:], len(seq) - 40, name))
reads.update(_noise(seq, name))
reads.update(_noise(seq, name, 25))
return reads
def _mature(subseq, absolute, c, size=33, total=5000):
"""Create mature sequences around start/end"""
reads = dict()
probs = [0.1, 0.2, 0.4, 0.2, 0.1]
end = 5 + size
error = [-2, -1, 0, 1, 2]
for error5 in error:
for error3 in error:
s = 5 - error5
e = end - error3
seen = subseq[s:e]
counts = int(probs[error5 + 2] * probs[error3 + 2] * total) + 1
name = "seq_%s_%s_%s_x%s" % (c, s + absolute, e + absolute, counts)
reads[name] = (seen, counts)
return reads
def _noise(seq, c, size=33, total=1000):
"""Create mature sequences around start/end"""
reads = dict()
seen = 0
while seen < total:
s = random.randint(0, len(seq) - size)
e = s + size + random.randint(-5,5)
p = random.uniform(0, 0.1)
counts = int(p * total) + 1
seen += counts
name = "seq_%s_%s_%s_x%s" % (c, s, e, counts)
reads[name] = (seq[s:e], counts)
return reads
def _write_reads(reads, prefix):
"""
Write fasta file, ma file and real position
"""
out_ma = prefix + ".ma"
out_fasta = prefix + ".fasta"
out_real = prefix + ".txt"
with open(out_ma, 'w') as ma_handle:
print("id\tseq\tsample", file=ma_handle)
with open(out_fasta, 'w') as fa_handle:
with open(out_real, 'w') as read_handle:
for idx, r in enumerate(reads):
info = r.split("_")
print("seq_%s\t%s\t%s" % (idx, reads[r][0], reads[r][1]), file=ma_handle)
print(">seq_%s\n%s" % (idx, reads[r][0]), file=fa_handle)
print("%s\t%s\t%s\t%s\t%s\t%s\t%s" % (idx, r, reads[r][0], reads[r][1], info[1], info[2], info[3]), file=read_handle)
def _get_precursor(bed_file, reference, out_fa):
"""
get sequence precursor from position
"""
get_fasta(bed_file, reference, out_fa)
return 0
def _get_spot(precursor):
"""
get spot that will be enriched
"""
return 0
def _get_type(pob):
"""
randomly decide if is small rna or degradation
"""
return 0
def _random_sequences(precursor, start= None, end=None):
"""
randomly get sequences around some nucleotides.
It could be enriched in some positions
"""
return 0
mirtop-0.4.23/mirtop/libs/spikeins.py 0000664 0000000 0000000 00000006471 13547635037 0017601 0 ustar 00root root 0000000 0000000 """This code helps to work with spikeins"""
import os
from collections import defaultdict
from mirtop.libs import fastq
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def convert(args):
out_dir = args.out if args.out else os.path.dirname(args.file)
gff_file = os.path.join(out_dir, "spikeins_pre.gff")
fasta_file = os.path.join(out_dir, "spikeins_pre.fasta")
spikes = read_spikeins(args.file)
write_gff(spikes, gff_file)
logger.info("GFF file is at %s" % gff_file)
write_precursors(spikes, fasta_file)
logger.info("FASTA file is at %s" % fasta_file)
def read_spikeins(in_file):
"""Read FASTA file containing small spikeins
Args:
*in_file(str)*: file name with sequences.
Returns:
*spikeins(dict)*: dictionary with keys being names
and values being: given spike-in, synthetic precursor and
position on the synthetic precursor.
"""
spikeins = defaultdict(dict)
with fastq.open_fastq(in_file) as inh:
for line in inh:
if line.startswith(">"):
spike = line.strip()[1:].split()[0]
else:
precursor = "GGGGG" + line.strip() + "GGGGG"
pos = [5, 4 + len(line.strip())]
logger.debug("SPIKE::NAME::%s -> %s" % (spike, line.strip()))
logger.debug("SPIKE::GENERATED::precursor::%s" % precursor)
logger.debug("SPIKE::GENERATED::position::%s" % pos)
spikeins[spike] = {'mature': line.strip(),
'precursor': precursor,
'position': pos}
return spikeins
def write_precursors(spikeins, out_file):
"""
Write FASTA file for precursors to be used to annotate isomiRs
Args:
*spikeins(dict)*: output from read_spikeins
*out_file*: file name to write the FASTA information
"""
with open(out_file, 'w') as outh:
for spike in spikeins:
outh.write(">pre-{0}\n{1}\n".format(spike,
spikeins[spike]['precursor']))
def write_gff(spikeins, out_file):
"""
Write GTF file for precursors to be used to annotate isomiRs
Args:
*spikeins(dict)*: output from read_spikeins
*out_file*: file name to write the GFF information
"""
with open(out_file, 'w') as outh:
outh.write("#microRNAs: spikeins_v1\n")
for spike in spikeins:
outh.write("\t".join(["chr%s" % spike, ".",
"miRNA_primary_transcript",
"1",
str(len(spikeins[spike]['precursor'])),
".", "+", ".",
"Name=pre-%s;ID=pre-%s" % (spike, spike),
"\n"]))
outh.write("\t".join(["chr%s" % spike, ".", "miRNA",
str(spikeins[spike]['position'][0] + 1),
str(spikeins[spike]['position'][1] + 1),
".", "+", ".",
"Derives_from=pre-%s;"
"Name=%s;ID=%s;" % (spike, spike, spike),
"\n"]))
mirtop-0.4.23/mirtop/libs/sql.py 0000664 0000000 0000000 00000002757 13547635037 0016556 0 ustar 00root root 0000000 0000000 import sqlite3
from sqlite3 import Error
def create_connection():
""" create a database connection to the SQLite database
specified by the db_file
:return: Connection object or None
"""
try:
conn = sqlite3.connect(":memory:")
return conn
except Error as e:
print(e)
return None
def create_reads_table(conn, key="sequence"):
""" create a table on the SQLite database
:param conn: connection of database
:return: Connection object or None
"""
c = conn.cursor()
c.execute("CREATE TABLE reads"
" (name text, sequence text,"
" chrom text, start int,"
" PRIMARY KEY(%s, chrom, start))" % key)
conn.commit()
def insert_row_in_reads_table(cur, fields):
""" create a table on the SQLite database
:param cur: connection of database
:param fields: list with columns to fill table
:return: Connection object or None
"""
# c = conn.cursor()
cur.execute("INSERT INTO reads VALUES"
" (\"%s\", \"%s\", \"%s\", %s)" % (fields[0],
fields[1],
fields[2],
fields[3]))
def select_all_reads(conn):
"""
Query all rows in the reads table
:param conn: the Connection object
:return:
"""
cur = conn.cursor()
cur.execute("SELECT * FROM reads")
rows = cur.fetchall()
return rows
mirtop-0.4.23/mirtop/libs/utils.py 0000664 0000000 0000000 00000001630 13547635037 0017104 0 ustar 00root root 0000000 0000000 """utils from http://www.github.com/chapmanb/bcbio-nextgen.git"""
import os
import shutil
import contextlib
@contextlib.contextmanager
def chdir(p):
"""Change dir temporaly using `with`:
>>> with chdir(temporal):
do_something()
"""
cur_dir = os.getcwd()
os.chdir(p)
try:
yield
finally:
os.chdir(cur_dir)
def safe_dirs(dirs):
"""Create folder if not exitsts
"""
if not os.path.exists(dirs):
os.makedirs(dirs)
return dirs
def safe_remove(fn):
"""Remove file skipping
"""
if os.path.exists(fn):
if os.path.isfile(fn):
os.remove(fn)
elif os.path.isdir(fn):
shutil.rmtree(fn)
def file_exists(fname):
"""Check if a file exists and is non-empty.
"""
try:
return fname and os.path.exists(fname) and os.path.getsize(fname) > 0
except OSError:
return False
mirtop-0.4.23/mirtop/mirna/ 0000775 0000000 0000000 00000000000 13547635037 0015547 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/mirna/README_TermsOfUse_MINTplates.txt 0000664 0000000 0000000 00000005036 13547635037 0023425 0 ustar 00root root 0000000 0000000 MINTcodes "license-plates"
------------------------------
1. General Information
----------------------
This code was created by Venetia Pliatsika, Isidore Rigoutsos, Jeffery Ma, Phillipe Loher
It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates"
back to sequences. While initially created for tRFs (tRNA fragments), this tool can be used for
any genomic sequences including but not limited to: tRFs, isomiRs, reference miRNA, etc.
For more information on "license-plates", visit https://cm.jefferson.edu/MINTbase and
refer to publications https://www.ncbi.nlm.nih.gov/pubmed/27153631/ and https://www.ncbi.nlm.nih.gov/pubmed/28220888/.
Contact us at: https://cm.jefferson.edu/contact-us/
2. Terms of Use
---------------
This code can be freely used for research, academic and other non-profit activities.
Only one instance of the code may be used at a time, and then for only one concurrent user. You may not
use the code to conduct any type of application service, service bureau or time-sharing operation or to
provide any remote processing, network processing, network telecommunications or similar services to
any person, entity or organization, whether on a fee basis or otherwise. The code can be copied and
compiled on any platform for the use authorized by these terms and conditions. All copies of the code
must be accompanied by this note. The code cannot be modified without the written permission of the
Computational Medicine Center of Thomas Jefferson University https://cm.jefferson.edu
Commercial use is strictly prohibited. If you wish to use these codes commercially please contact the
Computational Medicine Center of Thomas Jefferson University: https://cm.jefferson.edu/contact-us/
THE CODE IS PROVIDED “AS IS” WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESSED
OR IMPLIED. TO THE FULLEST EXTENT PERMISSIBLE PURSUANT TO APPLICABLE LAW. THOMAS JEFFERSON
UNIVERSITY, AND ITS AFFILIATES, DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NON-INFRINGEMENT.
NEITHER THOMAS JEFFERSON UNIVERSITY NOR ITS AFFILIATES MAKE ANY REPRESENTATION AS TO THE RESULTS
TO BE OBTAINED FROM USE OF THE CODE.
3. Usage Information
--------------------
Usage (Python 2 and 3 compatible):
python MINTplates.py example_sequences_to_encode.txt en --p [prefix to add to license plate]
python MINTplates.py example_license_plates_to_decode.txt de --p [optional prefix, not used in decoding] mirtop-0.4.23/mirtop/mirna/__init__.py 0000664 0000000 0000000 00000000000 13547635037 0017646 0 ustar 00root root 0000000 0000000 mirtop-0.4.23/mirtop/mirna/annotate.py 0000664 0000000 0000000 00000010160 13547635037 0017730 0 ustar 00root root 0000000 0000000 """ Read bam files"""
import copy
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def _coord(sequence, start, mirna, precursor, iso):
"""
Define t5 and t3 isomirs
"""
insertion = 0
deletion = 0
add = 0
if iso.subs:
insertion = sum([1 if s[-1] == "-" else 0 for s in iso.subs])
if iso.subs:
deletion = sum([1 if s[1] == "-" else 0 for s in iso.subs])
if iso.add:
add = len(iso.add)
end = (iso.end - add - insertion + deletion)
logger.debug("COOR:: s:%s len:%s end:%s fixedEnd:%s mirna:%s iso:%s" % (
start, len(sequence), iso.end, end, mirna, iso.format())
)
dif = abs(mirna[0] - start)
if start < mirna[0]:
iso.t5 = sequence[:dif].upper()
elif start > mirna[0]:
iso.t5 = precursor[mirna[0]:mirna[0] + dif].lower()
elif start == mirna[0]:
iso.t5 = 0
if dif > 6:
logger.debug("COOR::start > 6 start:%s len:%s dif:%s mirna:%s iso:%s" % (
start, len(sequence),
dif, mirna, iso.format()))
return None
dif = abs(mirna[1] - iso.end)
if iso.add:
iso.add = iso.add.replace("-", "")
sequence = sequence[:-len(iso.add)]
if end > mirna[1]:
iso.t3 = sequence[-dif:].upper()
elif end < mirna[1]:
iso.t3 = precursor[mirna[1] + 1 - dif:(mirna[1] + 1)].lower()
elif end == mirna[1]:
iso.t3 = 0
if dif > 7:
logger.debug("COOR::end > 7 len:%s end:%s dif:%s mirna:%s iso:%s" % (
len(sequence), end, dif, mirna, iso.format()))
return None
return True
def annotate(reads, mature_ref, precursors, quiet=False):
"""
Using coordinates, mismatches and realign to annotate isomiRs
Args:
*reads(dicts of hits)*:
dict object that comes from *mirotp.bam.bam.read_bam()*
*mirbase_ref (dict of mirna positions)*:
dict object that comers from *mirtop.mirna.read_mature()*
*precursors dict object (key : fasta)*:
that comes from *mirtop.mirna.fasta.read_precursor()*
*quiet(boolean)*:
verbosity state
Return:
*reads (dict)*:
dictionary where keys are read_id and
values are *mirtop.realign.hits*
"""
n_iso = 0
n_skip_precursor = 0
for r in reads:
logger.debug(("\nANN::READ::read {r}").format(**locals()))
for ps in reads[r].precursors:
p = list(ps)[0]
start = reads[r].precursors[ps].start
end = reads[r].precursors[ps].end
logger.debug(("\nANN::READ::precursor {start} {end}").format(**locals()))
for mature in mature_ref[p]:
mi = mature_ref[p][mature]
logger.debug(("\nANN::NEW::read:{s}\n pre:{p} start:{start} end: {end} "
"cigar: {cigar} "
"\n mir:{mature} mir_pos:{mi}\n mir_seqs:{mature_s}"
).format(s=reads[r].sequence,
mature_s = precursors[ps][mi[0]:mi[1] + 1],
cigar = reads[r].precursors[ps].cigar,
**locals()))
iso_copy = copy.deepcopy(reads[r].precursors[ps])
if not precursors[ps[0]]:
n_skip_precursor += 1
continue
is_iso = _coord(reads[r].sequence, start, mi, precursors[ps[0]], iso_copy)
logger.debug(("ANN::is_iso:{is_iso}").format(**locals()))
logger.debug("ANN::annotation:%s iso:%s" % (r, reads[r].precursors[ps].format()))
logger.debug("ANN::annotation:%s Variant:%s" % (r, reads[r].precursors[ps].formatGFF()))
if is_iso:
n_iso += 1
reads[r].precursors[ps] = iso_copy
reads[r].precursors[ps].mirna = mature
# break
if not quiet:
logger.info("Valid hits (+/- reference miRNA): %s" % n_iso)
logger.info("Skipped due to not precursor sequence: %s" % n_skip_precursor)
return reads
mirtop-0.4.23/mirtop/mirna/fasta.py 0000664 0000000 0000000 00000002364 13547635037 0017224 0 ustar 00root root 0000000 0000000 """Read precursor fasta file"""
from collections import defaultdict
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def read_precursor(precursor, sps=None):
"""
Load precursor file for that species
Args:
*precursor(str)*: file name with fasta sequences
*sps(str)*: if any, select species to keep.
It'll do a `header_sequence.find(sps)`.
Returns:
*hairpin(dict)*: keys are precursor names and
values are precursor sequences.
"""
hairpin = defaultdict(str)
name = None
with open(precursor) as in_handle:
for line in in_handle:
if line.startswith(">"):
if name in hairpin:
hairpin[name] = hairpin[name] + "NNNNNNNNNNNN"
if not sps or line.find(sps) > -1:
name = line.strip().replace(">", " ").split()[0]
else:
name = None
logger.debug("PRECURSOR::name %s" % name)
elif name:
hairpin[name] += line.strip().replace("U", "T")
logger.debug("PRECURSOR::sequence %s" % hairpin[name])
if name:
hairpin[name] = hairpin[name] + "NNNNNNNNNNNN"
return hairpin
mirtop-0.4.23/mirtop/mirna/keys.py 0000664 0000000 0000000 00000004031 13547635037 0017072 0 ustar 00root root 0000000 0000000 CODE2NT = {
'#': 'CCC',
'$': 'GGG',
'%': 'TTT',
'0': 'TCT',
'3': 'GTG',
'4': 'GAG',
'5': 'GTT',
'6': 'GCT',
'7': 'TGA',
'8': 'GAC',
'9': 'TCC',
'@': 'AAA',
'A': 'GGT',
'B': 'TGT',
'C': 'CGA',
'D': 'CAG',
'E': 'CGC',
'F': 'GAT',
'G': 'CGG',
'H': 'CTT',
'I': 'TGC',
'J': 'TAG',
'K': 'GGA',
'L': 'TAA',
'M': 'GGC',
'N': 'TAC',
'O': 'TTC',
'P': 'TCG',
'Q': 'TTA',
'R': 'TTG',
'S': 'CGT',
'T': 'GAA',
'U': 'TCA',
'V': 'GCA',
'W': 'GTA',
'X': 'GCC',
'Y': 'GTC',
'Z': 'GCG',
'a': 'ACC',
'b': 'ATG',
'c': 'AAG',
'd': 'ACG',
'e': 'ATC',
'f': 'AAC',
'g': 'ATA',
'h': 'AGG',
'i': 'CCT',
'j': 'CTC',
'k': 'AGC',
'l': 'ACA',
'm': 'AGA',
'n': 'CAT',
'o': 'AAT',
'p': 'ATT',
'q': 'CTG',
'r': 'CTA',
's': 'ACT',
't': 'CAC',
'u': 'TGG',
'v': 'CAA',
'w': 'AGT',
'x': 'CCA',
'y': 'CCG',
'z': 'TAT'}
NT2CODE = {
'AAA': '@',
'AAC': 'f',
'AAG': 'c',
'AAT': 'o',
'ACA': 'l',
'ACC': 'a',
'ACG': 'd',
'ACT': 's',
'AGA': 'm',
'AGC': 'k',
'AGG': 'h',
'AGT': 'w',
'ATA': 'g',
'ATC': 'e',
'ATG': 'b',
'ATT': 'p',
'CAA': 'v',
'CAC': 't',
'CAG': 'D',
'CAT': 'n',
'CCA': 'x',
'CCC': '#',
'CCG': 'y',
'CCT': 'i',
'CGA': 'C',
'CGC': 'E',
'CGG': 'G',
'CGT': 'S',
'CTA': 'r',
'CTC': 'j',
'CTG': 'q',
'CTT': 'H',
'GAA': 'T',
'GAC': '8',
'GAG': '4',
'GAT': 'F',
'GCA': 'V',
'GCC': 'X',
'GCG': 'Z',
'GCT': '6',
'GGA': 'K',
'GGC': 'M',
'GGG': '$',
'GGT': 'A',
'GTA': 'W',
'GTC': 'Y',
'GTG': '3',
'GTT': '5',
'TAA': 'L',
'TAC': 'N',
'TAG': 'J',
'TAT': 'z',
'TCA': 'U',
'TCC': '9',
'TCG': 'P',
'TCT': '0',
'TGA': '7',
'TGC': 'I',
'TGG': 'u',
'TGT': 'B',
'TTA': 'Q',
'TTC': 'O',
'TTG': 'R',
'TTT': '%'}
mirtop-0.4.23/mirtop/mirna/mapper.py 0000664 0000000 0000000 00000034512 13547635037 0017412 0 ustar 00root root 0000000 0000000 """Read database information"""
from collections import defaultdict
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def guess_database(args):
"""
Guess database name from GFF file.
Args:
*gtf(str)*: file name with GFF miRNA genomic positions and
header lines.
Returns:
*database(str)*: name of the database
TODO: this needs to be generic to other databases.
"""
return _guess_database_file(args.gtf, args.database)
def _guess_database_file(gff, database=None):
with open(gff) as in_handle:
for line in in_handle:
if not line.startswith("#"):
break
if line.find("miRBase") > -1:
database = line[line.find("miRBase"):].strip().replace(" ", "")
elif line.find("MirGeneDB") > -1:
database = line[line.find("MirGeneDB"):].strip().replace(" ", "")
elif line.find("microRNAs") > -1:
database = line.strip().split()[1]
if not database:
logger.error("Database not found in --mirna %s. "
"Use --database argument to add a custom source." % gff)
raise ValueError("Database not found in %s header" % gff)
return database
def get_primary_transcript(database):
"""
Get the ID to identify the primary transcript in the
GTF file with the miRNA and precursor coordinates
to be able to parse BAM files with genomic
coordinates.
"""
if database.find("miRBase") > -1:
return "miRNA_primary_transcript"
else:
raise ValueError("Only miRBase is supported for this action.")
def read_gtf_to_mirna(gtf):
"""
Load GTF file with precursor positions on genome.
Args:
*gtf(str)*: file name with GFF miRNA genomic positions and
header lines.
Returns:
*db_mir(dict)*: dictionary with keys being mirnas and values
genomic positions.
"""
if not gtf:
return gtf
if _guess_database_file(gtf).find("miRBase") > -1:
mapped = read_gtf_to_precursor_mirbase(gtf, format="genomic")
elif _guess_database_file(gtf).find("MirGeneDB") > -1:
mapped = read_gtf_to_precursor_mirgenedb(gtf, format="genomic")
else:
logger.info("Database different than miRBase or MirGeneDB")
logger.info("If you get an error when loading,")
logger.info("report it to https://github.com/miRTop/mirtop/issues")
mapped = read_gtf_to_precursor_mirbase(gtf)
return mapped
def read_gtf_chr2mirna(gtf): # read from read_gtf_to_precursor
"""
Load GTF file with precursor positions on genome.
Args:
*gtf(str)*: file name with GFF miRNA genomic positions and
header lines.
Returns:
*db_mir(dict)*: dictionary with keys being chr and values
mirna and genomic positions.
"""
if not gtf:
return gtf
if _guess_database_file(gtf).find("miRBase") > -1:
mapped = read_gtf_to_precursor_mirbase(gtf, format="chrom")
elif _guess_database_file(gtf).find("MirGeneDB") > -1:
mapped = read_gtf_to_precursor_mirgenedb(gtf, format="chrom")
else:
logger.info("Database different than miRBase or MirGeneDB")
logger.info("If you get an error when loading,")
logger.info("report it to https://github.com/miRTop/mirtop/issues")
mapped = read_gtf_to_precursor_mirbase(gtf)
return mapped
def read_gtf_chr2mirna2(gtf): # to remove
mir2hairpin = read_gtf_to_precursor(gtf)
if not gtf:
return gtf
db = defaultdict(list)
db_mir = defaultdict(list)
id_dict = dict()
with open(gtf) as in_handle:
for line in in_handle:
if line.startswith("#"):
continue
cols = line.strip().split("\t")
logger.debug("MAP:: line:%s" % cols)
name = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("Name")]
idname = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("ID")]
chrom, start, end, strand = cols[0], cols[3], cols[4], cols[6]
logger.debug("MAP:: idname:%s" % idname)
logger.debug("MAP:: name:%s" % name)
id_dict[idname[0]] = name[0] # MIMA to sps-Y-X-5/3p
if cols[2] == "miRNA_primary_transcript":
db[idname[0]] = [chrom, int(start), int(end), strand]
if cols[2] == "miRNA":
parent = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("Derives_from")]
parent_name = id_dict[parent[0]]
db_mir[chrom].append([name[0], start, end,
strand,
parent_name,
mir2hairpin[parent_name][name[0]][0]])
logger.debug("MAP:: mirna:%s" % name[0])
logger.debug("MAP:: precursor:%s" % parent_name)
logger.debug("MAP:: precursor pos %s" % mir2hairpin[parent_name][name[0]])
return db_mir
def read_gtf_to_precursor(gtf):
"""
Load GTF file with precursor positions on genome
Return dict with key being precursor name and
value a dict of mature miRNA with relative position
to precursor.
Args:
*gtf(str)*: file name with GFF miRNA genomic positions and
header lines.
Returns:
*map_dict(dict)*:
>>> {'parent': {mirna: [start, end]}}
"""
if not gtf:
return gtf
if _guess_database_file(gtf).find("miRBase") > -1:
mapped = read_gtf_to_precursor_mirbase(gtf)
elif _guess_database_file(gtf).find("MirGeneDB") > -1:
mapped = read_gtf_to_precursor_mirgenedb(gtf)
else:
logger.info("Database different than miRBase or MirGeneDB")
logger.info("If you get an error when loading,")
logger.info("report it to https://github.com/miRTop/mirtop/issues")
mapped = read_gtf_to_precursor_mirbase(gtf)
return mapped
def _parse_db_mir_chrom(db_mir, db, id_dict):
mir2hairpin = _parse_db_mir(db_mir, db, id_dict)
map_dict = defaultdict(list)
for mir in db_mir:
parent = db_mir[mir][4]
precursor = db[id_dict[parent]]
logger.debug("MAP::%s %s %s" % (
id_dict[parent], precursor[1], precursor[2]))
logger.debug("MAP::%s %s %s" % (mir, db_mir[mir][1], db_mir[mir][2]))
if precursor[3] != db_mir[mir][3]:
logger.warning("%s -> %s" % (id_dict[parent], mir))
logger.warning("miRNA strand doesn't match with precursor strand:"
" %s - %s" % (db_mir[mir][3], precursor[3]))
next
if precursor[0] != db_mir[mir][0]:
logger.warning("%s -> %s" % (id_dict[parent], mir))
logger.warning("miRNA chr doesn't match with precursor chr:"
" %s - %s" % (db_mir[mir][0], precursor[0]))
next
map_dict[db_mir[mir][0]].append([mir[1], db_mir[mir][1], db_mir[mir][2],
db_mir[mir][3],
id_dict[parent],
mir2hairpin[id_dict[parent]][mir[1]][0]])
return map_dict
def _parse_db_mir(db_mir, db, id_dict):
map_dict = defaultdict(dict)
for mir in db_mir:
parent = db_mir[mir][4]
precursor = db[id_dict[parent]]
logger.debug("MAP::%s %s %s" % (
id_dict[parent], precursor[1], precursor[2]))
logger.debug("MAP::%s %s %s" % (mir, db_mir[mir][1], db_mir[mir][2]))
if precursor[3] != db_mir[mir][3]:
logger.warning("%s -> %s" % (id_dict[parent], mir))
logger.warning("miRNA strand doesn't match with precursor strand:"
" %s - %s" % (db_mir[mir][3], precursor[3]))
next
if precursor[0] != db_mir[mir][0]:
logger.warning("%s -> %s" % (id_dict[parent], mir))
logger.warning("miRNA chr doesn't match with precursor chr:"
" %s - %s" % (db_mir[mir][0], precursor[0]))
next
if precursor[3] == "+":
start = db_mir[mir][1] - precursor[1]
end = db_mir[mir][2] - precursor[1]
if precursor[3] == "-":
end = precursor[2] - db_mir[mir][1]
start = precursor[2] - db_mir[mir][2]
logger.debug("MAP:: final:%s %s %s" % (mir[1], start, end))
map_dict[id_dict[parent]][mir[1]] = [start, end, db_mir[mir][3]]
return map_dict
def _parse_db_mir_genomic(db_mir, db, id_dict):
map_dict = defaultdict(dict)
for mir in db_mir:
parent = db_mir[mir][4]
precursor = db[id_dict[parent]]
logger.debug("MAP::%s %s %s" % (
id_dict[parent], precursor[1], precursor[2]))
logger.debug("MAP::%s %s %s" % (mir, db_mir[mir][1], db_mir[mir][2]))
if precursor[3] != db_mir[mir][3]:
logger.warning("%s -> %s" % (id_dict[parent], mir))
logger.warning("miRNA strand doesn't match with precursor strand:"
" %s - %s" % (db_mir[mir][3], precursor[3]))
next
if precursor[0] != db_mir[mir][0]:
logger.warning("%s -> %s" % (id_dict[parent], mir))
logger.warning("miRNA chr doesn't match with precursor chr:"
" %s - %s" % (db_mir[mir][0], precursor[0]))
next
map_dict[mir[1]].update({id_dict[parent]: db_mir[mir]})
return map_dict
def read_gtf_to_precursor_mirgenedb(gtf, format="precursor"):
"""
Load GTF file with precursor positions on genome
Return dict with key being precursor name and
value a dict of mature miRNA with relative position
to precursor. For MirGeneDB and similar GFF3 files.
Args:
*gtf(str)*: file name with GFF miRNA genomic positions and
header lines.
Returns:
*map_dict(dict)*:
>>> {'parent': {mirna: [start, end]}}
"""
if not gtf:
return gtf
db = defaultdict(list)
db_mir = defaultdict(list)
id_dict = dict()
with open(gtf) as in_handle:
for line in in_handle:
if line.startswith("#"):
continue
cols = line.strip().split("\t")
idname = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("ID")][0]
name = idname
chrom, start, end, strand = cols[0], cols[3], cols[4], cols[6]
id_dict[idname] = name
if cols[2] == "pre_miRNA":
db[name] = [chrom, int(start), int(end), strand]
if cols[2] == "miRNA":
idname_mi = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("ID")][0]
parent = "%s_pre" % idname_mi.split("_")[0]
db_mir[(parent, name)] = [chrom,
int(start), int(end),
strand, parent]
logger.debug("MAP:: mirna:%s" % name)
logger.debug("MAP:: pos %s" % db_mir[(parent, name)])
if format == "genomic":
return _parse_db_mir_genomic(db_mir, db, id_dict)
elif format == "chrom":
return _parse_db_mir_chrom(db_mir, db, id_dict)
return _parse_db_mir(db_mir, db, id_dict)
def read_gtf_to_precursor_mirbase(gtf, format="precursor"):
"""
Load GTF file with precursor positions on genome
Return dict with key being precursor name and
value a dict of mature miRNA with relative position
to precursor. For miRBase and similar GFF3 files.
Args:
*gtf(str)*: file name with GFF miRNA genomic positions and
header lines.
Returns:
*map_dict(dict)*:
>>> {'parent': {mirna: [start, end]}}
"""
if not gtf:
return gtf
db = defaultdict(list)
db_mir = defaultdict(list)
id_dict = dict()
with open(gtf) as in_handle:
for line in in_handle:
if line.startswith("#"):
continue
cols = line.strip().split("\t")
name = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("Name")]
idname = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("ID")]
chrom, start, end, strand = cols[0], cols[3], cols[4], cols[6]
id_dict[idname[0]] = name[0]
if cols[2] == "miRNA_primary_transcript":
db[name[0]] = [chrom, int(start), int(end), strand]
if cols[2] == "miRNA":
parent = [n.split("=")[1] for n in cols[-1].split(";")
if n.startswith("Derives_from")]
db_mir[(parent[0], name[0])] = [chrom,
int(start), int(end),
strand, parent[0]]
logger.debug("MAP:: mirna:%s" % name[0])
logger.debug("MAP:: pos %s" % db_mir[(parent[0], name[0])])
if format == "genomic":
return _parse_db_mir_genomic(db_mir, db, id_dict)
elif format == "chrom":
return _parse_db_mir_chrom(db_mir, db, id_dict)
return _parse_db_mir(db_mir, db, id_dict)
def liftover_genomic_precursor(read, genome, hairpin, expected=None):
# example 1 LESS (+) strand to miRNAX (+)1010 (->10)
# genome miRNAX [start, end, strand] (+)1009
# hairpin miRNAX [start, end] 9 (1 MORE = 8, 1 LESS = 10)
# hairpin_start - (genome_start - read_start)
# 9 - (1009 - 1010) = 9 - (-1) = 10
if read['strand'] != genome['strand']:
# Add warning
return None
logger.debug("MAPPER::liftover::genomic %s" % genome)
logger.debug("MAPPER::liftover::hairpin %s" % hairpin)
logger.debug("MAPPER::liftover::read %s" % read)
if genome['strand'] == "+":
lifted = hairpin["start"] - (genome["start"] - read["start"])
# example 1 MORE: 1008
# 9 - (1009 - 1008) = 9 - 1 = 8
# example 1 MORE (-) strand: 1010
# hairpin_start - (read_start - genome_start)
# 9 - (1010 - 1009) = 9 - 1 = 8
# example 1 LESS: 1008
# 9 - (1008 - 1009) = 9 - (-1) = 10
elif genome['strand'] == "-":
lifted = hairpin["start"] - (read["end"] - genome["end"])
logger.debug("MAPPER::liftover::lifted %s" % lifted)
if expected and expected != lifted:
raise ValueError("Bad liftover event.")
return lifted
mirtop-0.4.23/mirtop/mirna/mintplates.py 0000664 0000000 0000000 00000157167 13547635037 0020322 0 ustar 00root root 0000000 0000000 #!/usr/bin/env python
"""
MINTplates.py: Terms and conditions located in README_TermsOfUse_MINTplates.txt
This code was created by Venetia Pliatsika, Isidore Rigoutsos, Jeffery Ma, Phillipe Loher
It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates"
back to sequences. While initially created for tRFs (tRNA fragments), this tool can be used for
any genomic sequences including but not limited to: tRFs, isomiRs, reference miRNA, etc.
For more information on "license-plates", visit https://cm.jefferson.edu/MINTbase and
refer to publications https://www.ncbi.nlm.nih.gov/pubmed/27153631/ and https://www.ncbi.nlm.nih.gov/pubmed/28220888/.
Contact us at: https://cm.jefferson.edu/contact-us/
"""
import sys
import re
import argparse
encode_hash = {'AAAAA': 'BB', 'AAAAC': 'BD', 'AAAAG': 'B0', 'AAAAT': 'BE', 'AAACA': 'BF', 'AAACC': 'B1',
'AAACG': 'BH', 'AAACT': 'BI', 'AAAGA': 'B2', 'AAAGC': 'BJ', 'AAAGG': 'BK', 'AAAGT': 'B3',
'AAATA': 'BL', 'AAATC': 'BM', 'AAATG': 'B4', 'AAATT': 'BN', 'AACAA': 'BO', 'AACAC': 'B5',
'AACAG': 'BP', 'AACAT': 'BQ', 'AACCA': 'B6', 'AACCC': 'BR', 'AACCG': 'BS', 'AACCT': 'B7',
'AACGA': 'BU', 'AACGC': 'BV', 'AACGG': 'B8', 'AACGT': 'BW', 'AACTA': 'BX', 'AACTC': 'B9',
'AACTG': 'BY', 'AACTT': 'BZ', 'AAGAA': 'DB', 'AAGAC': 'DD', 'AAGAG': 'D0', 'AAGAT': 'DE',
'AAGCA': 'DF', 'AAGCC': 'D1', 'AAGCG': 'DH', 'AAGCT': 'DI', 'AAGGA': 'D2', 'AAGGC': 'DJ',
'AAGGG': 'DK', 'AAGGT': 'D3', 'AAGTA': 'DL', 'AAGTC': 'DM', 'AAGTG': 'D4', 'AAGTT': 'DN',
'AATAA': 'DO', 'AATAC': 'D5', 'AATAG': 'DP', 'AATAT': 'DQ', 'AATCA': 'D6', 'AATCC': 'DR',
'AATCG': 'DS', 'AATCT': 'D7', 'AATGA': 'DU', 'AATGC': 'DV', 'AATGG': 'D8', 'AATGT': 'DW',
'AATTA': 'DX', 'AATTC': 'D9', 'AATTG': 'DY', 'AATTT': 'DZ', 'ACAAA': '0B', 'ACAAC': '0D',
'ACAAG': '00', 'ACAAT': '0E', 'ACACA': '0F', 'ACACC': '01', 'ACACG': '0H', 'ACACT': '0I',
'ACAGA': '02', 'ACAGC': '0J', 'ACAGG': '0K', 'ACAGT': '03', 'ACATA': '0L', 'ACATC': '0M',
'ACATG': '04', 'ACATT': '0N', 'ACCAA': '0O', 'ACCAC': '05', 'ACCAG': '0P', 'ACCAT': '0Q',
'ACCCA': '06', 'ACCCC': '0R', 'ACCCG': '0S', 'ACCCT': '07', 'ACCGA': '0U', 'ACCGC': '0V',
'ACCGG': '08', 'ACCGT': '0W', 'ACCTA': '0X', 'ACCTC': '09', 'ACCTG': '0Y', 'ACCTT': '0Z',
'ACGAA': 'EB', 'ACGAC': 'ED', 'ACGAG': 'E0', 'ACGAT': 'EE', 'ACGCA': 'EF', 'ACGCC': 'E1',
'ACGCG': 'EH', 'ACGCT': 'EI', 'ACGGA': 'E2', 'ACGGC': 'EJ', 'ACGGG': 'EK', 'ACGGT': 'E3',
'ACGTA': 'EL', 'ACGTC': 'EM', 'ACGTG': 'E4', 'ACGTT': 'EN', 'ACTAA': 'EO', 'ACTAC': 'E5',
'ACTAG': 'EP', 'ACTAT': 'EQ', 'ACTCA': 'E6', 'ACTCC': 'ER', 'ACTCG': 'ES', 'ACTCT': 'E7',
'ACTGA': 'EU', 'ACTGC': 'EV', 'ACTGG': 'E8', 'ACTGT': 'EW', 'ACTTA': 'EX', 'ACTTC': 'E9',
'ACTTG': 'EY', 'ACTTT': 'EZ', 'AGAAA': 'FB', 'AGAAC': 'FD', 'AGAAG': 'F0', 'AGAAT': 'FE',
'AGACA': 'FF', 'AGACC': 'F1', 'AGACG': 'FH', 'AGACT': 'FI', 'AGAGA': 'F2', 'AGAGC': 'FJ',
'AGAGG': 'FK', 'AGAGT': 'F3', 'AGATA': 'FL', 'AGATC': 'FM', 'AGATG': 'F4', 'AGATT': 'FN',
'AGCAA': 'FO', 'AGCAC': 'F5', 'AGCAG': 'FP', 'AGCAT': 'FQ', 'AGCCA': 'F6', 'AGCCC': 'FR',
'AGCCG': 'FS', 'AGCCT': 'F7', 'AGCGA': 'FU', 'AGCGC': 'FV', 'AGCGG': 'F8', 'AGCGT': 'FW',
'AGCTA': 'FX', 'AGCTC': 'F9', 'AGCTG': 'FY', 'AGCTT': 'FZ', 'AGGAA': '1B', 'AGGAC': '1D',
'AGGAG': '10', 'AGGAT': '1E', 'AGGCA': '1F', 'AGGCC': '11', 'AGGCG': '1H', 'AGGCT': '1I',
'AGGGA': '12', 'AGGGC': '1J', 'AGGGG': '1K', 'AGGGT': '13', 'AGGTA': '1L', 'AGGTC': '1M',
'AGGTG': '14', 'AGGTT': '1N', 'AGTAA': '1O', 'AGTAC': '15', 'AGTAG': '1P', 'AGTAT': '1Q',
'AGTCA': '16', 'AGTCC': '1R', 'AGTCG': '1S', 'AGTCT': '17', 'AGTGA': '1U', 'AGTGC': '1V',
'AGTGG': '18', 'AGTGT': '1W', 'AGTTA': '1X', 'AGTTC': '19', 'AGTTG': '1Y', 'AGTTT': '1Z',
'ATAAA': 'HB', 'ATAAC': 'HD', 'ATAAG': 'H0', 'ATAAT': 'HE', 'ATACA': 'HF', 'ATACC': 'H1',
'ATACG': 'HH', 'ATACT': 'HI', 'ATAGA': 'H2', 'ATAGC': 'HJ', 'ATAGG': 'HK', 'ATAGT': 'H3',
'ATATA': 'HL', 'ATATC': 'HM', 'ATATG': 'H4', 'ATATT': 'HN', 'ATCAA': 'HO', 'ATCAC': 'H5',
'ATCAG': 'HP', 'ATCAT': 'HQ', 'ATCCA': 'H6', 'ATCCC': 'HR', 'ATCCG': 'HS', 'ATCCT': 'H7',
'ATCGA': 'HU', 'ATCGC': 'HV', 'ATCGG': 'H8', 'ATCGT': 'HW', 'ATCTA': 'HX', 'ATCTC': 'H9',
'ATCTG': 'HY', 'ATCTT': 'HZ', 'ATGAA': 'IB', 'ATGAC': 'ID', 'ATGAG': 'I0', 'ATGAT': 'IE',
'ATGCA': 'IF', 'ATGCC': 'I1', 'ATGCG': 'IH', 'ATGCT': 'II', 'ATGGA': 'I2', 'ATGGC': 'IJ',
'ATGGG': 'IK', 'ATGGT': 'I3', 'ATGTA': 'IL', 'ATGTC': 'IM', 'ATGTG': 'I4', 'ATGTT': 'IN',
'ATTAA': 'IO', 'ATTAC': 'I5', 'ATTAG': 'IP', 'ATTAT': 'IQ', 'ATTCA': 'I6', 'ATTCC': 'IR',
'ATTCG': 'IS', 'ATTCT': 'I7', 'ATTGA': 'IU', 'ATTGC': 'IV', 'ATTGG': 'I8', 'ATTGT': 'IW',
'ATTTA': 'IX', 'ATTTC': 'I9', 'ATTTG': 'IY', 'ATTTT': 'IZ', 'CAAAA': '2B', 'CAAAC': '2D',
'CAAAG': '20', 'CAAAT': '2E', 'CAACA': '2F', 'CAACC': '21', 'CAACG': '2H', 'CAACT': '2I',
'CAAGA': '22', 'CAAGC': '2J', 'CAAGG': '2K', 'CAAGT': '23', 'CAATA': '2L', 'CAATC': '2M',
'CAATG': '24', 'CAATT': '2N', 'CACAA': '2O', 'CACAC': '25', 'CACAG': '2P', 'CACAT': '2Q',
'CACCA': '26', 'CACCC': '2R', 'CACCG': '2S', 'CACCT': '27', 'CACGA': '2U', 'CACGC': '2V',
'CACGG': '28', 'CACGT': '2W', 'CACTA': '2X', 'CACTC': '29', 'CACTG': '2Y', 'CACTT': '2Z',
'CAGAA': 'JB', 'CAGAC': 'JD', 'CAGAG': 'J0', 'CAGAT': 'JE', 'CAGCA': 'JF', 'CAGCC': 'J1',
'CAGCG': 'JH', 'CAGCT': 'JI', 'CAGGA': 'J2', 'CAGGC': 'JJ', 'CAGGG': 'JK', 'CAGGT': 'J3',
'CAGTA': 'JL', 'CAGTC': 'JM', 'CAGTG': 'J4', 'CAGTT': 'JN', 'CATAA': 'JO', 'CATAC': 'J5',
'CATAG': 'JP', 'CATAT': 'JQ', 'CATCA': 'J6', 'CATCC': 'JR', 'CATCG': 'JS', 'CATCT': 'J7',
'CATGA': 'JU', 'CATGC': 'JV', 'CATGG': 'J8', 'CATGT': 'JW', 'CATTA': 'JX', 'CATTC': 'J9',
'CATTG': 'JY', 'CATTT': 'JZ', 'CCAAA': 'KB', 'CCAAC': 'KD', 'CCAAG': 'K0', 'CCAAT': 'KE',
'CCACA': 'KF', 'CCACC': 'K1', 'CCACG': 'KH', 'CCACT': 'KI', 'CCAGA': 'K2', 'CCAGC': 'KJ',
'CCAGG': 'KK', 'CCAGT': 'K3', 'CCATA': 'KL', 'CCATC': 'KM', 'CCATG': 'K4', 'CCATT': 'KN',
'CCCAA': 'KO', 'CCCAC': 'K5', 'CCCAG': 'KP', 'CCCAT': 'KQ', 'CCCCA': 'K6', 'CCCCC': 'KR',
'CCCCG': 'KS', 'CCCCT': 'K7', 'CCCGA': 'KU', 'CCCGC': 'KV', 'CCCGG': 'K8', 'CCCGT': 'KW',
'CCCTA': 'KX', 'CCCTC': 'K9', 'CCCTG': 'KY', 'CCCTT': 'KZ', 'CCGAA': '3B', 'CCGAC': '3D',
'CCGAG': '30', 'CCGAT': '3E', 'CCGCA': '3F', 'CCGCC': '31', 'CCGCG': '3H', 'CCGCT': '3I',
'CCGGA': '32', 'CCGGC': '3J', 'CCGGG': '3K', 'CCGGT': '33', 'CCGTA': '3L', 'CCGTC': '3M',
'CCGTG': '34', 'CCGTT': '3N', 'CCTAA': '3O', 'CCTAC': '35', 'CCTAG': '3P', 'CCTAT': '3Q',
'CCTCA': '36', 'CCTCC': '3R', 'CCTCG': '3S', 'CCTCT': '37', 'CCTGA': '3U', 'CCTGC': '3V',
'CCTGG': '38', 'CCTGT': '3W', 'CCTTA': '3X', 'CCTTC': '39', 'CCTTG': '3Y', 'CCTTT': '3Z',
'CGAAA': 'LB', 'CGAAC': 'LD', 'CGAAG': 'L0', 'CGAAT': 'LE', 'CGACA': 'LF', 'CGACC': 'L1',
'CGACG': 'LH', 'CGACT': 'LI', 'CGAGA': 'L2', 'CGAGC': 'LJ', 'CGAGG': 'LK', 'CGAGT': 'L3',
'CGATA': 'LL', 'CGATC': 'LM', 'CGATG': 'L4', 'CGATT': 'LN', 'CGCAA': 'LO', 'CGCAC': 'L5',
'CGCAG': 'LP', 'CGCAT': 'LQ', 'CGCCA': 'L6', 'CGCCC': 'LR', 'CGCCG': 'LS', 'CGCCT': 'L7',
'CGCGA': 'LU', 'CGCGC': 'LV', 'CGCGG': 'L8', 'CGCGT': 'LW', 'CGCTA': 'LX', 'CGCTC': 'L9',
'CGCTG': 'LY', 'CGCTT': 'LZ', 'CGGAA': 'MB', 'CGGAC': 'MD', 'CGGAG': 'M0', 'CGGAT': 'ME',
'CGGCA': 'MF', 'CGGCC': 'M1', 'CGGCG': 'MH', 'CGGCT': 'MI', 'CGGGA': 'M2', 'CGGGC': 'MJ',
'CGGGG': 'MK', 'CGGGT': 'M3', 'CGGTA': 'ML', 'CGGTC': 'MM', 'CGGTG': 'M4', 'CGGTT': 'MN',
'CGTAA': 'MO', 'CGTAC': 'M5', 'CGTAG': 'MP', 'CGTAT': 'MQ', 'CGTCA': 'M6', 'CGTCC': 'MR',
'CGTCG': 'MS', 'CGTCT': 'M7', 'CGTGA': 'MU', 'CGTGC': 'MV', 'CGTGG': 'M8', 'CGTGT': 'MW',
'CGTTA': 'MX', 'CGTTC': 'M9', 'CGTTG': 'MY', 'CGTTT': 'MZ', 'CTAAA': '4B', 'CTAAC': '4D',
'CTAAG': '40', 'CTAAT': '4E', 'CTACA': '4F', 'CTACC': '41', 'CTACG': '4H', 'CTACT': '4I',
'CTAGA': '42', 'CTAGC': '4J', 'CTAGG': '4K', 'CTAGT': '43', 'CTATA': '4L', 'CTATC': '4M',
'CTATG': '44', 'CTATT': '4N', 'CTCAA': '4O', 'CTCAC': '45', 'CTCAG': '4P', 'CTCAT': '4Q',
'CTCCA': '46', 'CTCCC': '4R', 'CTCCG': '4S', 'CTCCT': '47', 'CTCGA': '4U', 'CTCGC': '4V',
'CTCGG': '48', 'CTCGT': '4W', 'CTCTA': '4X', 'CTCTC': '49', 'CTCTG': '4Y', 'CTCTT': '4Z',
'CTGAA': 'NB', 'CTGAC': 'ND', 'CTGAG': 'N0', 'CTGAT': 'NE', 'CTGCA': 'NF', 'CTGCC': 'N1',
'CTGCG': 'NH', 'CTGCT': 'NI', 'CTGGA': 'N2', 'CTGGC': 'NJ', 'CTGGG': 'NK', 'CTGGT': 'N3',
'CTGTA': 'NL', 'CTGTC': 'NM', 'CTGTG': 'N4', 'CTGTT': 'NN', 'CTTAA': 'NO', 'CTTAC': 'N5',
'CTTAG': 'NP', 'CTTAT': 'NQ', 'CTTCA': 'N6', 'CTTCC': 'NR', 'CTTCG': 'NS', 'CTTCT': 'N7',
'CTTGA': 'NU', 'CTTGC': 'NV', 'CTTGG': 'N8', 'CTTGT': 'NW', 'CTTTA': 'NX', 'CTTTC': 'N9',
'CTTTG': 'NY', 'CTTTT': 'NZ', 'GAAAA': 'OB', 'GAAAC': 'OD', 'GAAAG': 'O0', 'GAAAT': 'OE',
'GAACA': 'OF', 'GAACC': 'O1', 'GAACG': 'OH', 'GAACT': 'OI', 'GAAGA': 'O2', 'GAAGC': 'OJ',
'GAAGG': 'OK', 'GAAGT': 'O3', 'GAATA': 'OL', 'GAATC': 'OM', 'GAATG': 'O4', 'GAATT': 'ON',
'GACAA': 'OO', 'GACAC': 'O5', 'GACAG': 'OP', 'GACAT': 'OQ', 'GACCA': 'O6', 'GACCC': 'OR',
'GACCG': 'OS', 'GACCT': 'O7', 'GACGA': 'OU', 'GACGC': 'OV', 'GACGG': 'O8', 'GACGT': 'OW',
'GACTA': 'OX', 'GACTC': 'O9', 'GACTG': 'OY', 'GACTT': 'OZ', 'GAGAA': '5B', 'GAGAC': '5D',
'GAGAG': '50', 'GAGAT': '5E', 'GAGCA': '5F', 'GAGCC': '51', 'GAGCG': '5H', 'GAGCT': '5I',
'GAGGA': '52', 'GAGGC': '5J', 'GAGGG': '5K', 'GAGGT': '53', 'GAGTA': '5L', 'GAGTC': '5M',
'GAGTG': '54', 'GAGTT': '5N', 'GATAA': '5O', 'GATAC': '55', 'GATAG': '5P', 'GATAT': '5Q',
'GATCA': '56', 'GATCC': '5R', 'GATCG': '5S', 'GATCT': '57', 'GATGA': '5U', 'GATGC': '5V',
'GATGG': '58', 'GATGT': '5W', 'GATTA': '5X', 'GATTC': '59', 'GATTG': '5Y', 'GATTT': '5Z',
'GCAAA': 'PB', 'GCAAC': 'PD', 'GCAAG': 'P0', 'GCAAT': 'PE', 'GCACA': 'PF', 'GCACC': 'P1',
'GCACG': 'PH', 'GCACT': 'PI', 'GCAGA': 'P2', 'GCAGC': 'PJ', 'GCAGG': 'PK', 'GCAGT': 'P3',
'GCATA': 'PL', 'GCATC': 'PM', 'GCATG': 'P4', 'GCATT': 'PN', 'GCCAA': 'PO', 'GCCAC': 'P5',
'GCCAG': 'PP', 'GCCAT': 'PQ', 'GCCCA': 'P6', 'GCCCC': 'PR', 'GCCCG': 'PS', 'GCCCT': 'P7',
'GCCGA': 'PU', 'GCCGC': 'PV', 'GCCGG': 'P8', 'GCCGT': 'PW', 'GCCTA': 'PX', 'GCCTC': 'P9',
'GCCTG': 'PY', 'GCCTT': 'PZ', 'GCGAA': 'QB', 'GCGAC': 'QD', 'GCGAG': 'Q0', 'GCGAT': 'QE',
'GCGCA': 'QF', 'GCGCC': 'Q1', 'GCGCG': 'QH', 'GCGCT': 'QI', 'GCGGA': 'Q2', 'GCGGC': 'QJ',
'GCGGG': 'QK', 'GCGGT': 'Q3', 'GCGTA': 'QL', 'GCGTC': 'QM', 'GCGTG': 'Q4', 'GCGTT': 'QN',
'GCTAA': 'QO', 'GCTAC': 'Q5', 'GCTAG': 'QP', 'GCTAT': 'QQ', 'GCTCA': 'Q6', 'GCTCC': 'QR',
'GCTCG': 'QS', 'GCTCT': 'Q7', 'GCTGA': 'QU', 'GCTGC': 'QV', 'GCTGG': 'Q8', 'GCTGT': 'QW',
'GCTTA': 'QX', 'GCTTC': 'Q9', 'GCTTG': 'QY', 'GCTTT': 'QZ', 'GGAAA': '6B', 'GGAAC': '6D',
'GGAAG': '60', 'GGAAT': '6E', 'GGACA': '6F', 'GGACC': '61', 'GGACG': '6H', 'GGACT': '6I',
'GGAGA': '62', 'GGAGC': '6J', 'GGAGG': '6K', 'GGAGT': '63', 'GGATA': '6L', 'GGATC': '6M',
'GGATG': '64', 'GGATT': '6N', 'GGCAA': '6O', 'GGCAC': '65', 'GGCAG': '6P', 'GGCAT': '6Q',
'GGCCA': '66', 'GGCCC': '6R', 'GGCCG': '6S', 'GGCCT': '67', 'GGCGA': '6U', 'GGCGC': '6V',
'GGCGG': '68', 'GGCGT': '6W', 'GGCTA': '6X', 'GGCTC': '69', 'GGCTG': '6Y', 'GGCTT': '6Z',
'GGGAA': 'RB', 'GGGAC': 'RD', 'GGGAG': 'R0', 'GGGAT': 'RE', 'GGGCA': 'RF', 'GGGCC': 'R1',
'GGGCG': 'RH', 'GGGCT': 'RI', 'GGGGA': 'R2', 'GGGGC': 'RJ', 'GGGGG': 'RK', 'GGGGT': 'R3',
'GGGTA': 'RL', 'GGGTC': 'RM', 'GGGTG': 'R4', 'GGGTT': 'RN', 'GGTAA': 'RO', 'GGTAC': 'R5',
'GGTAG': 'RP', 'GGTAT': 'RQ', 'GGTCA': 'R6', 'GGTCC': 'RR', 'GGTCG': 'RS', 'GGTCT': 'R7',
'GGTGA': 'RU', 'GGTGC': 'RV', 'GGTGG': 'R8', 'GGTGT': 'RW', 'GGTTA': 'RX', 'GGTTC': 'R9',
'GGTTG': 'RY', 'GGTTT': 'RZ', 'GTAAA': 'SB', 'GTAAC': 'SD', 'GTAAG': 'S0', 'GTAAT': 'SE',
'GTACA': 'SF', 'GTACC': 'S1', 'GTACG': 'SH', 'GTACT': 'SI', 'GTAGA': 'S2', 'GTAGC': 'SJ',
'GTAGG': 'SK', 'GTAGT': 'S3', 'GTATA': 'SL', 'GTATC': 'SM', 'GTATG': 'S4', 'GTATT': 'SN',
'GTCAA': 'SO', 'GTCAC': 'S5', 'GTCAG': 'SP', 'GTCAT': 'SQ', 'GTCCA': 'S6', 'GTCCC': 'SR',
'GTCCG': 'SS', 'GTCCT': 'S7', 'GTCGA': 'SU', 'GTCGC': 'SV', 'GTCGG': 'S8', 'GTCGT': 'SW',
'GTCTA': 'SX', 'GTCTC': 'S9', 'GTCTG': 'SY', 'GTCTT': 'SZ', 'GTGAA': '7B', 'GTGAC': '7D',
'GTGAG': '70', 'GTGAT': '7E', 'GTGCA': '7F', 'GTGCC': '71', 'GTGCG': '7H', 'GTGCT': '7I',
'GTGGA': '72', 'GTGGC': '7J', 'GTGGG': '7K', 'GTGGT': '73', 'GTGTA': '7L', 'GTGTC': '7M',
'GTGTG': '74', 'GTGTT': '7N', 'GTTAA': '7O', 'GTTAC': '75', 'GTTAG': '7P', 'GTTAT': '7Q',
'GTTCA': '76', 'GTTCC': '7R', 'GTTCG': '7S', 'GTTCT': '77', 'GTTGA': '7U', 'GTTGC': '7V',
'GTTGG': '78', 'GTTGT': '7W', 'GTTTA': '7X', 'GTTTC': '79', 'GTTTG': '7Y', 'GTTTT': '7Z',
'TAAAA': 'UB', 'TAAAC': 'UD', 'TAAAG': 'U0', 'TAAAT': 'UE', 'TAACA': 'UF', 'TAACC': 'U1',
'TAACG': 'UH', 'TAACT': 'UI', 'TAAGA': 'U2', 'TAAGC': 'UJ', 'TAAGG': 'UK', 'TAAGT': 'U3',
'TAATA': 'UL', 'TAATC': 'UM', 'TAATG': 'U4', 'TAATT': 'UN', 'TACAA': 'UO', 'TACAC': 'U5',
'TACAG': 'UP', 'TACAT': 'UQ', 'TACCA': 'U6', 'TACCC': 'UR', 'TACCG': 'US', 'TACCT': 'U7',
'TACGA': 'UU', 'TACGC': 'UV', 'TACGG': 'U8', 'TACGT': 'UW', 'TACTA': 'UX', 'TACTC': 'U9',
'TACTG': 'UY', 'TACTT': 'UZ', 'TAGAA': 'VB', 'TAGAC': 'VD', 'TAGAG': 'V0', 'TAGAT': 'VE',
'TAGCA': 'VF', 'TAGCC': 'V1', 'TAGCG': 'VH', 'TAGCT': 'VI', 'TAGGA': 'V2', 'TAGGC': 'VJ',
'TAGGG': 'VK', 'TAGGT': 'V3', 'TAGTA': 'VL', 'TAGTC': 'VM', 'TAGTG': 'V4', 'TAGTT': 'VN',
'TATAA': 'VO', 'TATAC': 'V5', 'TATAG': 'VP', 'TATAT': 'VQ', 'TATCA': 'V6', 'TATCC': 'VR',
'TATCG': 'VS', 'TATCT': 'V7', 'TATGA': 'VU', 'TATGC': 'VV', 'TATGG': 'V8', 'TATGT': 'VW',
'TATTA': 'VX', 'TATTC': 'V9', 'TATTG': 'VY', 'TATTT': 'VZ', 'TCAAA': '8B', 'TCAAC': '8D',
'TCAAG': '80', 'TCAAT': '8E', 'TCACA': '8F', 'TCACC': '81', 'TCACG': '8H', 'TCACT': '8I',
'TCAGA': '82', 'TCAGC': '8J', 'TCAGG': '8K', 'TCAGT': '83', 'TCATA': '8L', 'TCATC': '8M',
'TCATG': '84', 'TCATT': '8N', 'TCCAA': '8O', 'TCCAC': '85', 'TCCAG': '8P', 'TCCAT': '8Q',
'TCCCA': '86', 'TCCCC': '8R', 'TCCCG': '8S', 'TCCCT': '87', 'TCCGA': '8U', 'TCCGC': '8V',
'TCCGG': '88', 'TCCGT': '8W', 'TCCTA': '8X', 'TCCTC': '89', 'TCCTG': '8Y', 'TCCTT': '8Z',
'TCGAA': 'WB', 'TCGAC': 'WD', 'TCGAG': 'W0', 'TCGAT': 'WE', 'TCGCA': 'WF', 'TCGCC': 'W1',
'TCGCG': 'WH', 'TCGCT': 'WI', 'TCGGA': 'W2', 'TCGGC': 'WJ', 'TCGGG': 'WK', 'TCGGT': 'W3',
'TCGTA': 'WL', 'TCGTC': 'WM', 'TCGTG': 'W4', 'TCGTT': 'WN', 'TCTAA': 'WO', 'TCTAC': 'W5',
'TCTAG': 'WP', 'TCTAT': 'WQ', 'TCTCA': 'W6', 'TCTCC': 'WR', 'TCTCG': 'WS', 'TCTCT': 'W7',
'TCTGA': 'WU', 'TCTGC': 'WV', 'TCTGG': 'W8', 'TCTGT': 'WW', 'TCTTA': 'WX', 'TCTTC': 'W9',
'TCTTG': 'WY', 'TCTTT': 'WZ', 'TGAAA': 'XB', 'TGAAC': 'XD', 'TGAAG': 'X0', 'TGAAT': 'XE',
'TGACA': 'XF', 'TGACC': 'X1', 'TGACG': 'XH', 'TGACT': 'XI', 'TGAGA': 'X2', 'TGAGC': 'XJ',
'TGAGG': 'XK', 'TGAGT': 'X3', 'TGATA': 'XL', 'TGATC': 'XM', 'TGATG': 'X4', 'TGATT': 'XN',
'TGCAA': 'XO', 'TGCAC': 'X5', 'TGCAG': 'XP', 'TGCAT': 'XQ', 'TGCCA': 'X6', 'TGCCC': 'XR',
'TGCCG': 'XS', 'TGCCT': 'X7', 'TGCGA': 'XU', 'TGCGC': 'XV', 'TGCGG': 'X8', 'TGCGT': 'XW',
'TGCTA': 'XX', 'TGCTC': 'X9', 'TGCTG': 'XY', 'TGCTT': 'XZ', 'TGGAA': '9B', 'TGGAC': '9D',
'TGGAG': '90', 'TGGAT': '9E', 'TGGCA': '9F', 'TGGCC': '91', 'TGGCG': '9H', 'TGGCT': '9I',
'TGGGA': '92', 'TGGGC': '9J', 'TGGGG': '9K', 'TGGGT': '93', 'TGGTA': '9L', 'TGGTC': '9M',
'TGGTG': '94', 'TGGTT': '9N', 'TGTAA': '9O', 'TGTAC': '95', 'TGTAG': '9P', 'TGTAT': '9Q',
'TGTCA': '96', 'TGTCC': '9R', 'TGTCG': '9S', 'TGTCT': '97', 'TGTGA': '9U', 'TGTGC': '9V',
'TGTGG': '98', 'TGTGT': '9W', 'TGTTA': '9X', 'TGTTC': '99', 'TGTTG': '9Y', 'TGTTT': '9Z',
'TTAAA': 'YB', 'TTAAC': 'YD', 'TTAAG': 'Y0', 'TTAAT': 'YE', 'TTACA': 'YF', 'TTACC': 'Y1',
'TTACG': 'YH', 'TTACT': 'YI', 'TTAGA': 'Y2', 'TTAGC': 'YJ', 'TTAGG': 'YK', 'TTAGT': 'Y3',
'TTATA': 'YL', 'TTATC': 'YM', 'TTATG': 'Y4', 'TTATT': 'YN', 'TTCAA': 'YO', 'TTCAC': 'Y5',
'TTCAG': 'YP', 'TTCAT': 'YQ', 'TTCCA': 'Y6', 'TTCCC': 'YR', 'TTCCG': 'YS', 'TTCCT': 'Y7',
'TTCGA': 'YU', 'TTCGC': 'YV', 'TTCGG': 'Y8', 'TTCGT': 'YW', 'TTCTA': 'YX', 'TTCTC': 'Y9',
'TTCTG': 'YY', 'TTCTT': 'YZ', 'TTGAA': 'ZB', 'TTGAC': 'ZD', 'TTGAG': 'Z0', 'TTGAT': 'ZE',
'TTGCA': 'ZF', 'TTGCC': 'Z1', 'TTGCG': 'ZH', 'TTGCT': 'ZI', 'TTGGA': 'Z2', 'TTGGC': 'ZJ',
'TTGGG': 'ZK', 'TTGGT': 'Z3', 'TTGTA': 'ZL', 'TTGTC': 'ZM', 'TTGTG': 'Z4', 'TTGTT': 'ZN',
'TTTAA': 'ZO', 'TTTAC': 'Z5', 'TTTAG': 'ZP', 'TTTAT': 'ZQ', 'TTTCA': 'Z6', 'TTTCC': 'ZR',
'TTTCG': 'ZS', 'TTTCT': 'Z7', 'TTTGA': 'ZU', 'TTTGC': 'ZV', 'TTTGG': 'Z8', 'TTTGT': 'ZW',
'TTTTA': 'ZX', 'TTTTC': 'Z9', 'TTTTG': 'ZY', 'TTTTT': 'ZZ', 'A': 'B', 'C': 'D',
'G': '0', 'T': 'E', 'AA': 'F', 'AC': '1', 'AG': 'H', 'AT': 'I',
'CA': '2', 'CC': 'J', 'CG': 'K', 'CT': '3', 'GA': 'L', 'GC': 'M',
'GG': '4', 'GT': 'N', 'TA': 'O', 'TC': '5', 'TG': 'P', 'TT': 'Q',
'AAA': '6', 'AAC': 'R', 'AAG': 'S', 'AAT': '7', 'ACA': 'U', 'ACC': 'V',
'ACG': '8', 'ACT': 'W', 'AGA': 'X', 'AGC': '9', 'AGG': 'Y', 'AGT': 'Z',
'ATA': 'DB', 'ATC': 'DD', 'ATG': 'D0', 'ATT': 'DE', 'CAA': 'DF', 'CAC': 'D1',
'CAG': 'DH', 'CAT': 'DI', 'CCA': 'D2', 'CCC': 'DJ', 'CCG': 'DK', 'CCT': 'D3',
'CGA': 'DL', 'CGC': 'DM', 'CGG': 'D4', 'CGT': 'DN', 'CTA': 'DO', 'CTC': 'D5',
'CTG': 'DP', 'CTT': 'DQ', 'GAA': 'D6', 'GAC': 'DR', 'GAG': 'DS', 'GAT': 'D7',
'GCA': 'DU', 'GCC': 'DV', 'GCG': 'D8', 'GCT': 'DW', 'GGA': 'DX', 'GGC': 'D9',
'GGG': 'DY', 'GGT': 'DZ', 'GTA': '0B', 'GTC': '0D', 'GTG': '00', 'GTT': '0E',
'TAA': '0F', 'TAC': '01', 'TAG': '0H', 'TAT': '0I', 'TCA': '02', 'TCC': '0J',
'TCG': '0K', 'TCT': '03', 'TGA': '0L', 'TGC': '0M', 'TGG': '04', 'TGT': '0N',
'TTA': '0O', 'TTC': '05', 'TTG': '0P', 'TTT': '0Q', 'AAAA': '06', 'AAAC': '0R',
'AAAG': '0S', 'AAAT': '07', 'AACA': '0U', 'AACC': '0V', 'AACG': '08', 'AACT': '0W',
'AAGA': '0X', 'AAGC': '09', 'AAGG': '0Y', 'AAGT': '0Z', 'AATA': 'EB', 'AATC': 'ED',
'AATG': 'E0', 'AATT': 'EE', 'ACAA': 'EF', 'ACAC': 'E1', 'ACAG': 'EH', 'ACAT': 'EI',
'ACCA': 'E2', 'ACCC': 'EJ', 'ACCG': 'EK', 'ACCT': 'E3', 'ACGA': 'EL', 'ACGC': 'EM',
'ACGG': 'E4', 'ACGT': 'EN', 'ACTA': 'EO', 'ACTC': 'E5', 'ACTG': 'EP', 'ACTT': 'EQ',
'AGAA': 'E6', 'AGAC': 'ER', 'AGAG': 'ES', 'AGAT': 'E7', 'AGCA': 'EU', 'AGCC': 'EV',
'AGCG': 'E8', 'AGCT': 'EW', 'AGGA': 'EX', 'AGGC': 'E9', 'AGGG': 'EY', 'AGGT': 'EZ',
'AGTA': 'FB', 'AGTC': 'FD', 'AGTG': 'F0', 'AGTT': 'FE', 'ATAA': 'FF', 'ATAC': 'F1',
'ATAG': 'FH', 'ATAT': 'FI', 'ATCA': 'F2', 'ATCC': 'FJ', 'ATCG': 'FK', 'ATCT': 'F3',
'ATGA': 'FL', 'ATGC': 'FM', 'ATGG': 'F4', 'ATGT': 'FN', 'ATTA': 'FO', 'ATTC': 'F5',
'ATTG': 'FP', 'ATTT': 'FQ', 'CAAA': 'F6', 'CAAC': 'FR', 'CAAG': 'FS', 'CAAT': 'F7',
'CACA': 'FU', 'CACC': 'FV', 'CACG': 'F8', 'CACT': 'FW', 'CAGA': 'FX', 'CAGC': 'F9',
'CAGG': 'FY', 'CAGT': 'FZ', 'CATA': '1B', 'CATC': '1D', 'CATG': '10', 'CATT': '1E',
'CCAA': '1F', 'CCAC': '11', 'CCAG': '1H', 'CCAT': '1I', 'CCCA': '12', 'CCCC': '1J',
'CCCG': '1K', 'CCCT': '13', 'CCGA': '1L', 'CCGC': '1M', 'CCGG': '14', 'CCGT': '1N',
'CCTA': '1O', 'CCTC': '15', 'CCTG': '1P', 'CCTT': '1Q', 'CGAA': '16', 'CGAC': '1R',
'CGAG': '1S', 'CGAT': '17', 'CGCA': '1U', 'CGCC': '1V', 'CGCG': '18', 'CGCT': '1W',
'CGGA': '1X', 'CGGC': '19', 'CGGG': '1Y', 'CGGT': '1Z', 'CGTA': 'HB', 'CGTC': 'HD',
'CGTG': 'H0', 'CGTT': 'HE', 'CTAA': 'HF', 'CTAC': 'H1', 'CTAG': 'HH', 'CTAT': 'HI',
'CTCA': 'H2', 'CTCC': 'HJ', 'CTCG': 'HK', 'CTCT': 'H3', 'CTGA': 'HL', 'CTGC': 'HM',
'CTGG': 'H4', 'CTGT': 'HN', 'CTTA': 'HO', 'CTTC': 'H5', 'CTTG': 'HP', 'CTTT': 'HQ',
'GAAA': 'H6', 'GAAC': 'HR', 'GAAG': 'HS', 'GAAT': 'H7', 'GACA': 'HU', 'GACC': 'HV',
'GACG': 'H8', 'GACT': 'HW', 'GAGA': 'HX', 'GAGC': 'H9', 'GAGG': 'HY', 'GAGT': 'HZ',
'GATA': 'IB', 'GATC': 'ID', 'GATG': 'I0', 'GATT': 'IE', 'GCAA': 'IF', 'GCAC': 'I1',
'GCAG': 'IH', 'GCAT': 'II', 'GCCA': 'I2', 'GCCC': 'IJ', 'GCCG': 'IK', 'GCCT': 'I3',
'GCGA': 'IL', 'GCGC': 'IM', 'GCGG': 'I4', 'GCGT': 'IN', 'GCTA': 'IO', 'GCTC': 'I5',
'GCTG': 'IP', 'GCTT': 'IQ', 'GGAA': 'I6', 'GGAC': 'IR', 'GGAG': 'IS', 'GGAT': 'I7',
'GGCA': 'IU', 'GGCC': 'IV', 'GGCG': 'I8', 'GGCT': 'IW', 'GGGA': 'IX', 'GGGC': 'I9',
'GGGG': 'IY', 'GGGT': 'IZ', 'GGTA': '2B', 'GGTC': '2D', 'GGTG': '20', 'GGTT': '2E',
'GTAA': '2F', 'GTAC': '21', 'GTAG': '2H', 'GTAT': '2I', 'GTCA': '22', 'GTCC': '2J',
'GTCG': '2K', 'GTCT': '23', 'GTGA': '2L', 'GTGC': '2M', 'GTGG': '24', 'GTGT': '2N',
'GTTA': '2O', 'GTTC': '25', 'GTTG': '2P', 'GTTT': '2Q', 'TAAA': '26', 'TAAC': '2R',
'TAAG': '2S', 'TAAT': '27', 'TACA': '2U', 'TACC': '2V', 'TACG': '28', 'TACT': '2W',
'TAGA': '2X', 'TAGC': '29', 'TAGG': '2Y', 'TAGT': '2Z', 'TATA': 'JB', 'TATC': 'JD',
'TATG': 'J0', 'TATT': 'JE', 'TCAA': 'JF', 'TCAC': 'J1', 'TCAG': 'JH', 'TCAT': 'JI',
'TCCA': 'J2', 'TCCC': 'JJ', 'TCCG': 'JK', 'TCCT': 'J3', 'TCGA': 'JL', 'TCGC': 'JM',
'TCGG': 'J4', 'TCGT': 'JN', 'TCTA': 'JO', 'TCTC': 'J5', 'TCTG': 'JP', 'TCTT': 'JQ',
'TGAA': 'J6', 'TGAC': 'JR', 'TGAG': 'JS', 'TGAT': 'J7', 'TGCA': 'JU', 'TGCC': 'JV',
'TGCG': 'J8', 'TGCT': 'JW', 'TGGA': 'JX', 'TGGC': 'J9', 'TGGG': 'JY', 'TGGT': 'JZ',
'TGTA': 'KB', 'TGTC': 'KD', 'TGTG': 'K0', 'TGTT': 'KE', 'TTAA': 'KF', 'TTAC': 'K1',
'TTAG': 'KH', 'TTAT': 'KI', 'TTCA': 'K2', 'TTCC': 'KJ', 'TTCG': 'KK', 'TTCT': 'K3',
'TTGA': 'KL', 'TTGC': 'KM', 'TTGG': 'K4', 'TTGT': 'KN', 'TTTA': 'KO', 'TTTC': 'K5',
'TTTG': 'KP', 'TTTT': 'KQ'}
decode_hash = {'BB-5': 'AAAAA', 'BD-5': 'AAAAC', 'B0-5': 'AAAAG', 'BE-5': 'AAAAT', 'BF-5': 'AAACA', 'B1-5': 'AAACC',
'BH-5': 'AAACG', 'BI-5': 'AAACT', 'B2-5': 'AAAGA', 'BJ-5': 'AAAGC', 'BK-5': 'AAAGG', 'B3-5': 'AAAGT',
'BL-5': 'AAATA', 'BM-5': 'AAATC', 'B4-5': 'AAATG', 'BN-5': 'AAATT', 'BO-5': 'AACAA', 'B5-5': 'AACAC',
'BP-5': 'AACAG', 'BQ-5': 'AACAT', 'B6-5': 'AACCA', 'BR-5': 'AACCC', 'BS-5': 'AACCG', 'B7-5': 'AACCT',
'BU-5': 'AACGA', 'BV-5': 'AACGC', 'B8-5': 'AACGG', 'BW-5': 'AACGT', 'BX-5': 'AACTA', 'B9-5': 'AACTC',
'BY-5': 'AACTG', 'BZ-5': 'AACTT', 'DB-5': 'AAGAA', 'DD-5': 'AAGAC', 'D0-5': 'AAGAG', 'DE-5': 'AAGAT',
'DF-5': 'AAGCA', 'D1-5': 'AAGCC', 'DH-5': 'AAGCG', 'DI-5': 'AAGCT', 'D2-5': 'AAGGA', 'DJ-5': 'AAGGC',
'DK-5': 'AAGGG', 'D3-5': 'AAGGT', 'DL-5': 'AAGTA', 'DM-5': 'AAGTC', 'D4-5': 'AAGTG', 'DN-5': 'AAGTT',
'DO-5': 'AATAA', 'D5-5': 'AATAC', 'DP-5': 'AATAG', 'DQ-5': 'AATAT', 'D6-5': 'AATCA', 'DR-5': 'AATCC',
'DS-5': 'AATCG', 'D7-5': 'AATCT', 'DU-5': 'AATGA', 'DV-5': 'AATGC', 'D8-5': 'AATGG', 'DW-5': 'AATGT',
'DX-5': 'AATTA', 'D9-5': 'AATTC', 'DY-5': 'AATTG', 'DZ-5': 'AATTT', '0B-5': 'ACAAA', '0D-5': 'ACAAC',
'00-5': 'ACAAG', '0E-5': 'ACAAT', '0F-5': 'ACACA', '01-5': 'ACACC', '0H-5': 'ACACG', '0I-5': 'ACACT',
'02-5': 'ACAGA', '0J-5': 'ACAGC', '0K-5': 'ACAGG', '03-5': 'ACAGT', '0L-5': 'ACATA', '0M-5': 'ACATC',
'04-5': 'ACATG', '0N-5': 'ACATT', '0O-5': 'ACCAA', '05-5': 'ACCAC', '0P-5': 'ACCAG', '0Q-5': 'ACCAT',
'06-5': 'ACCCA', '0R-5': 'ACCCC', '0S-5': 'ACCCG', '07-5': 'ACCCT', '0U-5': 'ACCGA', '0V-5': 'ACCGC',
'08-5': 'ACCGG', '0W-5': 'ACCGT', '0X-5': 'ACCTA', '09-5': 'ACCTC', '0Y-5': 'ACCTG', '0Z-5': 'ACCTT',
'EB-5': 'ACGAA', 'ED-5': 'ACGAC', 'E0-5': 'ACGAG', 'EE-5': 'ACGAT', 'EF-5': 'ACGCA', 'E1-5': 'ACGCC',
'EH-5': 'ACGCG', 'EI-5': 'ACGCT', 'E2-5': 'ACGGA', 'EJ-5': 'ACGGC', 'EK-5': 'ACGGG', 'E3-5': 'ACGGT',
'EL-5': 'ACGTA', 'EM-5': 'ACGTC', 'E4-5': 'ACGTG', 'EN-5': 'ACGTT', 'EO-5': 'ACTAA', 'E5-5': 'ACTAC',
'EP-5': 'ACTAG', 'EQ-5': 'ACTAT', 'E6-5': 'ACTCA', 'ER-5': 'ACTCC', 'ES-5': 'ACTCG', 'E7-5': 'ACTCT',
'EU-5': 'ACTGA', 'EV-5': 'ACTGC', 'E8-5': 'ACTGG', 'EW-5': 'ACTGT', 'EX-5': 'ACTTA', 'E9-5': 'ACTTC',
'EY-5': 'ACTTG', 'EZ-5': 'ACTTT', 'FB-5': 'AGAAA', 'FD-5': 'AGAAC', 'F0-5': 'AGAAG', 'FE-5': 'AGAAT',
'FF-5': 'AGACA', 'F1-5': 'AGACC', 'FH-5': 'AGACG', 'FI-5': 'AGACT', 'F2-5': 'AGAGA', 'FJ-5': 'AGAGC',
'FK-5': 'AGAGG', 'F3-5': 'AGAGT', 'FL-5': 'AGATA', 'FM-5': 'AGATC', 'F4-5': 'AGATG', 'FN-5': 'AGATT',
'FO-5': 'AGCAA', 'F5-5': 'AGCAC', 'FP-5': 'AGCAG', 'FQ-5': 'AGCAT', 'F6-5': 'AGCCA', 'FR-5': 'AGCCC',
'FS-5': 'AGCCG', 'F7-5': 'AGCCT', 'FU-5': 'AGCGA', 'FV-5': 'AGCGC', 'F8-5': 'AGCGG', 'FW-5': 'AGCGT',
'FX-5': 'AGCTA', 'F9-5': 'AGCTC', 'FY-5': 'AGCTG', 'FZ-5': 'AGCTT', '1B-5': 'AGGAA', '1D-5': 'AGGAC',
'10-5': 'AGGAG', '1E-5': 'AGGAT', '1F-5': 'AGGCA', '11-5': 'AGGCC', '1H-5': 'AGGCG', '1I-5': 'AGGCT',
'12-5': 'AGGGA', '1J-5': 'AGGGC', '1K-5': 'AGGGG', '13-5': 'AGGGT', '1L-5': 'AGGTA', '1M-5': 'AGGTC',
'14-5': 'AGGTG', '1N-5': 'AGGTT', '1O-5': 'AGTAA', '15-5': 'AGTAC', '1P-5': 'AGTAG', '1Q-5': 'AGTAT',
'16-5': 'AGTCA', '1R-5': 'AGTCC', '1S-5': 'AGTCG', '17-5': 'AGTCT', '1U-5': 'AGTGA', '1V-5': 'AGTGC',
'18-5': 'AGTGG', '1W-5': 'AGTGT', '1X-5': 'AGTTA', '19-5': 'AGTTC', '1Y-5': 'AGTTG', '1Z-5': 'AGTTT',
'HB-5': 'ATAAA', 'HD-5': 'ATAAC', 'H0-5': 'ATAAG', 'HE-5': 'ATAAT', 'HF-5': 'ATACA', 'H1-5': 'ATACC',
'HH-5': 'ATACG', 'HI-5': 'ATACT', 'H2-5': 'ATAGA', 'HJ-5': 'ATAGC', 'HK-5': 'ATAGG', 'H3-5': 'ATAGT',
'HL-5': 'ATATA', 'HM-5': 'ATATC', 'H4-5': 'ATATG', 'HN-5': 'ATATT', 'HO-5': 'ATCAA', 'H5-5': 'ATCAC',
'HP-5': 'ATCAG', 'HQ-5': 'ATCAT', 'H6-5': 'ATCCA', 'HR-5': 'ATCCC', 'HS-5': 'ATCCG', 'H7-5': 'ATCCT',
'HU-5': 'ATCGA', 'HV-5': 'ATCGC', 'H8-5': 'ATCGG', 'HW-5': 'ATCGT', 'HX-5': 'ATCTA', 'H9-5': 'ATCTC',
'HY-5': 'ATCTG', 'HZ-5': 'ATCTT', 'IB-5': 'ATGAA', 'ID-5': 'ATGAC', 'I0-5': 'ATGAG', 'IE-5': 'ATGAT',
'IF-5': 'ATGCA', 'I1-5': 'ATGCC', 'IH-5': 'ATGCG', 'II-5': 'ATGCT', 'I2-5': 'ATGGA', 'IJ-5': 'ATGGC',
'IK-5': 'ATGGG', 'I3-5': 'ATGGT', 'IL-5': 'ATGTA', 'IM-5': 'ATGTC', 'I4-5': 'ATGTG', 'IN-5': 'ATGTT',
'IO-5': 'ATTAA', 'I5-5': 'ATTAC', 'IP-5': 'ATTAG', 'IQ-5': 'ATTAT', 'I6-5': 'ATTCA', 'IR-5': 'ATTCC',
'IS-5': 'ATTCG', 'I7-5': 'ATTCT', 'IU-5': 'ATTGA', 'IV-5': 'ATTGC', 'I8-5': 'ATTGG', 'IW-5': 'ATTGT',
'IX-5': 'ATTTA', 'I9-5': 'ATTTC', 'IY-5': 'ATTTG', 'IZ-5': 'ATTTT', '2B-5': 'CAAAA', '2D-5': 'CAAAC',
'20-5': 'CAAAG', '2E-5': 'CAAAT', '2F-5': 'CAACA', '21-5': 'CAACC', '2H-5': 'CAACG', '2I-5': 'CAACT',
'22-5': 'CAAGA', '2J-5': 'CAAGC', '2K-5': 'CAAGG', '23-5': 'CAAGT', '2L-5': 'CAATA', '2M-5': 'CAATC',
'24-5': 'CAATG', '2N-5': 'CAATT', '2O-5': 'CACAA', '25-5': 'CACAC', '2P-5': 'CACAG', '2Q-5': 'CACAT',
'26-5': 'CACCA', '2R-5': 'CACCC', '2S-5': 'CACCG', '27-5': 'CACCT', '2U-5': 'CACGA', '2V-5': 'CACGC',
'28-5': 'CACGG', '2W-5': 'CACGT', '2X-5': 'CACTA', '29-5': 'CACTC', '2Y-5': 'CACTG', '2Z-5': 'CACTT',
'JB-5': 'CAGAA', 'JD-5': 'CAGAC', 'J0-5': 'CAGAG', 'JE-5': 'CAGAT', 'JF-5': 'CAGCA', 'J1-5': 'CAGCC',
'JH-5': 'CAGCG', 'JI-5': 'CAGCT', 'J2-5': 'CAGGA', 'JJ-5': 'CAGGC', 'JK-5': 'CAGGG', 'J3-5': 'CAGGT',
'JL-5': 'CAGTA', 'JM-5': 'CAGTC', 'J4-5': 'CAGTG', 'JN-5': 'CAGTT', 'JO-5': 'CATAA', 'J5-5': 'CATAC',
'JP-5': 'CATAG', 'JQ-5': 'CATAT', 'J6-5': 'CATCA', 'JR-5': 'CATCC', 'JS-5': 'CATCG', 'J7-5': 'CATCT',
'JU-5': 'CATGA', 'JV-5': 'CATGC', 'J8-5': 'CATGG', 'JW-5': 'CATGT', 'JX-5': 'CATTA', 'J9-5': 'CATTC',
'JY-5': 'CATTG', 'JZ-5': 'CATTT', 'KB-5': 'CCAAA', 'KD-5': 'CCAAC', 'K0-5': 'CCAAG', 'KE-5': 'CCAAT',
'KF-5': 'CCACA', 'K1-5': 'CCACC', 'KH-5': 'CCACG', 'KI-5': 'CCACT', 'K2-5': 'CCAGA', 'KJ-5': 'CCAGC',
'KK-5': 'CCAGG', 'K3-5': 'CCAGT', 'KL-5': 'CCATA', 'KM-5': 'CCATC', 'K4-5': 'CCATG', 'KN-5': 'CCATT',
'KO-5': 'CCCAA', 'K5-5': 'CCCAC', 'KP-5': 'CCCAG', 'KQ-5': 'CCCAT', 'K6-5': 'CCCCA', 'KR-5': 'CCCCC',
'KS-5': 'CCCCG', 'K7-5': 'CCCCT', 'KU-5': 'CCCGA', 'KV-5': 'CCCGC', 'K8-5': 'CCCGG', 'KW-5': 'CCCGT',
'KX-5': 'CCCTA', 'K9-5': 'CCCTC', 'KY-5': 'CCCTG', 'KZ-5': 'CCCTT', '3B-5': 'CCGAA', '3D-5': 'CCGAC',
'30-5': 'CCGAG', '3E-5': 'CCGAT', '3F-5': 'CCGCA', '31-5': 'CCGCC', '3H-5': 'CCGCG', '3I-5': 'CCGCT',
'32-5': 'CCGGA', '3J-5': 'CCGGC', '3K-5': 'CCGGG', '33-5': 'CCGGT', '3L-5': 'CCGTA', '3M-5': 'CCGTC',
'34-5': 'CCGTG', '3N-5': 'CCGTT', '3O-5': 'CCTAA', '35-5': 'CCTAC', '3P-5': 'CCTAG', '3Q-5': 'CCTAT',
'36-5': 'CCTCA', '3R-5': 'CCTCC', '3S-5': 'CCTCG', '37-5': 'CCTCT', '3U-5': 'CCTGA', '3V-5': 'CCTGC',
'38-5': 'CCTGG', '3W-5': 'CCTGT', '3X-5': 'CCTTA', '39-5': 'CCTTC', '3Y-5': 'CCTTG', '3Z-5': 'CCTTT',
'LB-5': 'CGAAA', 'LD-5': 'CGAAC', 'L0-5': 'CGAAG', 'LE-5': 'CGAAT', 'LF-5': 'CGACA', 'L1-5': 'CGACC',
'LH-5': 'CGACG', 'LI-5': 'CGACT', 'L2-5': 'CGAGA', 'LJ-5': 'CGAGC', 'LK-5': 'CGAGG', 'L3-5': 'CGAGT',
'LL-5': 'CGATA', 'LM-5': 'CGATC', 'L4-5': 'CGATG', 'LN-5': 'CGATT', 'LO-5': 'CGCAA', 'L5-5': 'CGCAC',
'LP-5': 'CGCAG', 'LQ-5': 'CGCAT', 'L6-5': 'CGCCA', 'LR-5': 'CGCCC', 'LS-5': 'CGCCG', 'L7-5': 'CGCCT',
'LU-5': 'CGCGA', 'LV-5': 'CGCGC', 'L8-5': 'CGCGG', 'LW-5': 'CGCGT', 'LX-5': 'CGCTA', 'L9-5': 'CGCTC',
'LY-5': 'CGCTG', 'LZ-5': 'CGCTT', 'MB-5': 'CGGAA', 'MD-5': 'CGGAC', 'M0-5': 'CGGAG', 'ME-5': 'CGGAT',
'MF-5': 'CGGCA', 'M1-5': 'CGGCC', 'MH-5': 'CGGCG', 'MI-5': 'CGGCT', 'M2-5': 'CGGGA', 'MJ-5': 'CGGGC',
'MK-5': 'CGGGG', 'M3-5': 'CGGGT', 'ML-5': 'CGGTA', 'MM-5': 'CGGTC', 'M4-5': 'CGGTG', 'MN-5': 'CGGTT',
'MO-5': 'CGTAA', 'M5-5': 'CGTAC', 'MP-5': 'CGTAG', 'MQ-5': 'CGTAT', 'M6-5': 'CGTCA', 'MR-5': 'CGTCC',
'MS-5': 'CGTCG', 'M7-5': 'CGTCT', 'MU-5': 'CGTGA', 'MV-5': 'CGTGC', 'M8-5': 'CGTGG', 'MW-5': 'CGTGT',
'MX-5': 'CGTTA', 'M9-5': 'CGTTC', 'MY-5': 'CGTTG', 'MZ-5': 'CGTTT', '4B-5': 'CTAAA', '4D-5': 'CTAAC',
'40-5': 'CTAAG', '4E-5': 'CTAAT', '4F-5': 'CTACA', '41-5': 'CTACC', '4H-5': 'CTACG', '4I-5': 'CTACT',
'42-5': 'CTAGA', '4J-5': 'CTAGC', '4K-5': 'CTAGG', '43-5': 'CTAGT', '4L-5': 'CTATA', '4M-5': 'CTATC',
'44-5': 'CTATG', '4N-5': 'CTATT', '4O-5': 'CTCAA', '45-5': 'CTCAC', '4P-5': 'CTCAG', '4Q-5': 'CTCAT',
'46-5': 'CTCCA', '4R-5': 'CTCCC', '4S-5': 'CTCCG', '47-5': 'CTCCT', '4U-5': 'CTCGA', '4V-5': 'CTCGC',
'48-5': 'CTCGG', '4W-5': 'CTCGT', '4X-5': 'CTCTA', '49-5': 'CTCTC', '4Y-5': 'CTCTG', '4Z-5': 'CTCTT',
'NB-5': 'CTGAA', 'ND-5': 'CTGAC', 'N0-5': 'CTGAG', 'NE-5': 'CTGAT', 'NF-5': 'CTGCA', 'N1-5': 'CTGCC',
'NH-5': 'CTGCG', 'NI-5': 'CTGCT', 'N2-5': 'CTGGA', 'NJ-5': 'CTGGC', 'NK-5': 'CTGGG', 'N3-5': 'CTGGT',
'NL-5': 'CTGTA', 'NM-5': 'CTGTC', 'N4-5': 'CTGTG', 'NN-5': 'CTGTT', 'NO-5': 'CTTAA', 'N5-5': 'CTTAC',
'NP-5': 'CTTAG', 'NQ-5': 'CTTAT', 'N6-5': 'CTTCA', 'NR-5': 'CTTCC', 'NS-5': 'CTTCG', 'N7-5': 'CTTCT',
'NU-5': 'CTTGA', 'NV-5': 'CTTGC', 'N8-5': 'CTTGG', 'NW-5': 'CTTGT', 'NX-5': 'CTTTA', 'N9-5': 'CTTTC',
'NY-5': 'CTTTG', 'NZ-5': 'CTTTT', 'OB-5': 'GAAAA', 'OD-5': 'GAAAC', 'O0-5': 'GAAAG', 'OE-5': 'GAAAT',
'OF-5': 'GAACA', 'O1-5': 'GAACC', 'OH-5': 'GAACG', 'OI-5': 'GAACT', 'O2-5': 'GAAGA', 'OJ-5': 'GAAGC',
'OK-5': 'GAAGG', 'O3-5': 'GAAGT', 'OL-5': 'GAATA', 'OM-5': 'GAATC', 'O4-5': 'GAATG', 'ON-5': 'GAATT',
'OO-5': 'GACAA', 'O5-5': 'GACAC', 'OP-5': 'GACAG', 'OQ-5': 'GACAT', 'O6-5': 'GACCA', 'OR-5': 'GACCC',
'OS-5': 'GACCG', 'O7-5': 'GACCT', 'OU-5': 'GACGA', 'OV-5': 'GACGC', 'O8-5': 'GACGG', 'OW-5': 'GACGT',
'OX-5': 'GACTA', 'O9-5': 'GACTC', 'OY-5': 'GACTG', 'OZ-5': 'GACTT', '5B-5': 'GAGAA', '5D-5': 'GAGAC',
'50-5': 'GAGAG', '5E-5': 'GAGAT', '5F-5': 'GAGCA', '51-5': 'GAGCC', '5H-5': 'GAGCG', '5I-5': 'GAGCT',
'52-5': 'GAGGA', '5J-5': 'GAGGC', '5K-5': 'GAGGG', '53-5': 'GAGGT', '5L-5': 'GAGTA', '5M-5': 'GAGTC',
'54-5': 'GAGTG', '5N-5': 'GAGTT', '5O-5': 'GATAA', '55-5': 'GATAC', '5P-5': 'GATAG', '5Q-5': 'GATAT',
'56-5': 'GATCA', '5R-5': 'GATCC', '5S-5': 'GATCG', '57-5': 'GATCT', '5U-5': 'GATGA', '5V-5': 'GATGC',
'58-5': 'GATGG', '5W-5': 'GATGT', '5X-5': 'GATTA', '59-5': 'GATTC', '5Y-5': 'GATTG', '5Z-5': 'GATTT',
'PB-5': 'GCAAA', 'PD-5': 'GCAAC', 'P0-5': 'GCAAG', 'PE-5': 'GCAAT', 'PF-5': 'GCACA', 'P1-5': 'GCACC',
'PH-5': 'GCACG', 'PI-5': 'GCACT', 'P2-5': 'GCAGA', 'PJ-5': 'GCAGC', 'PK-5': 'GCAGG', 'P3-5': 'GCAGT',
'PL-5': 'GCATA', 'PM-5': 'GCATC', 'P4-5': 'GCATG', 'PN-5': 'GCATT', 'PO-5': 'GCCAA', 'P5-5': 'GCCAC',
'PP-5': 'GCCAG', 'PQ-5': 'GCCAT', 'P6-5': 'GCCCA', 'PR-5': 'GCCCC', 'PS-5': 'GCCCG', 'P7-5': 'GCCCT',
'PU-5': 'GCCGA', 'PV-5': 'GCCGC', 'P8-5': 'GCCGG', 'PW-5': 'GCCGT', 'PX-5': 'GCCTA', 'P9-5': 'GCCTC',
'PY-5': 'GCCTG', 'PZ-5': 'GCCTT', 'QB-5': 'GCGAA', 'QD-5': 'GCGAC', 'Q0-5': 'GCGAG', 'QE-5': 'GCGAT',
'QF-5': 'GCGCA', 'Q1-5': 'GCGCC', 'QH-5': 'GCGCG', 'QI-5': 'GCGCT', 'Q2-5': 'GCGGA', 'QJ-5': 'GCGGC',
'QK-5': 'GCGGG', 'Q3-5': 'GCGGT', 'QL-5': 'GCGTA', 'QM-5': 'GCGTC', 'Q4-5': 'GCGTG', 'QN-5': 'GCGTT',
'QO-5': 'GCTAA', 'Q5-5': 'GCTAC', 'QP-5': 'GCTAG', 'QQ-5': 'GCTAT', 'Q6-5': 'GCTCA', 'QR-5': 'GCTCC',
'QS-5': 'GCTCG', 'Q7-5': 'GCTCT', 'QU-5': 'GCTGA', 'QV-5': 'GCTGC', 'Q8-5': 'GCTGG', 'QW-5': 'GCTGT',
'QX-5': 'GCTTA', 'Q9-5': 'GCTTC', 'QY-5': 'GCTTG', 'QZ-5': 'GCTTT', '6B-5': 'GGAAA', '6D-5': 'GGAAC',
'60-5': 'GGAAG', '6E-5': 'GGAAT', '6F-5': 'GGACA', '61-5': 'GGACC', '6H-5': 'GGACG', '6I-5': 'GGACT',
'62-5': 'GGAGA', '6J-5': 'GGAGC', '6K-5': 'GGAGG', '63-5': 'GGAGT', '6L-5': 'GGATA', '6M-5': 'GGATC',
'64-5': 'GGATG', '6N-5': 'GGATT', '6O-5': 'GGCAA', '65-5': 'GGCAC', '6P-5': 'GGCAG', '6Q-5': 'GGCAT',
'66-5': 'GGCCA', '6R-5': 'GGCCC', '6S-5': 'GGCCG', '67-5': 'GGCCT', '6U-5': 'GGCGA', '6V-5': 'GGCGC',
'68-5': 'GGCGG', '6W-5': 'GGCGT', '6X-5': 'GGCTA', '69-5': 'GGCTC', '6Y-5': 'GGCTG', '6Z-5': 'GGCTT',
'RB-5': 'GGGAA', 'RD-5': 'GGGAC', 'R0-5': 'GGGAG', 'RE-5': 'GGGAT', 'RF-5': 'GGGCA', 'R1-5': 'GGGCC',
'RH-5': 'GGGCG', 'RI-5': 'GGGCT', 'R2-5': 'GGGGA', 'RJ-5': 'GGGGC', 'RK-5': 'GGGGG', 'R3-5': 'GGGGT',
'RL-5': 'GGGTA', 'RM-5': 'GGGTC', 'R4-5': 'GGGTG', 'RN-5': 'GGGTT', 'RO-5': 'GGTAA', 'R5-5': 'GGTAC',
'RP-5': 'GGTAG', 'RQ-5': 'GGTAT', 'R6-5': 'GGTCA', 'RR-5': 'GGTCC', 'RS-5': 'GGTCG', 'R7-5': 'GGTCT',
'RU-5': 'GGTGA', 'RV-5': 'GGTGC', 'R8-5': 'GGTGG', 'RW-5': 'GGTGT', 'RX-5': 'GGTTA', 'R9-5': 'GGTTC',
'RY-5': 'GGTTG', 'RZ-5': 'GGTTT', 'SB-5': 'GTAAA', 'SD-5': 'GTAAC', 'S0-5': 'GTAAG', 'SE-5': 'GTAAT',
'SF-5': 'GTACA', 'S1-5': 'GTACC', 'SH-5': 'GTACG', 'SI-5': 'GTACT', 'S2-5': 'GTAGA', 'SJ-5': 'GTAGC',
'SK-5': 'GTAGG', 'S3-5': 'GTAGT', 'SL-5': 'GTATA', 'SM-5': 'GTATC', 'S4-5': 'GTATG', 'SN-5': 'GTATT',
'SO-5': 'GTCAA', 'S5-5': 'GTCAC', 'SP-5': 'GTCAG', 'SQ-5': 'GTCAT', 'S6-5': 'GTCCA', 'SR-5': 'GTCCC',
'SS-5': 'GTCCG', 'S7-5': 'GTCCT', 'SU-5': 'GTCGA', 'SV-5': 'GTCGC', 'S8-5': 'GTCGG', 'SW-5': 'GTCGT',
'SX-5': 'GTCTA', 'S9-5': 'GTCTC', 'SY-5': 'GTCTG', 'SZ-5': 'GTCTT', '7B-5': 'GTGAA', '7D-5': 'GTGAC',
'70-5': 'GTGAG', '7E-5': 'GTGAT', '7F-5': 'GTGCA', '71-5': 'GTGCC', '7H-5': 'GTGCG', '7I-5': 'GTGCT',
'72-5': 'GTGGA', '7J-5': 'GTGGC', '7K-5': 'GTGGG', '73-5': 'GTGGT', '7L-5': 'GTGTA', '7M-5': 'GTGTC',
'74-5': 'GTGTG', '7N-5': 'GTGTT', '7O-5': 'GTTAA', '75-5': 'GTTAC', '7P-5': 'GTTAG', '7Q-5': 'GTTAT',
'76-5': 'GTTCA', '7R-5': 'GTTCC', '7S-5': 'GTTCG', '77-5': 'GTTCT', '7U-5': 'GTTGA', '7V-5': 'GTTGC',
'78-5': 'GTTGG', '7W-5': 'GTTGT', '7X-5': 'GTTTA', '79-5': 'GTTTC', '7Y-5': 'GTTTG', '7Z-5': 'GTTTT',
'UB-5': 'TAAAA', 'UD-5': 'TAAAC', 'U0-5': 'TAAAG', 'UE-5': 'TAAAT', 'UF-5': 'TAACA', 'U1-5': 'TAACC',
'UH-5': 'TAACG', 'UI-5': 'TAACT', 'U2-5': 'TAAGA', 'UJ-5': 'TAAGC', 'UK-5': 'TAAGG', 'U3-5': 'TAAGT',
'UL-5': 'TAATA', 'UM-5': 'TAATC', 'U4-5': 'TAATG', 'UN-5': 'TAATT', 'UO-5': 'TACAA', 'U5-5': 'TACAC',
'UP-5': 'TACAG', 'UQ-5': 'TACAT', 'U6-5': 'TACCA', 'UR-5': 'TACCC', 'US-5': 'TACCG', 'U7-5': 'TACCT',
'UU-5': 'TACGA', 'UV-5': 'TACGC', 'U8-5': 'TACGG', 'UW-5': 'TACGT', 'UX-5': 'TACTA', 'U9-5': 'TACTC',
'UY-5': 'TACTG', 'UZ-5': 'TACTT', 'VB-5': 'TAGAA', 'VD-5': 'TAGAC', 'V0-5': 'TAGAG', 'VE-5': 'TAGAT',
'VF-5': 'TAGCA', 'V1-5': 'TAGCC', 'VH-5': 'TAGCG', 'VI-5': 'TAGCT', 'V2-5': 'TAGGA', 'VJ-5': 'TAGGC',
'VK-5': 'TAGGG', 'V3-5': 'TAGGT', 'VL-5': 'TAGTA', 'VM-5': 'TAGTC', 'V4-5': 'TAGTG', 'VN-5': 'TAGTT',
'VO-5': 'TATAA', 'V5-5': 'TATAC', 'VP-5': 'TATAG', 'VQ-5': 'TATAT', 'V6-5': 'TATCA', 'VR-5': 'TATCC',
'VS-5': 'TATCG', 'V7-5': 'TATCT', 'VU-5': 'TATGA', 'VV-5': 'TATGC', 'V8-5': 'TATGG', 'VW-5': 'TATGT',
'VX-5': 'TATTA', 'V9-5': 'TATTC', 'VY-5': 'TATTG', 'VZ-5': 'TATTT', '8B-5': 'TCAAA', '8D-5': 'TCAAC',
'80-5': 'TCAAG', '8E-5': 'TCAAT', '8F-5': 'TCACA', '81-5': 'TCACC', '8H-5': 'TCACG', '8I-5': 'TCACT',
'82-5': 'TCAGA', '8J-5': 'TCAGC', '8K-5': 'TCAGG', '83-5': 'TCAGT', '8L-5': 'TCATA', '8M-5': 'TCATC',
'84-5': 'TCATG', '8N-5': 'TCATT', '8O-5': 'TCCAA', '85-5': 'TCCAC', '8P-5': 'TCCAG', '8Q-5': 'TCCAT',
'86-5': 'TCCCA', '8R-5': 'TCCCC', '8S-5': 'TCCCG', '87-5': 'TCCCT', '8U-5': 'TCCGA', '8V-5': 'TCCGC',
'88-5': 'TCCGG', '8W-5': 'TCCGT', '8X-5': 'TCCTA', '89-5': 'TCCTC', '8Y-5': 'TCCTG', '8Z-5': 'TCCTT',
'WB-5': 'TCGAA', 'WD-5': 'TCGAC', 'W0-5': 'TCGAG', 'WE-5': 'TCGAT', 'WF-5': 'TCGCA', 'W1-5': 'TCGCC',
'WH-5': 'TCGCG', 'WI-5': 'TCGCT', 'W2-5': 'TCGGA', 'WJ-5': 'TCGGC', 'WK-5': 'TCGGG', 'W3-5': 'TCGGT',
'WL-5': 'TCGTA', 'WM-5': 'TCGTC', 'W4-5': 'TCGTG', 'WN-5': 'TCGTT', 'WO-5': 'TCTAA', 'W5-5': 'TCTAC',
'WP-5': 'TCTAG', 'WQ-5': 'TCTAT', 'W6-5': 'TCTCA', 'WR-5': 'TCTCC', 'WS-5': 'TCTCG', 'W7-5': 'TCTCT',
'WU-5': 'TCTGA', 'WV-5': 'TCTGC', 'W8-5': 'TCTGG', 'WW-5': 'TCTGT', 'WX-5': 'TCTTA', 'W9-5': 'TCTTC',
'WY-5': 'TCTTG', 'WZ-5': 'TCTTT', 'XB-5': 'TGAAA', 'XD-5': 'TGAAC', 'X0-5': 'TGAAG', 'XE-5': 'TGAAT',
'XF-5': 'TGACA', 'X1-5': 'TGACC', 'XH-5': 'TGACG', 'XI-5': 'TGACT', 'X2-5': 'TGAGA', 'XJ-5': 'TGAGC',
'XK-5': 'TGAGG', 'X3-5': 'TGAGT', 'XL-5': 'TGATA', 'XM-5': 'TGATC', 'X4-5': 'TGATG', 'XN-5': 'TGATT',
'XO-5': 'TGCAA', 'X5-5': 'TGCAC', 'XP-5': 'TGCAG', 'XQ-5': 'TGCAT', 'X6-5': 'TGCCA', 'XR-5': 'TGCCC',
'XS-5': 'TGCCG', 'X7-5': 'TGCCT', 'XU-5': 'TGCGA', 'XV-5': 'TGCGC', 'X8-5': 'TGCGG', 'XW-5': 'TGCGT',
'XX-5': 'TGCTA', 'X9-5': 'TGCTC', 'XY-5': 'TGCTG', 'XZ-5': 'TGCTT', '9B-5': 'TGGAA', '9D-5': 'TGGAC',
'90-5': 'TGGAG', '9E-5': 'TGGAT', '9F-5': 'TGGCA', '91-5': 'TGGCC', '9H-5': 'TGGCG', '9I-5': 'TGGCT',
'92-5': 'TGGGA', '9J-5': 'TGGGC', '9K-5': 'TGGGG', '93-5': 'TGGGT', '9L-5': 'TGGTA', '9M-5': 'TGGTC',
'94-5': 'TGGTG', '9N-5': 'TGGTT', '9O-5': 'TGTAA', '95-5': 'TGTAC', '9P-5': 'TGTAG', '9Q-5': 'TGTAT',
'96-5': 'TGTCA', '9R-5': 'TGTCC', '9S-5': 'TGTCG', '97-5': 'TGTCT', '9U-5': 'TGTGA', '9V-5': 'TGTGC',
'98-5': 'TGTGG', '9W-5': 'TGTGT', '9X-5': 'TGTTA', '99-5': 'TGTTC', '9Y-5': 'TGTTG', '9Z-5': 'TGTTT',
'YB-5': 'TTAAA', 'YD-5': 'TTAAC', 'Y0-5': 'TTAAG', 'YE-5': 'TTAAT', 'YF-5': 'TTACA', 'Y1-5': 'TTACC',
'YH-5': 'TTACG', 'YI-5': 'TTACT', 'Y2-5': 'TTAGA', 'YJ-5': 'TTAGC', 'YK-5': 'TTAGG', 'Y3-5': 'TTAGT',
'YL-5': 'TTATA', 'YM-5': 'TTATC', 'Y4-5': 'TTATG', 'YN-5': 'TTATT', 'YO-5': 'TTCAA', 'Y5-5': 'TTCAC',
'YP-5': 'TTCAG', 'YQ-5': 'TTCAT', 'Y6-5': 'TTCCA', 'YR-5': 'TTCCC', 'YS-5': 'TTCCG', 'Y7-5': 'TTCCT',
'YU-5': 'TTCGA', 'YV-5': 'TTCGC', 'Y8-5': 'TTCGG', 'YW-5': 'TTCGT', 'YX-5': 'TTCTA', 'Y9-5': 'TTCTC',
'YY-5': 'TTCTG', 'YZ-5': 'TTCTT', 'ZB-5': 'TTGAA', 'ZD-5': 'TTGAC', 'Z0-5': 'TTGAG', 'ZE-5': 'TTGAT',
'ZF-5': 'TTGCA', 'Z1-5': 'TTGCC', 'ZH-5': 'TTGCG', 'ZI-5': 'TTGCT', 'Z2-5': 'TTGGA', 'ZJ-5': 'TTGGC',
'ZK-5': 'TTGGG', 'Z3-5': 'TTGGT', 'ZL-5': 'TTGTA', 'ZM-5': 'TTGTC', 'Z4-5': 'TTGTG', 'ZN-5': 'TTGTT',
'ZO-5': 'TTTAA', 'Z5-5': 'TTTAC', 'ZP-5': 'TTTAG', 'ZQ-5': 'TTTAT', 'Z6-5': 'TTTCA', 'ZR-5': 'TTTCC',
'ZS-5': 'TTTCG', 'Z7-5': 'TTTCT', 'ZU-5': 'TTTGA', 'ZV-5': 'TTTGC', 'Z8-5': 'TTTGG', 'ZW-5': 'TTTGT',
'ZX-5': 'TTTTA', 'Z9-5': 'TTTTC', 'ZY-5': 'TTTTG', 'ZZ-5': 'TTTTT', 'B-1': 'A', 'D-1': 'C',
'0-1': 'G', 'E-1': 'T', 'F-2': 'AA', '1-2': 'AC', 'H-2': 'AG', 'I-2': 'AT',
'2-2': 'CA', 'J-2': 'CC', 'K-2': 'CG', '3-2': 'CT', 'L-2': 'GA', 'M-2': 'GC',
'4-2': 'GG', 'N-2': 'GT', 'O-2': 'TA', '5-2': 'TC', 'P-2': 'TG', 'Q-2': 'TT',
'6-3': 'AAA', 'R-3': 'AAC', 'S-3': 'AAG', '7-3': 'AAT', 'U-3': 'ACA', 'V-3': 'ACC',
'8-3': 'ACG', 'W-3': 'ACT', 'X-3': 'AGA', '9-3': 'AGC', 'Y-3': 'AGG', 'Z-3': 'AGT',
'DB-3': 'ATA', 'DD-3': 'ATC', 'D0-3': 'ATG', 'DE-3': 'ATT', 'DF-3': 'CAA', 'D1-3': 'CAC',
'DH-3': 'CAG', 'DI-3': 'CAT', 'D2-3': 'CCA', 'DJ-3': 'CCC', 'DK-3': 'CCG', 'D3-3': 'CCT',
'DL-3': 'CGA', 'DM-3': 'CGC', 'D4-3': 'CGG', 'DN-3': 'CGT', 'DO-3': 'CTA', 'D5-3': 'CTC',
'DP-3': 'CTG', 'DQ-3': 'CTT', 'D6-3': 'GAA', 'DR-3': 'GAC', 'DS-3': 'GAG', 'D7-3': 'GAT',
'DU-3': 'GCA', 'DV-3': 'GCC', 'D8-3': 'GCG', 'DW-3': 'GCT', 'DX-3': 'GGA', 'D9-3': 'GGC',
'DY-3': 'GGG', 'DZ-3': 'GGT', '0B-3': 'GTA', '0D-3': 'GTC', '00-3': 'GTG', '0E-3': 'GTT',
'0F-3': 'TAA', '01-3': 'TAC', '0H-3': 'TAG', '0I-3': 'TAT', '02-3': 'TCA', '0J-3': 'TCC',
'0K-3': 'TCG', '03-3': 'TCT', '0L-3': 'TGA', '0M-3': 'TGC', '04-3': 'TGG', '0N-3': 'TGT',
'0O-3': 'TTA', '05-3': 'TTC', '0P-3': 'TTG', '0Q-3': 'TTT', '06-4': 'AAAA', '0R-4': 'AAAC',
'0S-4': 'AAAG', '07-4': 'AAAT', '0U-4': 'AACA', '0V-4': 'AACC', '08-4': 'AACG', '0W-4': 'AACT',
'0X-4': 'AAGA', '09-4': 'AAGC', '0Y-4': 'AAGG', '0Z-4': 'AAGT', 'EB-4': 'AATA', 'ED-4': 'AATC',
'E0-4': 'AATG', 'EE-4': 'AATT', 'EF-4': 'ACAA', 'E1-4': 'ACAC', 'EH-4': 'ACAG', 'EI-4': 'ACAT',
'E2-4': 'ACCA', 'EJ-4': 'ACCC', 'EK-4': 'ACCG', 'E3-4': 'ACCT', 'EL-4': 'ACGA', 'EM-4': 'ACGC',
'E4-4': 'ACGG', 'EN-4': 'ACGT', 'EO-4': 'ACTA', 'E5-4': 'ACTC', 'EP-4': 'ACTG', 'EQ-4': 'ACTT',
'E6-4': 'AGAA', 'ER-4': 'AGAC', 'ES-4': 'AGAG', 'E7-4': 'AGAT', 'EU-4': 'AGCA', 'EV-4': 'AGCC',
'E8-4': 'AGCG', 'EW-4': 'AGCT', 'EX-4': 'AGGA', 'E9-4': 'AGGC', 'EY-4': 'AGGG', 'EZ-4': 'AGGT',
'FB-4': 'AGTA', 'FD-4': 'AGTC', 'F0-4': 'AGTG', 'FE-4': 'AGTT', 'FF-4': 'ATAA', 'F1-4': 'ATAC',
'FH-4': 'ATAG', 'FI-4': 'ATAT', 'F2-4': 'ATCA', 'FJ-4': 'ATCC', 'FK-4': 'ATCG', 'F3-4': 'ATCT',
'FL-4': 'ATGA', 'FM-4': 'ATGC', 'F4-4': 'ATGG', 'FN-4': 'ATGT', 'FO-4': 'ATTA', 'F5-4': 'ATTC',
'FP-4': 'ATTG', 'FQ-4': 'ATTT', 'F6-4': 'CAAA', 'FR-4': 'CAAC', 'FS-4': 'CAAG', 'F7-4': 'CAAT',
'FU-4': 'CACA', 'FV-4': 'CACC', 'F8-4': 'CACG', 'FW-4': 'CACT', 'FX-4': 'CAGA', 'F9-4': 'CAGC',
'FY-4': 'CAGG', 'FZ-4': 'CAGT', '1B-4': 'CATA', '1D-4': 'CATC', '10-4': 'CATG', '1E-4': 'CATT',
'1F-4': 'CCAA', '11-4': 'CCAC', '1H-4': 'CCAG', '1I-4': 'CCAT', '12-4': 'CCCA', '1J-4': 'CCCC',
'1K-4': 'CCCG', '13-4': 'CCCT', '1L-4': 'CCGA', '1M-4': 'CCGC', '14-4': 'CCGG', '1N-4': 'CCGT',
'1O-4': 'CCTA', '15-4': 'CCTC', '1P-4': 'CCTG', '1Q-4': 'CCTT', '16-4': 'CGAA', '1R-4': 'CGAC',
'1S-4': 'CGAG', '17-4': 'CGAT', '1U-4': 'CGCA', '1V-4': 'CGCC', '18-4': 'CGCG', '1W-4': 'CGCT',
'1X-4': 'CGGA', '19-4': 'CGGC', '1Y-4': 'CGGG', '1Z-4': 'CGGT', 'HB-4': 'CGTA', 'HD-4': 'CGTC',
'H0-4': 'CGTG', 'HE-4': 'CGTT', 'HF-4': 'CTAA', 'H1-4': 'CTAC', 'HH-4': 'CTAG', 'HI-4': 'CTAT',
'H2-4': 'CTCA', 'HJ-4': 'CTCC', 'HK-4': 'CTCG', 'H3-4': 'CTCT', 'HL-4': 'CTGA', 'HM-4': 'CTGC',
'H4-4': 'CTGG', 'HN-4': 'CTGT', 'HO-4': 'CTTA', 'H5-4': 'CTTC', 'HP-4': 'CTTG', 'HQ-4': 'CTTT',
'H6-4': 'GAAA', 'HR-4': 'GAAC', 'HS-4': 'GAAG', 'H7-4': 'GAAT', 'HU-4': 'GACA', 'HV-4': 'GACC',
'H8-4': 'GACG', 'HW-4': 'GACT', 'HX-4': 'GAGA', 'H9-4': 'GAGC', 'HY-4': 'GAGG', 'HZ-4': 'GAGT',
'IB-4': 'GATA', 'ID-4': 'GATC', 'I0-4': 'GATG', 'IE-4': 'GATT', 'IF-4': 'GCAA', 'I1-4': 'GCAC',
'IH-4': 'GCAG', 'II-4': 'GCAT', 'I2-4': 'GCCA', 'IJ-4': 'GCCC', 'IK-4': 'GCCG', 'I3-4': 'GCCT',
'IL-4': 'GCGA', 'IM-4': 'GCGC', 'I4-4': 'GCGG', 'IN-4': 'GCGT', 'IO-4': 'GCTA', 'I5-4': 'GCTC',
'IP-4': 'GCTG', 'IQ-4': 'GCTT', 'I6-4': 'GGAA', 'IR-4': 'GGAC', 'IS-4': 'GGAG', 'I7-4': 'GGAT',
'IU-4': 'GGCA', 'IV-4': 'GGCC', 'I8-4': 'GGCG', 'IW-4': 'GGCT', 'IX-4': 'GGGA', 'I9-4': 'GGGC',
'IY-4': 'GGGG', 'IZ-4': 'GGGT', '2B-4': 'GGTA', '2D-4': 'GGTC', '20-4': 'GGTG', '2E-4': 'GGTT',
'2F-4': 'GTAA', '21-4': 'GTAC', '2H-4': 'GTAG', '2I-4': 'GTAT', '22-4': 'GTCA', '2J-4': 'GTCC',
'2K-4': 'GTCG', '23-4': 'GTCT', '2L-4': 'GTGA', '2M-4': 'GTGC', '24-4': 'GTGG', '2N-4': 'GTGT',
'2O-4': 'GTTA', '25-4': 'GTTC', '2P-4': 'GTTG', '2Q-4': 'GTTT', '26-4': 'TAAA', '2R-4': 'TAAC',
'2S-4': 'TAAG', '27-4': 'TAAT', '2U-4': 'TACA', '2V-4': 'TACC', '28-4': 'TACG', '2W-4': 'TACT',
'2X-4': 'TAGA', '29-4': 'TAGC', '2Y-4': 'TAGG', '2Z-4': 'TAGT', 'JB-4': 'TATA', 'JD-4': 'TATC',
'J0-4': 'TATG', 'JE-4': 'TATT', 'JF-4': 'TCAA', 'J1-4': 'TCAC', 'JH-4': 'TCAG', 'JI-4': 'TCAT',
'J2-4': 'TCCA', 'JJ-4': 'TCCC', 'JK-4': 'TCCG', 'J3-4': 'TCCT', 'JL-4': 'TCGA', 'JM-4': 'TCGC',
'J4-4': 'TCGG', 'JN-4': 'TCGT', 'JO-4': 'TCTA', 'J5-4': 'TCTC', 'JP-4': 'TCTG', 'JQ-4': 'TCTT',
'J6-4': 'TGAA', 'JR-4': 'TGAC', 'JS-4': 'TGAG', 'J7-4': 'TGAT', 'JU-4': 'TGCA', 'JV-4': 'TGCC',
'J8-4': 'TGCG', 'JW-4': 'TGCT', 'JX-4': 'TGGA', 'J9-4': 'TGGC', 'JY-4': 'TGGG', 'JZ-4': 'TGGT',
'KB-4': 'TGTA', 'KD-4': 'TGTC', 'K0-4': 'TGTG', 'KE-4': 'TGTT', 'KF-4': 'TTAA', 'K1-4': 'TTAC',
'KH-4': 'TTAG', 'KI-4': 'TTAT', 'K2-4': 'TTCA', 'KJ-4': 'TTCC', 'KK-4': 'TTCG', 'K3-4': 'TTCT',
'KL-4': 'TTGA', 'KM-4': 'TTGC', 'K4-4': 'TTGG', 'KN-4': 'TTGT', 'KO-4': 'TTTA', 'K5-4': 'TTTC',
'KP-4': 'TTTG', 'KQ-4': 'TTTT'}
def is_sequence(sequence):
"""
Checks if sequence is only made up of ATCG's
:param sequence: Sequence to be checked
:return: boolean
"""
valid = re.compile('^[ATCG]+$', re.IGNORECASE)
return valid.match(sequence)
def is_license_plate(length, code):
"""
Checks if the license plate is in the proper format
:param length: Encoded sequence length
:param code: license plate for the sequence
:return: Boolean value of if it is valid or not
"""
if not length.isdigit():
return False
if any(c in ('A', 'T', 'G', 'C') or (not c.isalpha() and not c.isdigit()) for c in code):
return False
return True
def encode_sequence(sequence, prefix):
"""
Encodes the sequence into its corresponding license plate with given prefix (if given one)
:param sequence: The sequence being encoded
:param prefix: The prefix to use for the license plate
:return: The license plate it encodes to
"""
length = len(sequence)
# Encode label
if prefix is '':
final_result = [(str(length) + '-')]
else:
final_result = [prefix + "-" + str(length) + "-"]
work_sequence = sequence
while work_sequence != '':
try:
final_result.append(encode_hash[work_sequence[0:5]])
except KeyError as err:
if not err.args:
err.args = ('',)
err.args = err.args + ("Error, exiting: Segment '" + work_sequence[0:5] +
"' from sequence '" + sequence + "' is invalid.",)
raise
work_sequence = work_sequence[5:]
return ''.join(final_result)
def decode_sequence(plate):
"""
Decode the license-plate using the lookup table
:param plate: license plate being decoded
:return: The sequence it decodes to
"""
if plate.count('-') == 2:
fields = plate.split('-', 2)
# Discard prefix, it isn't used at all
fields = fields[1:]
elif plate.count('-') == 1:
fields = plate.split('-', 1)
else:
raise KeyError("Error, exiting: Provided license plate '" + plate + "' is not in a valid format.")
if not is_license_plate(fields[0], fields[1]):
raise KeyError("Error, exiting: Provided license plate '" + plate + "' is not in a valid format.")
length = int(fields[0])
code = fields[1]
# Retrieve sequence
remainder = length
raw_result = []
while code != '' and remainder > 0:
if remainder >= 5:
try:
raw_result.append(decode_hash[code[0:2] + '-5'])
except KeyError as err:
if not err.args:
err.args = ('',)
err.args = err.args + ("Error, exiting: Segment '" + code[0:2] + "' from license plate '"
+ plate + "' is invalid.",)
raise
else:
try:
raw_result.append(decode_hash[code[0:2] + '-' + str(remainder)])
except KeyError as err:
if not err.args:
err.args = ('',)
err.args = err.args + ("Error, exiting: Segment '" + code[0:2] + "' from license plate '"
+ plate + "' is invalid.",)
raise
remainder -= 5
code = code[2:]
# Check if label make sense
final_result = ''.join(raw_result)
if len(final_result) != length or code != '':
raise KeyError("Error, exiting: Invalid license plate '" + plate + "'.")
return final_result
def convert(seq, encode, prefix):
if prefix is None:
prefix = ''
else:
if '-' in prefix or ' ' in prefix:
sys.stderr.write("Warning: Dashes and spaces are not permitted in the license plate prefix."
"Program will remove all instances automatically from prefix '" + prefix + "'.\n")
prefix = prefix.replace('-', '')
prefix = prefix.replace(' ', '')
if encode:
# Encode
if seq != '':
cleaned = seq.upper().replace('U', 'T')
if is_sequence(cleaned):
return encode_sequence(cleaned, prefix)
else:
raise KeyError('Error, exiting: Illegal characters in line "' + seq + '"')
else:
# Decode
if seq != '':
cleaned = seq.upper()
return decode_sequence(cleaned)
def run_as_script():
"""
Main function
"""
from argparse import RawDescriptionHelpFormatter
parser = argparse.ArgumentParser(
description="Program to generate license plates from given sequence or decode license plate to a sequence. "
"An optional prefix can be provided to the program such as 'tRF', 'rRF', 'iso', etc, if needed.",
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('sequencefile', type=str, help='Sequences that are to be encoded or decoded')
parser.add_argument('encode_choice', type=str, choices=['en', 'de'],
help='Choice of encoding (en) or decoding (de)')
parser.add_argument('--p', '--prefix', type=str, default=None, dest='prefix',
help="Prefix to be used for license plates. 'tRF', 'rRF', 'iso', etc")
args = parser.parse_args()
encode = None
if args.encode_choice == 'en':
encode = True
elif args.encode_choice == 'de':
encode = False
illegal_characters = ['\n', '\r', '\t', '\0', '\f', '`', '?', '*', '\\', '<', '>', '|', '\"', ': ']
for item in illegal_characters:
if item in args.sequencefile.split('/')[-1]:
raise KeyError('Error, exiting: Illegal character "' + item + '" in filename')
try:
sequence_file = open(args.sequencefile, 'r')
except IOError:
sys.stderr.write('Error, exiting: File ' + args.sequencefile + ' not found.\n')
sys.exit(1)
if sequence_file is None:
sys.stderr.write('Error: An unexpected error has occurred, please ensure that the file ' + args.sequencefile +
' exists\n')
sys.exit(1)
sequences = []
for line in sequence_file:
sequences.append(line.rstrip())
sequence_file.close()
done = {}
for seq in sequences:
try:
done[seq] = convert(seq, encode, args.prefix)
except KeyError as error:
print(error)
sys.exit(1)
for item in done:
sys.stdout.write(item + '\t' + done[item] + '\n')
if __name__ == "__main__":
run_as_script()
mirtop-0.4.23/mirtop/mirna/realign.py 0000664 0000000 0000000 00000037527 13547635037 0017560 0 ustar 00root root 0000000 0000000 import re
from Bio import pairwise2
from Bio.Seq import Seq
from collections import defaultdict
from mirtop.mirna.mintplates import convert
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
class hits:
""""Class with alignment information."""
def __init__(self):
self.sequence = ""
self.idseq = ""
self.precursors = defaultdict(isomir)
self.score = []
self.best_hits = [] # maybe sam object?
self.counts = 0
def set_sequence(self, seq):
self.sequence = seq
self.idseq = make_id(seq)
def set_precursor(self, precursor, isomir):
self.precursors[(precursor, isomir.start)] = isomir
def remove_precursor(self, precursor):
del self.precursors[precursor]
class isomir:
"""
Class to represent isomiRs information.
"""
def __init__(self):
self.t5 = []
self.t3 = []
self.add = []
self.subs = []
self.external = ""
self.align = None
self.cigar = None
self.filter = "Pass"
self.map_score = 0
self.end = None
self.start = None
self.mirna = None
self.strand = "+"
def set_pos(self, start, l, strand="+"):
"""Set end position"""
if start < 0:
# l = l + start
start = 0
self.strand = strand
self.start = start
self.end = start + l - 1
if strand == "-":
self.start = start + l - 1
self.end = start
def formatGFF(self):
"""Create Variant attribute."""
value = []
subs = self.subs
if self.external != "notsure" and self.external != "":
return self.external
for sub in subs:
if sub:
if sub[0] > 1 and sub[0] < 8:
value.append("iso_snv_seed")
elif sub[0] == 8:
value.append("iso_snv_central_offset")
elif sub[0] > 8 and sub[0] < 13:
value.append("iso_snv_central")
elif sub[0] > 12 and sub[0] < 18:
value.append("iso_snv_central_supp")
else:
value.append("iso_snv")
if self.add:
value.append("iso_add3p:%s" % len(self.add))
if self.t5:
size = len(self.t5)
direction = "-" if self.t5.isupper() else "+"
value.append("iso_5p:%s%s" % (direction, size))
if self.t3:
size = len(self.t3)
direction = "+" if self.t3.isupper() else "-"
value.append("iso_3p:%s%s" % (direction, size))
if not value:
value = ["NA"]
return ",".join(list(set(value)))
def format(self, sep="\t"):
"""Create tabular line from variant fields."""
subs = "".join(["".join(map(str, mism)) for mism in self.subs])
if not subs:
subs = "0"
add = "0" if not self.add else self.add
return "%s%s%s%s%s%s%s" % (subs, sep, add, sep,
self.t5, sep, self.t3)
def format_id(self, sep="\t"):
"""Create simple identifier from variant fields."""
subs = ["".join(["".join([c[2], str(c[0]), c[1]]) for c in self.subs])]
if not subs:
subs = []
add = [] if not self.add else ["e%s" % self.add]
t5 = ["s%s" % self.t5] if self.t5 and self.t5 != "NA" else []
t3 = ["%s" % self.t3] if self.t3 and self.t3 != "NA" else []
full = t5 + subs + t3 + add
return sep.join([f for f in full if f])
def get_score(self, sc):
"""Get score from variant fields."""
for a in self.add:
if a in ['A', 'T']:
sc -= 0.25
else:
sc -= 0.75
for e in self.subs:
sc -= 1
return sc
def is_iso(self):
"""Define whether element is isomiR or not."""
if self.external == "NA":
return False
if self.t5 or self.t3 or self.add or self.subs or self.external != "":
return True
return False
def read_id(idu):
"""
Read a unique identifier for the sequence and
convert it to the nucleotides,
replacing an unique code for 5 nts.
It uses the code from *mirtop.mirna.keys()*.
Inspired by MINTplate: https://cm.jefferson.edu/MINTbase
https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates
Args:
*idu(str)*: unique identifier for the sequence.
Returns:
*seq(str)*: nucleotides sequences.
"""
try:
seq = convert(idu, False, 'iso')
except KeyError:
logger.error("UID is not valid " + idu)
return False
return seq
def make_id(seq):
"""
Create a unique identifier for the sequence from the nucleotides,
replacing 5 nts for a unique sequence.
It uses the code from *mirtop.mirna.keys()*.
Inspired by MINTplate: https://cm.jefferson.edu/MINTbase
https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates
Args:
*seq(str)*: nucleotides sequences.
Returns:
*idName(str)*: unique identifier for the sequence.
"""
try:
idu = convert(seq, True, 'iso')
except KeyError as error:
logger.error("Sequence is not valid " + seq)
raise
# If you wanted to add "iso-" into the license plate as the prefix
# idu = convert(seq, True, "iso")
return idu
def is_sequence(seq):
"""
This function check whether the sequence is valid or not.
Args:
*seq(str)*: string acting as a sequence.
Returns:
*boolean*: whether is or not a valid nucleotide sequence.
"""
alphabet = re.compile('^[ACTG]*$', re.IGNORECASE)
return alphabet.match(seq)
def align(x, y, local=False):
"""
Pairwise alignments between two sequenes.
https://medium.com/towards-data-science/pairwise-sequence-alignment-using-biopython-d1a9d0ba861f
Args:
*x(str)*: short sequence.
*y(str)*: long sequence.
*local(boolean)*: local or global alignment.
Returns:
*aligned_x(hit)*: alignment information, socre and positions.
"""
if local:
aligned_x = pairwise2.align.localxx(x, y)[0]
else:
aligned_x = pairwise2.align.globalms(x, y, 1, -1, -1, -0.5)[0]
aligned_x = list(aligned_x)
n_x = aligned_x[0]
if "N" in n_x:
N_indices = [i for i, ltr in enumerate(n_x) if ltr == 'N']
n_x = list(n_x)
for N_index in N_indices:
n_x[N_index] = y[N_index]
n_x = ''.join(n_x)
aligned_x[0] = n_x
return tuple(aligned_x)
def _add_cigar_char(counter, cache):
if counter == 1:
return cache
else:
return str(counter) + cache
def make_cigar(seq, mature):
"""
Function that will create CIGAR string from aligment
between read and reference sequence.
Args:
*seq(str)*: read sequence.
*mature(str)*: short sequence.
Return:
*short(str)*: CIGAR string.
"""
cigar = ""
for pos in range(0, len(seq)):
if seq[pos] == mature[pos]:
cigar += "M"
elif seq[pos] != mature[pos] and seq[pos] != "-" and mature[pos] != "-":
cigar += seq[pos]
elif seq[pos] == "-":
cigar += "D"
elif mature[pos] == "-":
cigar += "I"
cache = ""
counter = 1
short = ""
for c in cigar:
if c != cache and cache != "" and cache == "M":
short += _add_cigar_char(counter, cache)
counter = 1
cache = c
if c != "M":
short += c
if c == cache and c == "M":
counter += 1
cache = c
if cache == "M":
short += _add_cigar_char(counter, cache)
return short
def cigar_correction(cigarLine, query, target):
"""
Read from CIGAR in BAM file to define mismatches.
Args:
*cirgarLine(str)*: CIGAR string from BAM file.
*query(str)*: read sequence.
*target(str)*: target sequence.
Returns:
*(list)*: [query_nts, target_nts]
"""
query_pos = 0
target_pos = 0
query_fixed = []
target_fixed = []
for (cigarType, cigarLength) in cigarLine:
if cigarType == 0: # match
query_fixed.append(query[query_pos:query_pos+cigarLength])
target_fixed.append(target[target_pos:target_pos+cigarLength])
query_pos = query_pos + cigarLength
target_pos = target_pos + cigarLength
elif cigarType == 1: # insertions
query_fixed.append(query[query_pos:query_pos+cigarLength])
target_fixed.append("".join(["-"] * cigarLength))
query_pos = query_pos + cigarLength
elif cigarType == 2: # deletion
target_fixed.append(target[target_pos:target_pos+cigarLength])
query_fixed.append("".join(["-"] * cigarLength))
target_pos = target_pos + cigarLength
return ["".join(query_fixed), "".join(target_fixed)]
def expand_cigar(cigar):
"""
From short CIGAR version to long CIGAR version
where each character is each nts in the sequence.
Args:
*cigar(str)*: CIGAR string.
>>> 10MA3M
Returns:
*cigar_long(str)*: CIGAR long.
>>> MMMMMMMMMMAMMM
"""
cigar_long = ""
n = 0
for nt in cigar:
if nt in ["D", "M", "I", "A", "T", "C", "G"]:
if n > 0:
cigar_long += nt * int(n)
else:
cigar_long += nt
n = 0
else:
if n > 0:
n = int("%s%s" % (n, nt))
else:
n = int(nt)
return cigar_long
def cigar2snp(cigar, reference):
"""
From a CIGAR string and reference sequence
detect mistmatches positions and reference and
target nucleotides.
Args:
*cigar(str)*: CIGAR string.
*reference(str)*: reference sequence.
Returns:
*snp(list)*: position of mismatches (indels included) as:
>>> [pos, seq_nt, ref_nt]
"""
snp = []
pos_seq = 0
pos_ref = 0
for nt in expand_cigar(cigar):
if nt != "M":
if nt == "I":
snp.append([pos_seq, nt, "-"])
pos_seq += 1
elif nt == "D":
snp.append([pos_seq, "-", reference[pos_ref]])
pos_ref += 1
else:
snp.append([pos_seq, nt, reference[pos_ref]])
pos_ref += 1
pos_seq += 1
else:
pos_ref += 1
pos_seq += 1
return snp
def reverse_complement(seq):
"""Get reverse complement of a sequences
Args:
*seq(str)*: sequence.
>>> GCAT
Returns:
*(str)*: reverse complemente sequence:
>>> ATGC
"""
return str(Seq(seq).reverse_complement())
def get_mature_sequence(precursor, mature, exact=False, nt = 5):
"""
From precursor and mature positions
get mature sequence with +/- 4 flanking nts.
Args:
*precursor(str)*: long sequence.
*mature(list)*: [start, end].
*exact(boolean)*: not add 4+/- flanking nts.
*nt(int)*: number of nts to get.
Returns:
*(str)*: mature sequence.
"""
p = "%s%s" % ("".join(["N"]*nt), precursor)
s = mature[0] + nt
e = mature[1] + nt
if exact:
return p[s:e + 1]
return p[s - (nt - 1) :e + nt]
def align_from_variants(sequence, mature, variants):
"""
Giving the sequence read,
the mature from get_mature_sequence,
and the variant GFF annotation:
get a list of substitutions
Args:
*sequence(str)*: read sequence.
*mature(str)*: mature sequence from
*mirtop.mirna.realing.get_mature_sequence()*.
*variants(str)*: string from Variant attribute in GFF file.
Returns:
*snp(list)*: [[pos, target, reference]]
"""
init_log = "iso:%s -> %s\nref:%s" % (sequence, variants, mature)
snps = []
k = [v.split(":")[0] for v in variants.split(",") if v.find(":") > -1]
v = [int(v.split(":")[1]) for v in variants.split(",") if v.find(":") > -1]
var_dict = dict(zip(k, v))
logger.debug("realign::align_from_variants::sequence %s" % sequence)
logger.debug("realign::align_from_variants::mature %s" % mature)
logger.debug("realign::align_from_variants::variants %s" % variants)
snp = ["iso_snv" for v in variants.split(",") if v.find("snv") > -1]
fix_5p = 7
if "iso_5p" in k:
fix_5p = 7 + var_dict["iso_5p"]
mature = mature[fix_5p:]
if "iso_add3p" in k:
sequence = sequence[:-1 * var_dict["iso_add3p"]]
if "iso_3p" in k:
shift = 7 + (-1 * var_dict["iso_3p"])
if shift != 0:
mature = mature[:-(shift)]
else:
mature = mature[:-7]
logger.debug("realign::align_from_variants::snp %s" % snp)
logger.debug("realign::align_from_variants::sequence %s" % sequence)
logger.debug("realign::align_from_variants::mature %s" % mature)
if len(sequence) != len(mature): # in case of indels, align again
a = align(sequence, mature)
sequence = a[0]
mature = a[1]
if len(sequence) > len(mature):
logger.warning("Invalid isomiR definition:\n%s\niso:%s\nref:%s" % (init_log, sequence, mature))
return "Invalid"
for p in range(0, len(sequence)):
if sequence[p] != mature[p]:
if mature[p] == "N":
continue
value = ""
pos = p + 1
value = "iso_snv"
logger.debug("realign::align_from_variants::value %s at %s" % (value, pos))
if value in snp:
snps.append([pos, sequence[p], mature[p]])
logger.debug("realign::align_from_variants::snps %s" % snps)
return snps
def variant_to_5p(hairpin, pos, variant):
"""
From a sequence and a start position get the nts
+/- indicated by iso_5p. Pos option is 0-base-index
Args:
*hairpin(str)*: long sequence:
>>> AAATTTT
*position(int)*: >>> 3
*variant(int)*: number of nts involved in the variant:
>>> -1
Returns:
*(str)*: nucleotide involved in the variant:
>>> T
"""
pos = pos[0]
iso_t5 = [v for v in variant.split(",") if v.startswith("iso_5p")]
if iso_t5:
t5 = int(iso_t5[0].split(":")[-1][-1])
direction_t5 = int(iso_t5[0].split(":")[-1]) * -1
if direction_t5 > 0:
return hairpin[pos - t5:pos]
elif direction_t5 < 0:
return hairpin[pos:pos + t5].lower()
return "0"
def variant_to_3p(hairpin, pos, variant):
"""
From a sequence and a start position get the nts
+/- indicated by iso_3p. Pos option is 0-base-index
Args:
*hairpin(str)*: long sequence:
>>> AAATTTT
*position(int)*: >>> 3
*variant(int)*: number of nts involved in the variant:
>>> -1
Returns:
*(str)*: nucleotide involved in the variant:
>>> A
"""
pos = pos[1]
iso_t3 = [v for v in variant.split(",") if v.startswith("iso_3p")]
if iso_t3:
t3 = int(iso_t3[0].split(":")[-1][-1])
direction_t3 = int(iso_t3[0].split(":")[-1])
if direction_t3 > 0:
return hairpin[pos + 1:pos + t3 + 1]
elif direction_t3 < 0:
return hairpin[pos - t3 + 1:pos + 1].lower()
return "0"
def variant_to_add(read, variant):
"""
From a sequence and a start position get the nts
+/- indicated by iso_3p. Pos option is 0-base-index
Args:
*hairpin(str)*: long sequence:
>>> AAATTTT
*position(int)*: >>> 3
*variant(int)*: number of nts involved in the variant:
>>> 2
Returns:
*(str)*: nucleotide involved in the variant:
>>> TT
"""
add = [v for v in variant.split(",") if v.startswith("iso_add")]
if add:
add = int(add[0].split(":")[-1][-1]) * -1
return read[add:]
return "0"
mirtop-0.4.23/mirtop/mirna/snps.py 0000664 0000000 0000000 00000011575 13547635037 0017115 0 ustar 00root root 0000000 0000000 from __future__ import print_function;
import sys
import mirtop.libs.logger as mylog
STDOUT = sys.stdout
logger = mylog.getLogger(__name__)
def _parse_mut(mut):
"""
Parse mutation field to get position and nts.
"""
multiplier = 1
if mut.startswith("-"):
mut = mut[1:]
multiplier = -1
nt = mut.strip('0123456789')
pos = int(mut[:-2]) * multiplier
return nt, pos
def _get_reference_position(isomir):
"""
Liftover from isomir to reference mature
"""
mut = isomir.split(":")[1]
if mut == "0":
return mut
nt, pos = _parse_mut(mut)
trim5 = isomir.split(":")[-2]
off = -1 * len(trim5)
if trim5.islower():
off = len(trim5)
if trim5 == "NA" or trim5 == "0":
off = 0
# print(isomir)
# print([mut, pos, off, nt])
return "%s%s" % (pos + off, nt)
def _get_pct(isomirs, mirna):
"""
Get pct of variants respect to the reference
using reads and different sequences
"""
pass_pos = []
for isomir in isomirs.iterrows():
mir = isomir[1]["chrom"]
mut = isomir[1]["sv"]
mut_counts = isomir[1]["counts"]
total = mirna.loc[mir, "counts"] * 1.0 - mut_counts
mut_diff = isomir[1]["diff"]
ratio = mut_counts / total
if mut_counts > 10 and ratio > 0.4 and mut != "0" and mut_diff > 1:
isomir[1]["ratio"] = ratio
pass_pos.append(isomir[1])
return pass_pos
def _genotype(data):
"""Simple decision about genotype."""
if data['ratio'] > 0.9:
return "1/1"
return "1/0"
def _print_header(data):
"""
Create vcf header to make
a valid vcf.
"""
print("##fileformat=VCFv4.2", file=STDOUT)
print("##source=seqbuster2.3", file=STDOUT)
print("##reference=mirbase", file=STDOUT)
for pos in data:
print("##contig=" % pos["chrom"], file=STDOUT)
print('##INFO=', file=STDOUT)
print('##FORMAT=', file=STDOUT)
print('##FORMAT=', file=STDOUT)
print('##FORMAT=', file=STDOUT)
print("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMP001",file=STDOUT)
def print_vcf(data):
"""Print vcf line following rules."""
id_name = "."
qual = "."
chrom = data['chrom']
pos = data['pre_pos']
nt_ref = data['nt'][1]
nt_snp = data['nt'][0]
flt = "PASS"
info = "ID=%s" % data['mature']
frmt = "GT:NR:NS"
gntp = "%s:%s:%s" % (_genotype(data), data["counts"], data["diff"])
print("\t".join(map(str, [chrom, pos, id_name, nt_ref, nt_snp, qual, flt, info, frmt, gntp])),file=STDOUT)
def _make_header():
"""
Make vcf header for SNPs in miRs
"""
def liftover(pass_pos, matures):
"""Make position at precursor scale"""
fixed_pos = []
_print_header(pass_pos)
for pos in pass_pos:
mir = pos["mature"]
db_pos = matures[pos["chrom"]]
mut = _parse_mut(pos["sv"])
print([db_pos[mir], mut, pos["sv"]])
pos['pre_pos'] = db_pos[mir][0] + mut[1] - 1
pos['nt'] = list(mut[0])
fixed_pos.append(pos)
print_vcf(pos)
return fixed_pos
def create_vcf(isomirs, matures, gtf, vcf_file=None):
"""
Create vcf file of changes for all samples.
PASS will be ones with > 3 isomiRs supporting the position
and > 30% of reads, otherwise LOW
"""
global STDOUT
isomirs['sv'] = [_get_reference_position(m) for m in isomirs["isomir"]]
mirna = isomirs.groupby(['chrom']).sum()
sv = isomirs.groupby(['chrom', 'mature', 'sv'], as_index=False).sum()
sv["diff"] = isomirs.groupby(['chrom', 'mature', 'sv'], as_index=False).size().reset_index().loc[:,0]
pass_pos = _get_pct(sv, mirna)
if vcf_file:
with open(vcf_file, 'w') as out_handle:
STDOUT = out_handle
pass_pos = liftover(pass_pos, matures)
if gtf:
vcf_genome_file = vcf_file.replace(".vcf", "_genome.vcf")
with open(vcf_genome_file, 'w') as out_handle:
STDOUT = out_handle
pass_pos = liftover_to_genome(pass_pos, gtf)
def liftover_to_genome(pass_pos, gtf):
"""Liftover from precursor to genome"""
fixed_pos = []
for pos in pass_pos:
if pos["chrom"] not in gtf:
continue
db_pos = gtf[pos["chrom"]][0]
mut = _parse_mut(pos["sv"])
print([db_pos, pos])
if db_pos[3] == "+":
pos['pre_pos'] = db_pos[1] + pos["pre_pos"] + 1
else:
pos['pre_pos'] = db_pos[2] - (pos["pre_pos"] - 1)
pos['chrom'] = db_pos[0]
pos['nt'] = list(mut[0])
fixed_pos.append(pos)
_print_header(fixed_pos)
for pos in fixed_pos:
print_vcf(pos)
mirtop-0.4.23/requirements.txt 0000664 0000000 0000000 00000000070 13547635037 0016410 0 ustar 00root root 0000000 0000000 pysam
pybedtools
pandas
biopython
pyyaml
pybedtools
six
mirtop-0.4.23/run_test.sh 0000775 0000000 0000000 00000001517 13547635037 0015335 0 ustar 00root root 0000000 0000000 #!/usr/bin/env bash
# bash script inspared from bcbio-nextgen: https://github.com/chapmanb/bcbio-nextgen/blob/master/tests/run_tests.sh
# It allows to run specific test using the name like
# ./run_test.sh test_align
set -o pipefail # trace ERR through pipes
set -o errtrace # trace ERR through 'time command' and other functions
set -o nounset ## set -u : exit the script if you try to use an uninitialised variable
set -o errexit ## set -e : exit the script if any statement returns a non-true return value
set -v
set -x
export PS4='+(${BASH_SOURCE}:${LINENO}): ${FUNCNAME[0]:+${FUNCNAME[0]}(): }'
readlinkf(){ perl -MCwd -e 'print Cwd::abs_path shift' $1; }
SC_DIR=$(dirname "$(readlinkf `which mirtop`)")
unset PYTHONHOME
unset PYTHONPATH
export PYTHONNOUSERSITE=1
echo $SC_DIR
echo "Run module test."
"$SC_DIR/nosetests" -v -s -a "$@"
mirtop-0.4.23/scripts/ 0000775 0000000 0000000 00000000000 13547635037 0014616 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/scripts/create_mirgenedb.sh 0000664 0000000 0000000 00000000512 13547635037 0020427 0 ustar 00root root 0000000 0000000
SCRIPT="$1"
function run {
B="http://mirgenedb.org:81/static/data/$1-all.bed"
F="http://mirgenedb.org:81/static/data/$1-$2-pri-30-30.fas"
python $SCRIPT/prepare.py --bed ${B} --precursor30 ${F}
}
run hsa hg38
run mmu mm10
run rno rn6
run cpo cavPor3
run ocu oryCun2
run dno dasNov3
run gga galGal4
run dre danRer10
mirtop-0.4.23/scripts/import_gff3.py 0000664 0000000 0000000 00000021365 13547635037 0017416 0 ustar 00root root 0000000 0000000 # -*- coding: utf-8 -*-
"""
Function that loads a gff file into a pandas dataframe
"""
import pandas as pd
import numpy as np
def loadfile(filename,verbose=True):
try:
if verbose==True:
print 'Loading', filename
# obtaning sample names and number from 3rd line in header
num_header_lines=0
with open(filename) as f:
rowfile=f.readline()
num_header_lines+=1
while True:
if rowfile.startswith('## COLDATA'):
sample_names=rowfile.split()[2].split(',')
break
else:
rowfile=f.readline()
num_header_lines+=1
sample_number = len(sample_names)
if verbose==True:
print '--------------------------------------'
print sample_number,' samples in the file'
print '--------------------------------------'
for elem in sample_names:
print elem
print '--------------------------------------'
# number of columns in gff file
gff_cols = pd.read_table(filename, sep='\t', skiprows=num_header_lines, header=None).columns
# Adquiring non-attributes data
body_data=pd.read_table(filename, sep='\t', skiprows=num_header_lines, header=None, usecols=gff_cols[0:-1])
body_data.columns = ['SeqID', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase']
# Adquiring attributes data
atr_data = pd.read_table(filename, sep='\t', skiprows=num_header_lines, header=None, usecols=gff_cols[[-1]])
#print 'hasta aqui todo bien'
# Splitting the attributes column
list_atr = []
# cheking attributes present in first row
attr_names=[attr.split()[0] for attr in atr_data.values[0,0].split(';')]
#attributes in the column
#print attr_names
num_attr = len(attr_names) #number of attributes
#expression_colindex=attr_names.index ('Expression') #position of the expression column in the attr column
if verbose==True:
print num_attr,' attributes in the file '
print '--------------------------------------'
for attr in attr_names:
print attr
print '--------------------------------------'
# joining rows of attributes without the descriptor
for row in range(atr_data.shape[0]):
list_atr.append([attr.split()[1] for attr in atr_data.values[row,0].split(';')])
#list_atr.append(atr_data.values[row, 0].split()[1::2])
# appending observations
atr_data = pd.DataFrame(list_atr, columns=attr_names)
# desglosing the expression column in a column for each sample
list_expression=[]
for row in range(atr_data.shape[0]):
list_expression.append(atr_data.loc[row,'Expression'].split(','))
sample_names=['Expression_' +x for x in sample_names]
expression_data = pd.DataFrame(list_expression, columns=sample_names)
atr_data=atr_data.drop('Expression',axis=1) #Remove the expression column
atr_data=atr_data.join(expression_data)
# Joining the body and attributes dataframes
data = body_data.join(atr_data)
#Unlisting the variant column
tempframe=data[data.type=='isomiR']
list_variants_present=[]
for row in tempframe.itertuples():
actual_variant=tempframe.loc[row.Index,'Variant'].split(',')
for i in range(len(actual_variant)):
if actual_variant[i] not in list_variants_present:
list_variants_present.append(actual_variant[i])
for var in list_variants_present:
for row in data.itertuples():
try:
index=data.loc[row.Index,'Variant'].split(',').index(var)
except:
index=-1
if index>=0:
#print var, data.loc[row.Index,'Variant']
data.at[row.Index,var]=1
else:
data.at[row.Index,var]=np.nan
return data
except:
print 'Error loading the file'
"""
Function that check the header then load a gff file and check the content
Returns the dataframe if the format is ok, false if not
"""
def load_check_gff3(filename):
try:
Error = False
coldata_found=False
# Checking the format file
# Header and 1st data row
with open(filename) as file:
rowfile=file.readline()
while True:
if rowfile.startswith('##'):
if rowfile.startswith("## COLDATA"):
coldata_found=True
rowfile=file.readline()
else:
data_1=rowfile.split('\t')
break
if coldata_found==False:
print 'No COLDATA, bad header'
return False
#Number of columns without breaking down attributes column
if len(data_1) > 9:
Error=True
print(len(data_1))
print('Too much columns')
# Cheking the attributes column
attr_names=data_1[-1].split(';')
list_attr=[]
for atr in range(len(attr_names)-1):
list_attr.append(attr_names[atr].split()[0])
possible_attr = ['UID', 'Read', 'Name', 'Parent', 'Variant', 'Cigar', 'Hits', 'Alias', 'Genomic', 'Expression',
'Filter', 'Seed_fam']
for attr in list_attr:
if attr not in possible_attr:
Error=True
print attr,'is not a possible attribute'
break
if Error:
print 'File format error'
return False
# If not format error, loading content
try:
dataframe=loadfile(filename,True)
except:
print 'Error loading file'
return False
print 'Checking content'
for i in range(dataframe.shape[0]):
# Labels in type column
if dataframe.loc[i, 'type'] not in ['ref_miRNA', 'isomiR']:
Error = True
print'line', i, 'pip install Markdownbad type error'
# start= dataframe.loc[i, 'end']:
Error = True
print 'line', i, 'start >=end error'
# Strand + or -
if dataframe.loc[i, 'strand'] not in ['+', '-']:
Error = True
print 'line', i, 'bad strand error'
# Variant checking
possible_variant=['iso_5p','iso_3p','iso_add','iso_snp_seed','iso_snp_central_offset','iso_snp_central',
'iso_central_supp','iso_snp_central_supp','iso_snp']
variant_i=dataframe.loc[i,'Variant'].split(',')
if len(variant_i)==1 and variant_i[0]!='NA':
if variant_i[0].split(':')[0] not in possible_variant:
Error = True
print 'Variant error', variant_i[0].split(':')[0], 'line', i
elif variant_i[0]!='NA':
for var in range(len(variant_i)):
if variant_i[var].split(':')[0] not in possible_variant:
Error = True
print 'Variant error', variant_i[0].split(':')[0], 'line', i
#Checking expression data
expression_cols=[col for col in dataframe.columns if 'Expression_' in col]
for col in expression_cols:
for i in range(dataframe.shape[0]):
if not dataframe.loc[i,col].isdigit():
print dataframe.loc[i,col].isdigit()
print 'Expression count error line',i
Error= True
dataframe[col]=dataframe[col].astype(int) #setting the datatype of counts
dataframe[col]=dataframe[col].replace(0,np.nan) #Setting 0 reads to NaN
if 'Filter' in dataframe.columns:
for i in range(dataframe.shape[0]):
if dataframe.loc[i, 'Filter']!='Pass':
print 'Warning non-pass filter in line',i
if Error:
print 'File format error'
return False
print '--------------------------------------'
print dataframe.dtypes
print '--------------------------------------'
print 'Format ok'
return dataframe
except:
print 'Error checking the file'
return False
mirtop-0.4.23/scripts/make_spikeins.py 0000664 0000000 0000000 00000007356 13547635037 0020025 0 ustar 00root root 0000000 0000000 from __future__ import print_function
import argparse
import os
import random
from collections import defaultdict
import pysam
import mirtop.libs.logger as mylog
import mirtop.libs.do as runner
def _read_fasta(fa, size):
source = dict()
with open(fa) as inh:
for line in inh:
if line.startswith(">"):
name = line.strip().split()[0].replace(">", "")
else:
if len(line.strip()) >= size:
source.update({name: line.strip()[0:size]})
return source
def _update_ends(source):
nts = ["A", "T", "C", "G"]
start_idx = 0
end_idx = 0
for name in source:
source[name] = nts[start_idx] + source[name] + nts[end_idx]
if end_idx == 3 and start_idx == 3:
end_idx = -1
start_idx = 0
if end_idx == 3:
start_idx += 1
end_idx = 0
end_idx += 1
return source
def _write_fasta(sequences, filename):
with open(filename, 'w') as outh:
for name in sequences:
if sequences[name]:
print(">%s\n%s" % (name, sequences[name]), file=outh)
return filename
def _parse_hits(sam, source):
uniques = defaultdict(list)
# read sequences and score hits (ignore same sequence)
handle = pysam.Samfile(sam, "rb")
for line in handle:
reference = handle.getrname(line.reference_id)
name = line.query_name
# sequence = line.query_sequence if not line.is_reverse else reverse_complement(line.query_sequence)
if reference == name:
continue
# print([reference, name, line.get_tag("NM")])
distance = line.get_tag("NM")
uniques[name].append(distance)
uniques[reference].append(distance)
# read parsed data and keep the ones with score > 10 edit distance
for name in uniques:
if min(uniques[name]) < 4:
if name in source:
source[name] = None
return source
parser = argparse.ArgumentParser()
parser.add_argument("--fa",
help="File with mature sequences.", required=True)
parser.add_argument("-s", "--size", default=22,
help="Size of spike-ins to generate.")
parser.add_argument("-n", "--number", default=16,
help="Number of spike-ins to generate.")
parser.add_argument("-o", "--out", default="spikeins.fa",
help="Name used for output files.")
parser.add_argument("--seed", help="set up seed for reproducibility.",
default=42)
parser.add_argument("--universe", help="Set up universe sequences to avoid duplication.",
default=None)
args = parser.parse_args()
random.seed(args.seed)
mylog.initialize_logger(os.path.dirname(os.path.abspath(args.out)))
logger = mylog.getLogger(__name__)
# Read file to get all sequences longer than size - 2
size = args.size - 2
source = _read_fasta(args.fa, size)
logger.info("%s was read: %s sequences were loaded" % (args.fa, len(source)))
source = _update_ends(source)
logger.info("source updated with extended nts: %s" % source)
# Map all vs all with razers3
modified = _write_fasta(source, os.path.join(os.path.dirname(args.out), "modified.fa"))
sam = os.path.join(os.path.dirname(args.out), "modified.bam")
runner.run(("razers3 -i 75 -rr 80 -f -so 1 -o {output} {target} {query}").format(output=sam, target=modified, query=modified))
uniques = _parse_hits(sam, source)
print(uniques)
if args.universe:
sam = os.path.join(os.path.dirname(args.out), "modified_vs_universe.sam")
runner.run(("razers3 -i 75 -rr 80 -f -o {output} {target} {query}").format(output=sam, target=args.universe, query=modified))
uniques = _parse_hits(sam, uniques)
print(uniques)
# Write uniques to fasta
_write_fasta(uniques, args.out)
mirtop-0.4.23/scripts/make_unique.py 0000664 0000000 0000000 00000005567 13547635037 0017510 0 ustar 00root root 0000000 0000000 from __future__ import print_function
import argparse
import os
import random
from collections import defaultdict
import pysam
import mirtop.libs.logger as mylog
import mirtop.libs.do as runner
parser = argparse.ArgumentParser()
parser.add_argument("--fa",
help="File with mature sequences.", required=True)
parser.add_argument("-o", "--out", default="spikeins.fa",
help="Name used for output files.")
parser.add_argument("--seed", help="set up seed for reproducibility.",
default=42)
parser.add_argument("--max_size", help="maximum size allowed in the final output.",
default=25)
args = parser.parse_args()
random.seed(args.seed)
def _sam_to_bam(bam_fn):
bam_out = "%s.bam" % os.path.splitext(bam_fn)[0]
cmd = "samtools view -Sbh {bam_fn} -o {bam_out}"
runner.run(cmd.format(**locals()))
return bam_fn
def _bam_sort(bam_fn):
bam_sort_by_n = os.path.splitext(bam_fn)[0] + "_sort.bam"
runner.run(("samtools sort -n -o {bam_sort_by_n} {bam_fn}").format(
**locals()))
return bam_sort_by_n
def _read_fasta(fa):
source = dict()
with open(fa) as inh:
for line in inh:
if line.startswith(">"):
name = line.strip().split()[0].replace(">", "")
else:
source.update({name: line.strip()})
return source
def _write_fasta(sequences, filename, max=25):
with open(filename, 'w') as outh:
for name in sequences:
if sequences[name]:
if len(sequences[name]) < max:
print(">%s\n%s" % (name, sequences[name]), file=outh)
return filename
def _parse_hits(sam, source):
uniques = defaultdict(list)
# bam_fn = _sam_to_bam(sam)
# bam_fn = _bam_sort(bam_fn)
# read sequences and score hits (ignore same sequence)
handle = pysam.Samfile(sam, "rb")
for line in handle:
reference = handle.getrname(line.reference_id)
name = line.query_name
# sequence = line.query_sequence if not line.is_reverse else reverse_complement(line.query_sequence)
if reference == name:
continue
# print([reference, name, line.get_tag("NM")])
distance = line.get_tag("NM")
uniques[name].append(distance)
uniques[reference].append(distance)
# read parsed data and keep the ones with score > 10 edit distance
for name in uniques:
if min(uniques[name]) < 5:
if name in source:
source[name] = None
return source
# Map all vs all with razers3
source = _read_fasta(args.fa)
sam = os.path.join(os.path.dirname(args.out), "modified.bam")
runner.run(("razers3 -dr 5 -i 75 -rr 80 -f -so 1 -o {output} {target} {query}").format(output=sam, target=args.fa, query=args.fa))
uniques = _parse_hits(sam, source)
# Write uniques to fasta
_write_fasta(uniques, args.out, args.max_size)
mirtop-0.4.23/scripts/miRNA.simulator.py 0000664 0000000 0000000 00000012720 13547635037 0020156 0 ustar 00root root 0000000 0000000 from __future__ import print_function
from optparse import OptionParser
import os
import random
import numpy
from mirtop.mirna import fasta
from mirtop.mirna import mapper
from mirtop.mirna import realign
from mirtop.gff import body, header
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
def write_collapse_fastq(reads, out_fn):
idx = 0
with open(out_fn, 'a') as outh:
for r in reads:
idx += 1
print(">name%s_x%s" % (idx, r[1]), file=outh)
print(r[0], file=outh)
def write_fastq(reads, out_fn):
idx = 0
with open(out_fn, 'a') as outh:
for r in reads:
idx += 1
print("@name_read:%s" % idx, file=outh)
print(r, file=outh)
print("+", file=outh)
print("I" * len(r), file=outh)
def create_read(read, count, adapter="TGGAATTCTCGGGTGCCAAGGAACTC", size=36):
reads = list()
for i in range(0, count):
rest = size - len(read)
part = adapter[:rest]
reads.append(read + part)
return reads
def variation(info, seq):
randS = random.randint(info[0] - 2, info[0] + 2) + 1
randE = random.randint(info[1] - 1, info[1] + 2) + 1
if randS < 1:
randS = 1
if randE > len(seq):
randE = info[1] - 1
randSeq = seq[randS:randE]
t5Lab = ""
t5Lab = seq[randS:info[0]] if randS < info[0] else t5Lab
t5Lab = seq[info[0]:randS].lower() if randS > info[0] else t5Lab
t3Lab = ""
t3Lab = seq[randE:info[1] + 1].lower() if randE < info[1] + 1 else t3Lab
t3Lab = seq[info[1] + 1:randE] if randE > info[1] + 1 else t3Lab
# mutation
isMut = random.randint(0, 10)
mutLab = []
if isMut == 3:
ntMut = random.randint(0, 3)
posMut = random.randint(0, len(randSeq) - 1)
if not randSeq[posMut] == nt[ntMut]:
temp = list(randSeq)
mutLab = [[posMut, nt[ntMut], randSeq[posMut]]]
temp[posMut] = nt[ntMut]
randSeq = "".join(temp)
# addition
isAdd = random.randint(0, 3)
addTag = ""
if isAdd == 2:
posAdd = random.randint(1, 3)
for numadd in range(posAdd):
ntAdd = random.randint(0, 1)
print([randSeq, seq[randS + len(randSeq)]])
if nt[ntAdd] == seq[randS + len(randSeq)]:
ntAdd = 1 if ntAdd == 0 else 0
randSeq += nt[ntAdd]
addTag += nt[ntAdd]
print([randSeq, randE, info[1]])
return [randSeq, randS, t5Lab, t3Lab, mutLab, addTag]
def create_iso(name, mir, seq, numsim, exp):
reads = dict()
full_read = list()
clean_read = list()
seen = set()
for mirna in mir[name]:
info = mir[name][mirna]
for rand in range(int(numsim)):
e = 1
if exp:
trial = random.randint(1, 100)
p = random.randint(1, 50) / 50.0
e = numpy.random.negative_binomial(trial, p, 1)[0]
iso = realign.isomir()
randSeq, iso.start, iso.t5, iso.t3, iso.subs, iso.add = variation(info, seq)
if randSeq in seen:
continue
seen.add(randSeq)
iso.end = iso.start + len(randSeq)
aln = realign.align(randSeq, seq[iso.start:iso.end])
iso.cigar = realign.make_cigar(aln[0], aln[1])
iso.mirna = mirna
query_name = "%s.%s.%s" % (mirna, iso.format_id("."), randSeq)
reads[query_name] = realign.hits()
reads[query_name].set_sequence(randSeq)
reads[query_name].counts = e
reads[query_name].set_precursor(name, iso)
full_read.extend(create_read(randSeq, e))
clean_read.append([randSeq, e])
# print([randSeq, mutLab, addTag, t5Lab, t3Lab, mirSeq])
# data[randSeq] = [exp, iso] # create real object used in code to generate GFF
write_fastq(full_read, full_fq)
write_collapse_fastq(clean_read, clean_fq)
gff = body.create(reads, "miRBase21", "sim1")
return gff
def _write(lines, header, fn):
out_handle = open(fn, 'w')
print(header, file=out_handle)
for m in lines:
for s in sorted(lines[m].keys()):
for hit in lines[m][s]:
print(hit[4], file=out_handle)
out_handle.close()
usagetxt = "usage: %prog --fa precurso.fa --gtf miRNA.gtf -n 10"
parser = OptionParser(usage=usagetxt, version="%prog 1.0")
parser.add_option("--fa",
help="", metavar="FILE")
parser.add_option("--gtf",
help="", metavar="FILE")
parser.add_option("-n", "--num", dest="numsim",
help="")
parser.add_option("-e", "--exp", dest="exp", action="store_true",
help="give expression", default=False)
parser.add_option("-p", "--prefix", help="output name")
parser.add_option("--seed", help="set up seed for reproducibility.", default=None)
(options, args) = parser.parse_args()
if options.seed:
random.seed(options.seed)
full_fq = "%s_full.fq" % options.prefix
clean_fq = "%s_clean.fq" % options.prefix
out_gff = "%s.gff" % options.prefix
if os.path.exists(full_fq):
os.remove(full_fq)
if os.path.exists(clean_fq):
os.remove(clean_fq)
pre = fasta.read_precursor(options.fa, "")
mir = mapper.read_gtf_to_precursor(options.gtf)
nt = ['A', 'T', 'G', 'C']
gffs = dict()
h = header.create(["sampleX"], "miRBase1", "")
for precursor in pre:
seq = pre[precursor]
gffs.update(create_iso(precursor, mir, seq, options.numsim, options.exp))
_write(gffs, h, out_gff)
mirtop-0.4.23/scripts/prepare.py 0000664 0000000 0000000 00000005656 13547635037 0016642 0 ustar 00root root 0000000 0000000 import os
import sys
from collections import defaultdict
from argparse import ArgumentParser
def _read_pri(fn):
pri = dict()
with open(fn) as inh:
for line in inh:
if line.startswith(">") & line.strip().endswith("pri"):
name = line.strip()[1:-4]
else:
pri[name] = line.strip()
return pri
def _read_bed(fn):
bed = defaultdict(dict)
with open(fn) as inh:
for line in inh:
cols = line.strip().split("\t")
if cols[3].find("pri") > 0:
continue
if cols[3].find("loop") > 0:
continue
if cols[3].find("seed") > 0:
continue
if cols[3].find("motif") > 0:
continue
if cols[3].find("co") > 0:
continue
bed[cols[3].split("_")[0]].update({cols[3]: [int(cols[1]), int(cols[2]), cols[5]]})
return bed
def _download(url, outfn):
if os.path.isfile(outfn):
return outfn
os.system('wget -O %s %s' % (outfn, url))
return outfn
if __name__ == "__main__":
parser = ArgumentParser(description="Prepare files from mirGeneDB to be used with seqbuster")
parser.add_argument("--bed", help="bed file with position of all sequence", required=1)
parser.add_argument("--precursor30", help="file or url with fasta of precursor + 30 nt", required=1)
args = parser.parse_args()
sps = os.path.basename(args.precursor30).split("-")[0]
if os.path.isfile(args.bed):
fnbed = args.bed
else:
fnbed = _download(args.bed, "%s.bed" % sps)
if os.path.isfile(args.precursor30):
fnfa = args.precursor30
else:
fnfa = _download(args.precursor30, "%s.fa" % sps)
fa = _read_pri(fnfa)
bed = _read_bed(fnbed)
OUT = open("%s.miRNA.str" % sps, 'w')
OUTP = open("%s.hairpin.fa" % sps, 'w')
for mir in fa:
if mir in bed:
precursor = bed[mir][mir + "_pre"]
print precursor
mir5p = ""
mir3p = ""
for mature in bed[mir]:
info = bed[mir][mature]
# print info
if mature.endswith("pre"):
continue
if precursor[2] == "-":
start = int(precursor[1]) - int(info[1]) + 31
end = int(precursor[1]) - int(info[0]) + 30
else:
start = int(info[0]) - int(precursor[0]) + 31
end = int(info[1]) - int(precursor[0]) + 30
# print [mature, start, end, fa[mir][start:end]]
if mature.find("5p") > 0:
mir5p = "[%s:%s-%s]" % (mature, start, end)
if mature.find("3p") > 0:
mir3p = "[%s:%s-%s]" % (mature, start, end)
print >>OUT, ">%s (X) %s %s" % (mir, mir5p, mir3p)
print >>OUTP, ">%s\n%s" % (mir, fa[mir])
OUT.close()
OUTP.close()
mirtop-0.4.23/scripts/pyPlotM.py 0000664 0000000 0000000 00000004501 13547635037 0016574 0 ustar 00root root 0000000 0000000 import matplotlib.pyplot as plt
def makePlots(tsvFileN, pdfFileN, show):
#Reading file
with open(tsvFileN, "r") as ins:
lines = []
for line in ins:
lines.append(line.split('\t'))
#Calculating maximum number of plots
maxPlots = 0
for x in range(1, len(lines)):
idc = int(lines[x][0]) + 1
if maxPlots < idc:
maxPlots = idc
# Set up the matplotlib figure
cols = 3
rows = maxPlots/3
plt.subplots(3, rows, figsize=(8, 6), sharex=True)
#Creating array to store the values
array = []
for i in range(0, maxPlots):
arr2 = []
for j in range(0, 5):
arr2.append(0)
array.append(arr2)
#Filling the array with the values
for x in range(1, len(lines)):
idc = int(lines[x][0])
cnt = int(lines[x][3])
typ = lines[x][4].strip()
nam = lines[x][1].strip()
pos = 3;
if typ == 'synthetic':
pos = 2
if typ == 'bcbio':
pos = 0
if typ == 'mirge':
pos = 1
array[idc][pos] = cnt
array[idc][4] = nam
#Plotting the graphs
plt.figure(1)
#plt.xlabel('tool')
#plt.ylabel('Counts')
p = []
p.append(array[0][0])
p.append(array[0][1])
p.append(array[0][2])
n = array[0][4]
for i in range(0, maxPlots):
del(p[2])
del(p[1])
del(p[0])
p.append(array[i][0])
p.append(array[i][1])
p.append(array[i][2])
n = array[i][4]
pcd = rows * 100 + cols * 10 + 1 + i
plt.subplot(pcd)
ax = plt.gca()
ax.set_facecolor('lightgray')
plt.xticks([1,2,3], ('bcbio', 'mirge', 'synthetic'))
plt.yticks([0,10,20,30,40,50])
plt.tick_params(axis='both', which='major', labelsize=8)
plt.tick_params(axis='both', which='minor', labelsize=8)
plt.bar([1,2,3], p, color='gray')
plt.title(n)
for i, v in enumerate(p):
plt.text(i+0.9, 0, str(v), color='black', fontsize='8', fontweight='bold')
plt.subplots_adjust(top=0.92, bottom=0.10, left=0.10, right=0.95, hspace=0.50, wspace=0.35)
plt.savefig(pdfFileN, format="pdf")
if show == 1:
plt.show()
makePlots("../data/examples/plot/example_count.tsv", "kk.pdf", 1)
mirtop-0.4.23/setup.py 0000664 0000000 0000000 00000002474 13547635037 0014650 0 ustar 00root root 0000000 0000000 """small RNA-seq annotation"""
import os
from setuptools import setup, find_packages
version = '0.4.23'
url = 'http://github.com/mirtop/mirtop'
def readme():
with open('README.md') as f:
return f.read()
def write_version_py():
version_py = os.path.join(os.path.dirname(__file__), 'mirtop',
'version.py')
with open(version_py, "w") as out_handle:
out_handle.write("\n".join(['__version__ = "%s"' % version,
'__url__ = "%s"' % url]))
write_version_py()
setup(name='mirtop',
version=version,
description='Small RNA-seq annotation',
long_description=readme(),
long_description_content_type="text/markdown",
classifiers=[
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 2.7',
"Programming Language :: Python :: 3",
'Topic :: Scientific/Engineering :: Bio-Informatics'
],
keywords='RNA-seq miRNA isomiRs annotation',
url=url,
author='Lorena Pantano',
author_email='lorena.pantano@gmail.com',
license='MIT',
packages=find_packages(),
test_suite='nose',
entry_points={
'console_scripts': ['mirtop=mirtop.command_line:main'],
},
include_package_data=True,
zip_safe=False)
mirtop-0.4.23/test/ 0000775 0000000 0000000 00000000000 13547635037 0014106 5 ustar 00root root 0000000 0000000 mirtop-0.4.23/test/test_automated_analysis.py 0000664 0000000 0000000 00000040775 13547635037 0021422 0 ustar 00root root 0000000 0000000 """This directory is setup with configurations to run the main functional test.
Inspired in bcbio-nextgen code
"""
from __future__ import print_function
import os
import subprocess
import unittest
import shutil
import contextlib
import functools
from nose import SkipTest
from nose.plugins.attrib import attr
@contextlib.contextmanager
def make_workdir():
remove_old_dir = True
dirname = os.path.join(os.path.dirname(__file__), "test_automated_output")
if remove_old_dir:
if os.path.exists(dirname):
shutil.rmtree(dirname)
os.makedirs(dirname)
orig_dir = os.getcwd()
try:
os.chdir(dirname)
yield dirname
finally:
os.chdir(orig_dir)
def expected_failure(test):
"""Small decorator to mark tests as expected failure.
Useful for tests that are work-in-progress.
"""
@functools.wraps(test)
def inner(*args, **kwargs):
try:
test(*args, **kwargs)
except Exception:
raise SkipTest
else:
raise AssertionError('Failure expected')
return inner
class AutomatedAnalysisTest(unittest.TestCase):
"""Setup a full automated analysis and run the pipeline.
"""
def setUp(self):
self.data_dir = os.path.join(os.path.dirname(__file__), "data", "automated")
def _install_test_files(self, data_dir):
"""Download required sequence and reference files.
"""
# self._download_to_dir(url, dirname)
def _download_to_dir(self, url, dirname):
print(dirname)
cl = ["wget", url]
subprocess.check_call(cl)
cl = ["tar", "-xzvpf", os.path.basename(url)]
subprocess.check_call(cl)
shutil.move(os.path.basename(dirname), dirname)
os.remove(os.path.basename(url))
@attr(simulate=True)
def test_simulate(self):
"""Check simulated data"""
mirna = "TGAGGTAGTAGGTTGTATAGTT"
correct = 0
n = 0
with open("data/examples/simulation/res/reads.mirna") as inh:
header = inh.readline()
for line in inh:
cols = line.strip().split()
mut, add, t5, t3 = cols[6:10]
seq = cols[0]
if mut!="0":
pos = int(mut[:-2])
nt1 = mut[-2]
nt2 = mut[-1]
seql = list(seq)
seql[pos] = nt2
seq = "".join(seql)
if t5!="0" and t5.islower():
seq = "%s%s" % (t5.upper(), seq)
elif t5!="0" and t5.isupper():
seq = seq[len(t5):]
if add!="0":
seq = seq[:-len(add)]
if t3!="0" and t3.islower():
seq = "%s%s" % (seq, t3.upper())
elif t3!="0" and t3.isupper():
seq = seq[:-len(t3)]
if seq == mirna:
correct += 1
else:
print("\nerror:\n%s\n%s" % (seq, mirna))
n += 1
print("rate %s/%s" % (correct, n))
@attr(complete=True)
@attr(annotate=True)
@attr(bam=True)
@attr(cmd=True)
def test_srnaseq_annotation_bam(self):
"""Run miraligner analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--sps", "hsa", "--add-extra",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/annotate/sim_isomir.sam"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(low_memory=True)
@attr(cmd=True)
def test_srnaseq_annotation_bam_chunk(self):
"""Run miraligner analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff", "--low-memory",
"--sps", "hsa", "--add-extra",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/annotate/sim_isomir.sam"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(cmd_bam_genomic=True)
@attr(complete=True)
@attr(cmd=True)
def test_srnaseq_annotation_genomic_bam(self):
"""Run genomic bam analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--sps", "hsa", "--add-extra", "--genomic",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/db/mirbase/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/annotate/hsa-let-7a-nm.sam"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(cmd_bam_genomic_low_memory=True)
@attr(complete=True)
@attr(cmd=True)
def test_srnaseq_annotation_genomic_bam_low_memory(self):
"""Run genomic bam analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff", "--genomic", "--low-memory",
"--sps", "hsa", "--add-extra",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/db/mirbase/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/annotate/hsa-let-7a-nm.sam"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_seqbuster=True)
@attr(cmd=True)
def test_srnaseq_annotation_seqbuster(self):
"""Run miraligner analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--format", "seqbuster",
"--sps", "hsa",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/seqbuster/reads.mirna"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_seqbuster_low_memory=True)
@attr(cmd=True)
def test_srnaseq_annotation_seqbuster_low_memory(self):
"""Run miraligner analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff", "--low-memory",
"--format", "seqbuster",
"--sps", "hsa",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/seqbuster/reads.mirna"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_isomirsea=True)
@attr(cmd=True)
def test_srnaseq_annotation_isomirsea(self):
"""Run isomirsea analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--format", "isomirsea",
"--sps", "hsa",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/isomir-sea/tagMir-all.gff",
"-d", "-vd"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_srnabench=True)
@attr(cmd=True)
def test_srnaseq_annotation_srnabench(self):
"""Run srnabench analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--format", "srnabench",
"--sps", "hsa",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/srnabench/",
"-d", "-vd"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_optimir=True)
@attr(cmd=True)
def test_srnaseq_annotation_optimir(self):
"""Run optimir analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--format", "optimir",
"--sps", "hsa",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/optimir/synthetic_100_full.gff3",
"-d", "-vd"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_manatee=True)
@attr(cmd=True)
def test_srnaseq_annotation_manatee(self):
"""Run Manatee analysis
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--format", "manatee",
"--sps", "hsa",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/examples/manatee/simulated.sam",
"-d", "-vd"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_stats=True)
@attr(cmd=True)
def test_srnaseq_stats(self):
"""Run stats analysis
"""
with make_workdir():
clcode = ["mirtop",
"stats",
"-o", "test_out_mirs",
"../../data/examples/gff/correct_file.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
if not os.path.exists("test_out_mirs/mirtop_stats.txt"):
raise ValueError("File doesn't exist, something is wrong with stats cmd.")
if sum(1 for line in open('test_out_mirs/mirtop_stats.txt')) == 1:
raise ValueError("File is empty, something is wrong with stats cmd.")
@attr(complete=True)
@attr(cmd_merge=True)
@attr(cmd=True)
def test_merge_bam(self):
"""
Run collapse two samples
"""
with make_workdir():
clcode = ["mirtop",
"gff",
"--sps", "hsa", "--add-extra",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"-o", "test_out_mirs",
"../../data/merge/samples1.sam",
"../../data/merge/samples2.sam"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_export_seqbuster=True)
@attr(cmd=True)
def test_export_seqbuster(self):
"""
Run SEQBUSTER export command
"""
with make_workdir():
clcode = ["mirtop",
"export",
"-o", "test_out_mirs",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"../../data/examples/gff/correct_file.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_export_vcf=True)
@attr(cmd=True)
def test_export_vcf(self):
"""
Run VCF export command
"""
with make_workdir():
clcode = ["mirtop",
"export",
"-o", "test_out_mirs",
"--format", "vcf",
"-d", "-vd",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"../../data/examples/gff/correct_file.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_export_fasta=True)
@attr(cmd=True)
def test_export_fasta(self):
"""
Run FASTA export command
"""
with make_workdir():
clcode = ["mirtop",
"export",
"-o", "test_out_mirs",
"--format", "fasta",
"-d", "-vd",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"../../data/examples/gff/correct_file.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_count=True)
@attr(cmd=True)
def test_count(self):
"""
Run count command
"""
with make_workdir():
clcode = ["mirtop",
"counts",
"-o", "test_out_mirs",
"--hairpin", "../../data/examples/annotate/hairpin.fa",
"--gtf", "../../data/examples/annotate/hsa.gff3",
"--gff", "../../data/examples/synthetic/let7a-5p.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_spikeins=True)
@attr(cmd=True)
def test_spikeins_cmd(self):
"""Run spikeins analysis
"""
import platform
with make_workdir():
shutil.copy("../../data/examples/spikeins/spikeins.fa",
"spikeins.fa")
clcode = ["mirtop",
"spikein",
"spikeins.fa",
"-o",
"test_out_spikeins"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
if platform.system() == "Linux":
clcode = ["razers3", "-dr", "0", "-i", "80", "-rr", "90",
"-f", "-o", "spikeins.sam",
"test_out_spikeins/spikeins_pre.fasta",
"../../data/examples/spikeins/test-spikeins.fa"]
print(" ".join(clcode))
subprocess.check_call(clcode)
else:
shutil.copy("../../data/examples/spikeins/spikeins.sam",
"spikeins.sam")
clcode = ["mirtop",
"gff",
"--add-extra",
"--hairpin", "test_out_spikeins/spikeins_pre.fasta",
"--gtf", "test_out_spikeins/spikeins_pre.gff",
"-o", "test_out_mirs",
"spikeins.sam"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_update=True)
@attr(cmd=True)
def test_update_cmd(self):
"""Run update analysis
"""
with make_workdir():
clcode = ["mirtop",
"update",
"-o", "test_out_mirs",
"../../data/examples/versions/version1.0.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode)
@attr(complete=True)
@attr(cmd_validate=True)
@attr(cmd=True)
def test_validate_cmd(self):
"""Run update analysis
"""
with make_workdir():
clcode = ["mirtop",
"validate",
"../../data/examples/gff/correct_file.gff"]
print("")
print(" ".join(clcode))
subprocess.check_call(clcode) mirtop-0.4.23/test/test_functions.py 0000664 0000000 0000000 00000052572 13547635037 0017542 0 ustar 00root root 0000000 0000000 """
This directory is setup with configurations to run the main functional test.
Inspired in bcbio-nextgen code
"""
from __future__ import print_function
import os
import unittest
import argparse
import contextlib
import shutil
from nose.plugins.attrib import attr
@contextlib.contextmanager
def make_workdir():
remove_old_dir = True
dirname = os.path.join("test", "test_automated_output")
if remove_old_dir:
if os.path.exists(dirname):
shutil.rmtree(dirname)
os.makedirs(dirname)
orig_dir = os.getcwd()
try:
yield dirname
finally:
os.chdir(orig_dir)
def annotate(fn, read_file, load=False, create=True, keep_name=False,
gtf=None, genomic=None):
args = argparse.Namespace()
args.hairpin = "data/examples/annotate/hairpin.fa"
args.sps = "hsa"
args.gtf = "data/examples/annotate/hsa.gff3"
args.out = "test/test_automated_output"
args.database = None
if gtf:
args.gtf = gtf
args.genomic = genomic
args.add_extra = True
args.out_format = "gtf"
args.keep_name = keep_name
from mirtop.mirna import fasta, mapper
precursors = fasta.read_precursor(args.hairpin, args.sps)
matures = mapper.read_gtf_to_precursor(args.gtf)
args.precursors = precursors
args.matures = matures
args.database = mapper.guess_database(args)
from mirtop.mirna import annotate
from mirtop.gff import body
if not load:
reads = read_file(fn, args)
else:
reads = read_file
if create:
ann = annotate.annotate(reads, matures, precursors)
body = body.create(ann, "miRBase21", "Example", args)
return body
class FunctionsTest(unittest.TestCase):
"""Setup a full automated analysis and run the pipeline.
"""
@attr(database=True)
def test_database(self):
from mirtop.mirna import mapper
args = argparse.Namespace()
args.gtf = "data/examples/annotate/hsa.gff3"
args.database = None
db = mapper.guess_database(args)
print("Database is %s" % db)
if db != "miRBasev21":
raise ValueError("%s not eq to miRBasev21" % db)
@attr(read_hairpin=True)
def test_read_hairpin(self):
from mirtop.mirna import mapper, fasta
from mirtop.libs import logger
logger.initialize_logger("test_read_files", True, True)
map_mir = mapper.read_gtf_to_precursor(
"data/examples/annotate/hsa.gff3")
print(map_mir)
if map_mir["hsa-let-7a-1"]["hsa-let-7a-5p"][0] != 5:
raise ValueError("GFF is not loaded correctly.")
fasta_precursor = fasta.read_precursor(
"data/examples/annotate/hairpin.fa", "hsa")
print(fasta_precursor)
fasta_precursor2 = fasta.read_precursor(
"data/examples/annotate/hairpin.fa", None)
print(fasta_precursor2)
if fasta_precursor != fasta_precursor2:
raise ValueError("species value generates two different dicts.")
# read data/aligments/let7-perfect.bam
return True
@attr(read_hairpin_mirgenedb=True)
def test_read_hairpin_mirgenedb(self):
from mirtop.mirna import mapper
from mirtop.libs import logger
logger.initialize_logger("test_read_files", True, True)
map_mir = mapper.read_gtf_to_precursor(
"data/db/mirgenedb/hsa.gff")
print(map_mir)
@attr(read_mir2chr=True)
def test_read_mir2chr(self):
from mirtop.mirna import mapper
from mirtop.libs import logger
logger.initialize_logger("test_read_files", True, True)
map_mir = mapper.read_gtf_chr2mirna("data/examples/annotate/hsa.gff3")
print(map_mir)
# print(mapper.read_gtf_chr2mirna2("data/examples/annotate/hsa.gff3"))
@attr(read_mir2genomic=True)
def test_read_mir2genomic(self):
from mirtop.mirna import mapper
from mirtop.libs import logger
logger.initialize_logger("test_read_files", True, True)
map_mir = mapper.read_gtf_to_mirna("data/examples/annotate/hsa.gff3")
print(map_mir)
@attr(read_line=True)
def test_read_line(self):
"""Read GFF/GTF line"""
from mirtop.gff.body import read_gff_line
with open("data/examples/gff/2samples.gff") as inh:
for line in inh:
print(read_gff_line(line))
@attr(code=True)
def test_code(self):
"""testing code correction function"""
from mirtop.mirna.realign import make_id, read_id
def _convert(s, test, reverse=False):
code = read_id(s) if reverse else make_id(s)
if code != test:
raise ValueError("%s didn't result on %s but in %s" %
(s, test, code))
_convert("AAACCCTTTGGG", "iso-12-B1NY4")
_convert("AAACCCTTTGGGA", "iso-13-B1NYDX")
_convert("AAACCCTTTGGGAT", "iso-14-B1NYI7")
_convert("iso-12-B1NY4", "AAACCCTTTGGG", True)
_convert("iso-13-B1NYDX", "AAACCCTTTGGGA", True)
_convert("iso-14-B1NYI7", "AAACCCTTTGGGAT", True)
# if make_id("AGTFCVS"):
# raise ValueError("This should be False. Not valid sequence.")
# if read_id("asD(-"):
# raise ValueError("This should be False, Not valid code.")
@attr(code_convert=True)
def test_code_convert(self):
"""testing code correction function"""
from mirtop.mirna.realign import make_id
from mirtop.gff.update import read_uid_10
if not make_id(read_uid_10("@#%$")) == "iso-12-B1NY4":
raise ValueError("Update ID is not working.")
if not make_id(read_uid_10("@#%$@2")) == "iso-13-B1NYDX":
raise ValueError("Update ID is not working.")
@attr(cigar=True)
def test_cigar(self):
"""testing cigar correction function"""
cigar = [[0, 14], [1, 1], [0, 5]]
from mirtop.mirna.realign import cigar_correction, make_cigar, \
cigar2snp, expand_cigar
fixed = cigar_correction(cigar, "AAAAGCTGGGTTGAGGAGGA",
"AAAAGCTGGGTTGAGAGGA")
if not fixed[0] == "AAAAGCTGGGTTGAGGAGGA":
raise ValueError("Sequence 1 is not right.")
if not fixed[1] == "AAAAGCTGGGTTGA-GAGGA":
raise ValueError("Sequence 2 is not right.")
if not make_cigar("AAA-AAATAAA", "AGACAAA-AAA") == "MAMD3MI3M":
raise ValueError("Cigar not eq to MAMD3MI3M: %s" %
make_cigar("AAA-AAATAAA", "AGACAAA-AAA"))
# test expand cigar
if not expand_cigar("3MA3M") == "MMMAMMM":
raise ValueError("Cigar 3MA3M not eqaul to MMMAMMM but to %s" %
expand_cigar("3MA3M"))
# test cigar to snp
if not cigar2snp("3MA3M", "AAATCCC")[0] == [3, "A", "T"]:
raise ValueError("3MA3M not equal AAATCCC but %s" %
cigar2snp("3MA3M", "AAATCCC"))
@attr(sequence=True)
def test_is_sequence(self):
"""testing if string is valid sequence"""
from mirtop.mirna.realign import is_sequence
if not is_sequence("ACTGC"):
raise ValueError("ACTGC should return true.")
if is_sequence("AC2TGC"):
raise ValueError("AC2TGC should return false.")
@attr(locala=True)
def test_locala(self):
"""testing pairwise alignment"""
from mirtop.mirna.realign import align
print("\nExamples of perfect match, deletion, mutation")
print(align("TGAGTAGTAGGTTGTATAGTT", "TGAGGTAGTAGGTTGTATAGTT")[0])
print(align("TGAGGTGTAGGTTGTATAGTT", "TGAGGTAGTAGGTTGTATAGTT")[0])
print(align("TGAGGTAGTAGGCTGTATAGTT", "TGAGGTAGTAGGTTGTATAGTT")[0])
print(align("TGANTAGTAGNTTGTATNGTT", "TGAGTAGTAGGTTGTATAGTTT")[0])
print(align("TGANTAGTNGNTTGTATNGTT", "TGAGTATAGGCCTTGTATAGTT")[0])
print(align("NCANAGTCCAAGNTCATN", "TCATAGTCCAAGGTCATG")[0])
@attr(reverse=True)
def test_reverse(self):
"""Test reverse complement function"""
from mirtop.mirna.realign import reverse_complement
print("Testing ATGC complement")
if "GCAT" != reverse_complement("ATGC"):
raise ValueError("ATGC complement is not: %s" %
reverse_complement("ATGC"))
@attr(class_gff=True)
def test_class(self):
"""Test class to read GFF line"""
from mirtop.gff.classgff import feature
gff = feature("hsa-let-7a-5p\tmiRBasev21\tisomiR\t4\t25\t0\t+\t.\t"
"Read hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:"
"null_add:null_x861; UID bhJJ5WJL2;"
" Name hsa-let-7a-5p; Parent hsa-let-7a-1;"
" Variant iso_5p:+1,iso_3p:-1; Cigar 22M;"
" Expression 861; Filter Pass; Hits 1;")
print(gff.columns)
print(gff.attributes)
@attr(merge=True)
def test_merge(self):
"""Test merge functions"""
from mirtop.gff import merge
example_line = "hsa-let-7a-5p\tmiRBasev21\tisomiR\t4\t25"
if merge._chrom(example_line) != "hsa-let-7a-5p":
raise ValueError("Chrom should be hsa-let-7a-5p.")
if merge._start(example_line) != "4":
raise ValueError("Start should be 4.")
expression = merge._convert_to_string({'s': 1, 'x': 2}, ['s', 'x'])
print(merge._fix("hsa-let-7a-5p\tmiRBasev21\tisomiR\t4\t25\t0\t+\t.\t"
"Read hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:"
"null_add:null_x861; UID bhJJ5WJL2;"
" Name hsa-let-7a-5p; Parent hsa-let-7a-1;"
" Variant iso_5p:+1,iso_3p:-1; Cigar 22M;"
" Expression 861; Filter Pass; Hits 1;", expression))
if expression != "1,2":
raise ValueError("This is wrong: %s" % expression)
@attr(align_mature=True)
def test_variant(self):
"""testing get mature sequence"""
from mirtop.mirna import fasta, mapper
from mirtop.mirna.realign import get_mature_sequence, \
align_from_variants
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
matures = mapper.read_gtf_to_precursor(
"data/examples/annotate/hsa.gff3")
res = get_mature_sequence("GAAAATTTTTTTTTTTAAAAG", [5, 15])
if res != "AAAATTTTTTTTTTTAAAA":
raise ValueError("Results for GAAAATTTTTTTTTTTAAAAG was %s" % res)
mature = get_mature_sequence(precursors["hsa-let-7a-1"],
matures["hsa-let-7a-1"]["hsa-let-7a-5p"], nt = 8)
if mature != "NNTGGGATGAGGTAGTAGGTTGTATAGTTTTAGGGT":
raise ValueError("Results for hsa-let-7a-5p is %s" % mature)
res = align_from_variants("AGGTAGTAGTTGTATAGTT", mature,
"iso_5p:+2,iso_snv_central")
if not res or res[0][0] != 10:
raise ValueError("Wrong alignment for test 0 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTT", mature,
"iso_5p:+2")
if res:
raise ValueError("Wrong alignment for test 1 %s" % res)
res = align_from_variants("GATGAGGTAGTAGGTTGTATAGTT", mature,
"iso_5p:-2")
if res:
raise ValueError("Wrong alignment for test 2 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTTTT", mature,
"iso_5p:+2,iso_add3p:2")
if res:
raise ValueError("Wrong alignment for test 3 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTTTT", mature,
"iso_5p:+2,iso_3p:2")
if res:
raise ValueError("Wrong alignment for test 4 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAG", mature,
"iso_5p:+2,iso_3p:-2")
if res:
raise ValueError("Wrong alignment for test 5 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGAA", mature,
"iso_5p:+2,iso_3p:-2,iso_add3p:2")
if res:
raise ValueError("Wrong alignment for test 6 %s" % res)
res = align_from_variants("AGGTAGTAGGATGTATAGTT", mature,
"iso_5p:+2,iso_snv_central")
if not res:
if res[0][0] != 10:
raise ValueError("Wrong alignment for test 7 %s" % res)
res = align_from_variants("AGGTAGTAGGATGTATAGAA", mature,
"iso_5p:+2,iso_3p:-2,iso_add3p:2")
if res:
raise ValueError("Wrong alignment for test 8 %s" % res)
@attr(alignment=True)
def test_alignment(self):
"""testing alignments function"""
from mirtop.bam import bam
from mirtop.gff.classgff import feature
fns = {"let7-last1D.sam": {56:"iso_add3p:1,iso_snv"},
"let7-1D.sam": {5:"iso_snv,iso_3p:-5"},
"let7-last7M1I.sam": {5:"iso_add3p:1,iso_snv_seed"},
"let7-middle1D.sam": {5:"iso_snv_central_supp,iso_3p:-2"},
"let7-perfect.sam": {5:"NA"},
"let7-triming.sam": {5:"iso_3p:+2",4:"iso_5p:-1",6:"iso_5p:+1,iso_3p:-3"}}
#import pdb; pdb.set_trace()
for fn in fns:
gff = annotate("data/aligments/%s" % fn, bam.read_bam)
for pos in gff['hsa-let-7a-1']:
f = feature(gff['hsa-let-7a-1'][pos][0][4])
if not set(f.attributes['Variant'].split(",")) == set(fns[fn][pos].split(",")):
raise ValueError("Error in %s" % fn)
@attr(alignment_genomic=True)
def test_alignment_genomic(self):
"""testing alignments function"""
from mirtop.bam import bam
from mirtop.libs import logger
logger.initialize_logger("test_read_files", True, True)
# print(annotate("data/examples/annotate/hsa-let-7a-5ploss1_neg.sam",
# bam.read_bam,
# gtf="data/db/hsa.gff3", genomic=True))
print("\ngenomic\n")
with make_workdir():
for example in ["hsa-let-7a-nm", "hsa-let-7a-5ploss1",
"hsa-let-7a-3ploss1", "hsa-let-7a-5ploss1_neg"]:
print(annotate("data/examples/annotate/%s.sam" % example,
bam.read_bam,
gtf="data/db/mirbase/hsa.gff3", genomic=True))
@attr(keep_name=True)
def test_keep_name(self):
from mirtop.bam import bam
line = annotate("data/aligments/let7-perfect.sam",
bam.read_bam,
keep_name=True)
print(line)
if line["hsa-let-7a-1"][5][0][4].find("seq_perfect_x2") < 0:
raise ValueError("Keep name failed: %s" % line)
@attr(seqbuster=True)
def test_seqbuster(self):
"""testing reading seqbuster files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import seqbuster
print("\nperfect\n")
annotate("data/examples/seqbuster/reads20.mirna", seqbuster.read_file)
print("\naddition\n")
annotate("data/examples/seqbuster/readsAdd.mirna", seqbuster.read_file)
print("\nno frequency\n")
annotate("data/examples/seqbuster/seqbuster_nofreq.mirna", seqbuster.read_file)
@attr(srnabench=True)
def test_srnabench(self):
"""testing reading srnabench files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import srnabench
annotate("data/examples/srnabench", srnabench.read_file, create=False)
@attr(optimir=True)
def test_optimir(self):
"""testing reading optimir files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.importer import optimir
annotate("data/examples/optimir/synthetic_100_full.gff3", optimir.read_file, create=False)
@attr(prost=True)
def test_prost(self):
"""testing reading prost files function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.mirna import fasta
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
fn = "data/examples/prost/prost.example.txt"
from mirtop.importer import prost
reads = prost.read_file(
fn, precursors, "miRBasev21", "data/examples/annotate/hsa.gff3")
annotate("data/example/prost/prost.example.txt", reads, True)
@attr(gff=True)
def test_gff(self):
"""testing GFF function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.bam import bam
bam_fn = "data/aligments/let7-perfect.sam"
annotate(bam_fn, bam.read_bam)
return True
@attr(collapse=True)
def test_collapse(self):
"""testing GFF function"""
from mirtop.libs import logger
logger.initialize_logger("test", True, True)
logger = logger.getLogger(__name__)
from mirtop.bam import bam
bam_fn = "data/aligments/collapsing-isomirs.sam"
annotate(bam_fn, bam.read_bam)
return True
@attr(counts=True)
def test_counts(self):
"""testing convert_gff_counts in convert.py function"""
from mirtop.libs import logger
from mirtop.gff.convert import convert_gff_counts
import argparse
logger.initialize_logger("test counts", True, True)
logger = logger.getLogger(__name__)
args = argparse.Namespace()
args.hairpin = "data/examples/annotate/hairpin.fa"
args.sps = "hsa"
args.gtf = "data/examples/annotate/hsa.gff3"
args.gff = 'data/examples/synthetic/let7a-5p.gff'
args.out = 'data/examples/synthetic'
args.add_extra = True
convert_gff_counts(args)
os.remove(os.path.join(args.out, "let7a-5p.tsv"))
return True
@attr(stats=True)
def test_stats(self):
"""testing stats function"""
from mirtop.gff import stats
from mirtop import version
df = stats._calc_stats("data/examples/gff/correct_file.gff")
stats._dump_log(df, version, None)
print(df)
@attr(variant=True)
def test_string_variant(self):
"""testing parsing string variants"""
from mirtop.gff import body
gff = body.read_variant("iso_5p:-1,iso_add3p:2,iso_snp_central_supp")
truthk = ["iso_5p", "iso_add3p", "iso_snp_central_supp"]
truthv = [-1, 2, True]
if len(gff) != 3:
raise ValueError("Error size of output. Expectd 3.")
if (truthk > list(gff.keys())) - (list(gff.keys()) > truthk):
raise ValueError("Not found expected keys.")
if not isinstance(gff["iso_snp_central_supp"], bool):
raise ValueError("iso_snp_central_supp should be boolean.")
if (truthv > list(gff.values())) - (list(gff.values()) > truthv):
raise ValueError("Not found expected Values.")
@attr(validate=True)
def test_validator(self):
"""test validator functions"""
from mirtop.gff.validator import _check_file
for file in ["coldata_missing.gff", "3wrong_type.gff",
"missing_tools_header.gff"]:
errors = _check_file(os.path.join("data/examples/gff/", file))
if errors == 0:
raise ValueError("Validator didn't catch the error in %s." % file)
errors = _check_file("data/examples/gff/correct_file.gff")
if errors > 0:
raise ValueError("Validator did catch an unexpected error in correct_file.gff.")
@attr(spikeins=True)
def test_spikeins(self):
"""Test spikeins reading and annotation"""
from mirtop.libs import spikeins
from mirtop.mirna.realign import get_mature_sequence
load = spikeins.read_spikeins("data/examples/spikeins/spikeins.fa")
print(load)
load1 = load['spikein-1']
mature_from_data = get_mature_sequence(load1['precursor'],
load1['position'],
exact=True)
if mature_from_data != load1['mature']:
raise ValueError("Sequences doesn't match \n%s\n%s" %
(mature_from_data, load1['mature']))
file_fasta = "data/examples/spikeins/spikeins_pre.fasta"
file_gff = "data/examples/spikeins/spikeins_pre.gff"
spikeins.write_precursors(load, file_fasta)
spikeins.write_gff(load, file_gff)
from mirtop.mirna import mapper, fasta
map_mir = mapper.read_gtf_to_mirna(file_gff)
print(map_mir)
fasta_precursor = fasta.read_precursor(file_fasta, None)
print(fasta_precursor)
@attr(export_fasta=True)
def test_export_fasta(self):
from mirtop.exporter.fasta import _process
print("\n")
_process("data/examples/gff/2samples.gff", None)
@attr(update=True)
def test_update(self):
from mirtop.gff.update import update_file
print("\n")
update_file("data/examples/versions/version1.0.gff", None)