pax_global_header00006660000000000000000000000064137640105630014517gustar00rootroot0000000000000052 comment=84be444ede43a98173bdbd560dafae2f2c60a6cf seqmagick-0.8.4/000077500000000000000000000000001376401056300134745ustar00rootroot00000000000000seqmagick-0.8.4/.gitignore000066400000000000000000000001361376401056300154640ustar00rootroot00000000000000seqmagick/data/ver *.pyc .tox build/ dist/ MANIFEST doctrees/ seqmagick.egg-info/ docs/*.help seqmagick-0.8.4/.travis.yml000066400000000000000000000006751376401056300156150ustar00rootroot00000000000000language: python python: # - "2.7" # - "pypy" # - "3.4" # - "3.5" - "3.6" - "3.7" - "3.8" # Install numpy, then BioPython # BioPython doesn't always play well with pip install. install: - "if [[ $TRAVIS_PYTHON_VERSION != 'pypy' ]]; then pip install -q numpy; fi" - "pip install -q biopython nose pygtrie" - "pip install ." script: - seqmagick --version - nosetests notifications: email: - noah.hoffman@gmail.com seqmagick-0.8.4/CHANGELOG.rst000066400000000000000000000112441376401056300155170ustar00rootroot00000000000000Changes for seqmagick ===================== 0.8.0 ----- * Supports Python 3.5+ * Drops support for Python 3.4 * Fix issue: "seqmagick with no params gives KeyError:None" [GH-77] * Fix for Biopython 1.71 dual coding support [GH-76]; also fixes issue: "Translation error with new BioPython" [GH-79] * Send logging to stderr, not stdout [GH-75] 0.7.0 ----- * Supports Python 3.4+ * Drops support for python 2.7 * requires biopython >= 1.70 * Drops support for bz2 compression [see GH-66] * New option ``convert --sample-seed`` to make ``--sample`` deterministic. 0.6.2 ----- * New ``quality-filter --pct-ambiguous`` switch [GH-53] * setup.py enforces biopython>=1.58,<=1.66 (1.67 is not compatible) [GH-59] * This is the last release that will support Python 2! 0.6.1 ----- * Allow string wrapping when input isn't FASTA. [GH-45] * Fix ``--pattern-include``, ``--pattern-exclude``, and ``--pattern-replace`` for sequences without descriptions (e.g., from NEXUS files). [GH-47] * Fix mogrify example. [GH-52] 0.6.0 ----- * Map ``.nex`` extension to NEXUS-format (--alphabet must be specified if writing) * Use reservoir sampling in ``--sample`` selector (lower memory use) * Support specifying negative indices to ``--cut`` [GH-33] * Optionally allow invalid codons in ``backtrans-align`` [GH-34] * Map ``.fq`` extension to FASTQ format * Optional multithreaded I/O in ``info`` [GH-36] * Print sequence name on length mismatch in ``backtrans-align`` [GH-37] * Support for ``+`` and ``-`` in head and tail to mimick Linux head and tail commands. * Fix scoring for mixed-case sequences in ``primer-trim``. * Fix bug in ``primer-trim`` - failed when sequence had multiple 5' gaps compared to the primer. * Clarify documentation and fix bug in convert/mogrify ``--pattern-replace`` [GH-39] * Support for gzip files in ``seqmagick convert --sort`` 0.5.0 ----- * Change ``seqmagick extract-ids --source-format`` to ``--input-format`` to match other commands (GH-29) * Support gzip- and bzip2-compressed inputs and outputs for most commands (GH-30) * Change default input format for ``sff`` to ``sff-trim``, which respects the clipping locations embedded in each sequence record. * Add ``--details-out`` option to ``seqmagick quality-filter``, which writes details on each read processed. * Match barcode/primer ``seqmagick quality-filter`` against a trie; allows per-specimen barcodes. * Remove ``--failure-out`` option from ``seqmagick quality-filter``. See ``--details-out`` * Raise an error if number of codons does not match number of amino acids in ``seqmagick backtrans-align`` * Add ``--sample`` subcommand (GH-31) 0.4.0 ----- * Fix bug in ``--squeeze`` * More informative messages in ``seqmagick primer-trim`` * Added ``--alphabet`` flag to allow writing NEXUS (GH-23) * Exiting without error on SIGPIPE in extract-ids, info (GH-17) * Ambiguities are translated as 'X' in --translate (GH-16) * Allowing '.' or '-' as gap character (GH-18) * ``--name-prefix`` and ``--name-suffix`` no longer create a mangled description (GH-19) * Files owned by another user can be mogrified, as long as they are group writeable (GH-14) * Add ``backtrans-align`` subcommand, which maps unaligned nucleotides onto a protein alignment (GH-20) * Allow FASTQ as input to quality-filter * Significantly expand functionality of quality-filter: identify and trim barcodes/primers; report detailed failure information. * Cleanup, additional tests * Add ``--drop`` filter to convert and mogrify (GH-24) * Apply current umask when creating files (GH-26) * Support stdin in ``seqmagick info`` (GH-27) * Support translating ambiguous nucleotides, if codon translation is unambiguous 0.3.1 ----- * Fix bug in ``quality-filter`` MinLengthFilter * Case consistency in seqmagick 0.3.0 ----- * Internal reorganization - transformations are converted to partial functions, then applied. * Argument order now affects order of tranformation application. * Change default output format to 'align' for TTYs in seqmagick info * Add BioPython as dependency (closes GH-7) * Add ``primer-trim`` subcommand * Add option to apply custom function(s) to sequences * Add new filtering options: ``--squeeze-threshold``, ``--min-ungapped-length`` ``--include-from-file`` ``--exclude-from-file`` * Removed seqmagick muscle * Added new subcommand ``quality-filter`` * Added new subcommand ``extract-ids`` (closes GH-13) * Allow use of '-' to indicate stdin / stdout (closes GH-11) * Add mapping from .phyx to ``phylip-relaxed`` (targeted for BioPython 1.58) 0.2.0 ----- * Refactoring * Added hyphenation to multi-word command line options (e.g. ``--deduplicatetaxa`` -> ``--deduplicate-taxa``) * Add support for ``.needle``, ``.sff`` formats * Close GH-4 0.1.0 ----- Initial release seqmagick-0.8.4/CONTRIB000066400000000000000000000000731376401056300145170ustar00rootroot00000000000000See https://github.com/fhcrc/seqmagick/graphs/contributors seqmagick-0.8.4/DEVELOPING.rst000066400000000000000000000041251376401056300156640ustar00rootroot00000000000000====================== Developing seqmagick ====================== Requirements ============ Note that building docs, publishing to pypi, etc require some additional dependencies. It's best to work in a virtualenv:: python3 -m venv py3-env source py3-env/bin/activate pip install -r requirements.txt Git workflow ============ We aspire to more or less use a `feature branch workflow `_ for development. Briefly (for those working on the main fork): * Features or bugfixes should start life as a GitHub issue * Work on the feature occurs in a "feature branch" named like '%i-brief-description' % issue_number * When completed (with tests passing) the feature branch is merged into dev (a pull request at this point might be appropriate if you want to request a code review). * When it's time for a release, dev is merged into master (as a result, the head of the `master` branch is always on a release version). versioning ========== The package version is defined by the git tag (using ``git describe --tags --dirty``), in the form '..', eg:: git tag -a -m 'version 0.7.0' 0.7.0 Because setup.py determines the package version at the time the package tarball is created, the repo must be clean (ie, no uncommitted changes to versioned files) and there must be no further commits after adding the tag when preparing to upload a tarball to PyPi. preparing a release =================== First, make sure you have committed all changes. Run tests, and make sure docs build without errors:: nosetests (cd docs && make html) Push one last time to master to trigger tests on travis:: git push origin master Go to travis (https://travis-ci.org/fhcrc/seqmagick) and make sure the tests have completed. Add a new tag (see above). Push the tag to GitHub:: git push --tags Build and upload a tarball to PyPi:: python setup.py clean rm -r build dist python setup.py sdist twine upload dist/* Build and push docs to GutHub pages:: (cd docs && make html) ghp-import --no-jekyll -p docs/_build/html seqmagick-0.8.4/INSTALL000066400000000000000000000012611376401056300145250ustar00rootroot00000000000000The most convenient way to install is using pip (best to make sure you are using the most recent version of pip): pip install -U pip pip install seqmagick If the above doesn't work or you want to install from a clone of the project: First, install BioPython (http://www.biopython.org). NumPy (which parts of BioPython depend on) is not required for seqmagick to function but will most likely be installed as a dependency of BioPython. Once done, install system-wide with: sudo python setup.py install To install for a specific version of python: /path/to/python setup.py install Yet another installation option: python setup.py install --home=/home/username/local seqmagick-0.8.4/LICENSE000066400000000000000000001045141376401056300145060ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. 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But first, please read . seqmagick-0.8.4/MANIFEST.in000066400000000000000000000002541376401056300152330ustar00rootroot00000000000000include seqmagick/test/integration/data/* global-exclude *.so global-exclude *.pyd global-exclude *.pyc global-exclude .git* global-exclude .DS_Store global-exclude *.png seqmagick-0.8.4/README.rst000066400000000000000000000037331376401056300151710ustar00rootroot00000000000000========= seqmagick ========= .. image:: https://travis-ci.org/fhcrc/seqmagick.svg?branch=master :target: https://travis-ci.org/fhcrc/seqmagick We often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. ``seqmagick`` is a kickass little utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments:: seqmagick convert a.fasta b.phy # convert from fasta to phylip seqmagick mogrify --ungap a.fasta # remove all gaps from a.fasta, in place seqmagick info *.{fasta,sto} # describe all FASTA and Stockholm # files in the current directory Requirements ============ * Python >= 3.5 * biopython >= 1.78 Installation ============ Use pip:: pip install seqmagick Note that as of version 0.8.0, this package requires Python 3.5+. If you want to use the most recent version compatible with Python 2.7:: pip install seqmagick==0.6.2 Features ======== * Modifying sequences: Remove gaps, reverse complement, reverse, change case, - Remove gaps - Reverse & reverse complement - Trim to a range of residues - Change case - Sort by length or ID - `more`_ * Displaying `information `_ about sequence files * Subsetting sequence files by: - Position - ID - Deduplication - `more`_ * Filtering sequences by `quality score `_ * Trimming alignments to a `region of interest `_ defined by the forward and reverse primers Want to learn more? Head to the `Documentation`_. ``seqmagick`` is free software under the GPL v3. .. _`Documentation`: http://seqmagick.readthedocs.org/en/latest/ .. _`more`: http://seqmagick.readthedocs.org/en/latest/convert_mogrify.html seqmagick-0.8.4/docs/000077500000000000000000000000001376401056300144245ustar00rootroot00000000000000seqmagick-0.8.4/docs/.gitignore000066400000000000000000000000071376401056300164110ustar00rootroot00000000000000_build seqmagick-0.8.4/docs/Makefile000066400000000000000000000107721376401056300160730ustar00rootroot00000000000000# Makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = BUILDDIR = _build # Internal variables. 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The epub file is in $(BUILDDIR)/epub." latex: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." @echo "Run \`make' in that directory to run these through (pdf)latex" \ "(use \`make latexpdf' here to do that automatically)." latexpdf: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex @echo "Running LaTeX files through pdflatex..." make -C $(BUILDDIR)/latex all-pdf @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." text: $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text @echo @echo "Build finished. The text files are in $(BUILDDIR)/text." man: $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man @echo @echo "Build finished. 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Protein and nucleotide sequence files must contain the same number of sequences, in the same order, with the same IDs. .. literalinclude:: backtrans_align.help seqmagick-0.8.4/docs/changelog.rst000066400000000000000000000112441376401056300171070ustar00rootroot00000000000000Changes for seqmagick ===================== 0.8.0 ----- * Supports Python 3.5+ * Drops support for Python 3.4 * Fix issue: "seqmagick with no params gives KeyError:None" [GH-77] * Fix for Biopython 1.71 dual coding support [GH-76]; also fixes issue: "Translation error with new BioPython" [GH-79] * Send logging to stderr, not stdout [GH-75] 0.7.0 ----- * Supports Python 3.4+ * Drops support for python 2.7 * requires biopython >= 1.70 * Drops support for bz2 compression [see GH-66] * New option ``convert --sample-seed`` to make ``--sample`` deterministic. 0.6.2 ----- * New ``quality-filter --pct-ambiguous`` switch [GH-53] * setup.py enforces biopython>=1.58,<=1.66 (1.67 is not compatible) [GH-59] * This is the last release that will support Python 2! 0.6.1 ----- * Allow string wrapping when input isn't FASTA. [GH-45] * Fix ``--pattern-include``, ``--pattern-exclude``, and ``--pattern-replace`` for sequences without descriptions (e.g., from NEXUS files). [GH-47] * Fix mogrify example. [GH-52] 0.6.0 ----- * Map ``.nex`` extension to NEXUS-format (--alphabet must be specified if writing) * Use reservoir sampling in ``--sample`` selector (lower memory use) * Support specifying negative indices to ``--cut`` [GH-33] * Optionally allow invalid codons in ``backtrans-align`` [GH-34] * Map ``.fq`` extension to FASTQ format * Optional multithreaded I/O in ``info`` [GH-36] * Print sequence name on length mismatch in ``backtrans-align`` [GH-37] * Support for ``+`` and ``-`` in head and tail to mimick Linux head and tail commands. * Fix scoring for mixed-case sequences in ``primer-trim``. * Fix bug in ``primer-trim`` - failed when sequence had multiple 5' gaps compared to the primer. * Clarify documentation and fix bug in convert/mogrify ``--pattern-replace`` [GH-39] * Support for gzip files in ``seqmagick convert --sort`` 0.5.0 ----- * Change ``seqmagick extract-ids --source-format`` to ``--input-format`` to match other commands (GH-29) * Support gzip- and bzip2-compressed inputs and outputs for most commands (GH-30) * Change default input format for ``sff`` to ``sff-trim``, which respects the clipping locations embedded in each sequence record. * Add ``--details-out`` option to ``seqmagick quality-filter``, which writes details on each read processed. * Match barcode/primer ``seqmagick quality-filter`` against a trie; allows per-specimen barcodes. * Remove ``--failure-out`` option from ``seqmagick quality-filter``. See ``--details-out`` * Raise an error if number of codons does not match number of amino acids in ``seqmagick backtrans-align`` * Add ``--sample`` subcommand (GH-31) 0.4.0 ----- * Fix bug in ``--squeeze`` * More informative messages in ``seqmagick primer-trim`` * Added ``--alphabet`` flag to allow writing NEXUS (GH-23) * Exiting without error on SIGPIPE in extract-ids, info (GH-17) * Ambiguities are translated as 'X' in --translate (GH-16) * Allowing '.' or '-' as gap character (GH-18) * ``--name-prefix`` and ``--name-suffix`` no longer create a mangled description (GH-19) * Files owned by another user can be mogrified, as long as they are group writeable (GH-14) * Add ``backtrans-align`` subcommand, which maps unaligned nucleotides onto a protein alignment (GH-20) * Allow FASTQ as input to quality-filter * Significantly expand functionality of quality-filter: identify and trim barcodes/primers; report detailed failure information. * Cleanup, additional tests * Add ``--drop`` filter to convert and mogrify (GH-24) * Apply current umask when creating files (GH-26) * Support stdin in ``seqmagick info`` (GH-27) * Support translating ambiguous nucleotides, if codon translation is unambiguous 0.3.1 ----- * Fix bug in ``quality-filter`` MinLengthFilter * Case consistency in seqmagick 0.3.0 ----- * Internal reorganization - transformations are converted to partial functions, then applied. * Argument order now affects order of tranformation application. * Change default output format to 'align' for TTYs in seqmagick info * Add BioPython as dependency (closes GH-7) * Add ``primer-trim`` subcommand * Add option to apply custom function(s) to sequences * Add new filtering options: ``--squeeze-threshold``, ``--min-ungapped-length`` ``--include-from-file`` ``--exclude-from-file`` * Removed seqmagick muscle * Added new subcommand ``quality-filter`` * Added new subcommand ``extract-ids`` (closes GH-13) * Allow use of '-' to indicate stdin / stdout (closes GH-11) * Add mapping from .phyx to ``phylip-relaxed`` (targeted for BioPython 1.58) 0.2.0 ----- * Refactoring * Added hyphenation to multi-word command line options (e.g. ``--deduplicatetaxa`` -> ``--deduplicate-taxa``) * Add support for ``.needle``, ``.sff`` formats * Close GH-4 0.1.0 ----- Initial release seqmagick-0.8.4/docs/conf.py000066400000000000000000000166721376401056300157370ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # seqmagick documentation build configuration file, created by # sphinx-quickstart on Thu May 19 16:18:13 2011. # # 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. import sys import os import time import subprocess # 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. sys.path.insert(0, os.path.abspath('..')) from seqmagick import __version__ # -- 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 = [] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'seqmagick' copyright = u'2011-{}, The Matsen Group'.format(time.strftime('%Y')) # 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 = __version__.split('+')[0] # The full version, including alpha/beta/rc tags. release = __version__ # generate help text for each subcommand subcommands = [ 'backtrans-align', 'convert', 'extract-ids', 'info', 'primer-trim', 'quality-filter', ] for cmd in subcommands: print('generating help text for {}'.format(cmd)) p = subprocess.run(['../seqmagick.py', cmd, '-h'], stdout=subprocess.PIPE, universal_newlines=True) with open(cmd.replace('-', '_') + '.help', 'w') as f: f.write(p.stdout) # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = ['_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # -- 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 = 'sphinxdoc' # 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 = {} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. html_logo = '../logo/seqmagick_logo_small.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. #html_favicon = None # 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'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_domain_indices = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. #html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. #html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None # Output file base name for HTML help builder. htmlhelp_basename = 'seqmagickdoc' # -- Options for LaTeX output -------------------------------------------------- # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index', 'seqmagick.tex', u'seqmagick Documentation', u'Matsen Group', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # If true, show page references after internal links. #latex_show_pagerefs = False # If true, show URL addresses after external links. #latex_show_urls = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_domain_indices = True # -- Options for manual page output -------------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ ('index', 'seqmagick', u'seqmagick Documentation', [u'Matsen Group'], 1) ] seqmagick-0.8.4/docs/convert_mogrify.rst000066400000000000000000000045031376401056300203740ustar00rootroot00000000000000``convert`` and ``mogrify`` =========================== Convert and mogrify achieve similar goals. ``convert`` performs some operation on a file (from changing format to something more complicated) and writes to a new file. ``mogrify`` modifies a file in place, and would not normally be used to convert formats. The two have similar signatures:: seqmagick convert [options] infile outfile vs:: seqmagick mogrify [options] infile Options are shared between convert and mogrify. Examples -------- Basic Conversion ^^^^^^^^^^^^^^^^ ``convert`` can be used to convert between any file types BioPython supports (which is many). For a full list of supported types, see the `BioPython SeqIO wiki page`_. By default, file type is inferred from file extension, so:: seqmagick convert a.fasta a.sto converts an existing file ``a.fasta`` from FASTA to Stockholm format. **Neat!** But there's more. Sequence Modification ^^^^^^^^^^^^^^^^^^^^^ A wealth of options await you when you're ready to do something slightly more complicated with your sequences. Let's say I just want a few of my sequences:: $ seqmagick convert --head 5 examples/test.fasta examples/test.head.fasta $ seqmagick info examples/test*.fasta name alignment min_len max_len avg_len num_seqs examples/test.fasta FALSE 972 9719 1573.67 15 examples/test.head.fasta FALSE 978 990 984.00 5 Or I want to remove any gaps, reverse complement, select the last 5 sequences, and remove any duplicates from an alignment in place:: seqmagick mogrify --tail 5 --reverse-complement --ungap --deduplicate-sequences examples/test.fasta You can even define your own functions in python and use them via ``--apply-function``. .. note:: To maximize flexibility, most transformations passed as options to ``mogrify`` and ``convert`` are processed *in order*, so:: seqmagick convert --min-length 50 --cut 1:5 a.fasta b.fasta will work fine, but:: seqmagick convert --cut 1:5 --min-length 50 a.fasta b.fasta will never return records, since the cutting transformation happens before the minimum length predicate is applied. Command-line Arguments ********************** .. literalinclude:: convert.help .. _`BioPython SeqIO wiki page`: http://www.biopython.org/wiki/SeqIO#File_Formats seqmagick-0.8.4/docs/extensions.rst000066400000000000000000000012131376401056300173520ustar00rootroot00000000000000========= ============== Extension Format ========= ============== .afa fasta .aln clustal .fa fasta .faa fasta .fas fasta .fasta fasta .fastq fastq .ffn fasta .fna fasta .fq fastq .frn fasta .gb genbank .gbk genbank .needle emboss .nex nexus .phy phylip .phylip phylip .phyx phylip-relaxed .qual qual .sff sff-trim .sth stockholm .sto stockholm ========= ============== seqmagick-0.8.4/docs/extract_ids.rst000066400000000000000000000003311376401056300174640ustar00rootroot00000000000000``extract-ids`` =============== ``seqmagick extract-ids`` is extremely simple - all the IDs from a sequence file are printed to stdout (by default) or the file of your choosing: .. literalinclude:: extract_ids.help seqmagick-0.8.4/docs/index.rst000066400000000000000000000070541376401056300162730ustar00rootroot00000000000000.. seqmagick documentation master file, created by sphinx-quickstart on Thu May 19 16:18:13 2011. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. .. Contents: .. "Fork me on github" .. raw:: html Fork me on GitHub ========= seqmagick ========= .. contents:: :depth: 4 :class: new .. toctree:: :maxdepth: 1 changelog Motivation ========== We often have to convert between sequence formats and do little tasks on them, and it's not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick_ to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments:: seqmagick convert a.fasta b.phy # convert from fasta to phylip seqmagick mogrify --ungap a.fasta # remove all gaps from a.fasta, in place seqmagick info *.fasta # describe all FASTA files in the current directory And more. Installation ============ Install the latest release with:: pip install seqmagick This should also install `BioPython`_. NumPy (which parts of BioPython depend on) is not required for ``seqmagick`` to function, but may be installed as a dependency of ``BioPython``. To install the bleeding edge version:: pip install git+https://github.com/fhcrc/seqmagick.git@master#egg-info=seqmagick Note that as of version 0.8.0, this package requires Python 3.5+. If you want to use the most recent version compatible with Python 2.7:: pip install seqmagick==0.6.2 Use === Seqmagick can be used to query information about sequence files, convert between types, and modify sequence files. All functions are accessed through subcommands:: seqmagick [options] arguments List of Subcommands =================== .. toctree:: :maxdepth: 2 convert_mogrify backtrans_align extract_ids info quality_filter primer_trim Supported File Extensions ========================= By default, ``seqmagick`` infers the file type from extension. Currently mapped extensions are: .. include:: extensions.rst .. note:: NEXUS-format output requires the ``--alphabet`` flag. Default Format -------------- When reading from stdin or writing to stdout, ``seqmagick`` defaults to fasta format. This behavior may be overridden with the ``--input-format`` and ``--output-format`` flags. If an extension is not listed, you can either rename the file to a supported extension, or specify it manually via ``--input-format`` or ``--output-format``. Compressed file support ----------------------- most commands support gzip (files ending in ``.gz``) and bzip (files ending in ``.bz2`` or ``.bz``) compressed inputs and outputs. File types for these files are inferred using the extension of the file after stripping the file extension indicating that the file is compressed, so ``input.fasta.gz`` would be inferred to be in FASTA format. Acknowledgements ================ seqmagick is written and maintained by the `Matsen Group`_ at the Fred Hutchinson Cancer Research Center. Contributing ============ We welcome contributions! Simply fork the repository `on GitHub`_ and send a pull request. .. _`on GitHub`: http://github.com/fhcrc/seqmagick/ .. _`Matsen Group`: http://matsen.fhcrc.org/ .. _imagemagick: http://www.imagemagick.org/script/command-line-tools.php .. _`BioPython`: http://www.biopython.org/ seqmagick-0.8.4/docs/info.rst000066400000000000000000000013101376401056300161040ustar00rootroot00000000000000``info`` ======== ``seqmagick info`` describes one or more sequence files Example ******* :: seqmagick info examples/*.fasta name alignment min_len max_len avg_len num_seqs examples/aligned.fasta TRUE 9797 9797 9797.00 15 examples/dewrapped.fasta TRUE 240 240 240.00 148 examples/range.fasta TRUE 119 119 119.00 2 examples/test.fasta FALSE 972 9719 1573.67 15 examples/wrapped.fasta FALSE 120 237 178.50 2 Output can be in comma-separated, tab-separated, or aligned formats. See ``seqmagick info -h`` for details. Usage: .. literalinclude:: info.help seqmagick-0.8.4/docs/make_extensions.py000077500000000000000000000014251376401056300201770ustar00rootroot00000000000000#!/usr/bin/env python from seqmagick import fileformat extension_map = fileformat.EXTENSION_TO_TYPE items = extension_map.items() items.sort() max_key_length = max((len('Extension'), max(len(k) for k in extension_map.keys()))) max_val_length = max((len('Format'), max(len(v) for v in extension_map.values()))) format_string = '{0:' + str(max_key_length) + 's} {1:' + str(max_val_length) + 's}' with open('extensions.rst', 'w') as fp: def print_row(k, v): print >> fp, format_string.format(k, v) print_row('=' * max_key_length, '=' * max_val_length) print_row('Extension', 'Format') print_row('=' * max_key_length, '=' * max_val_length) for k, v in items: print_row(k, v) print_row('=' * max_key_length, '=' * max_val_length) print >> fp, '' seqmagick-0.8.4/docs/primer_trim.rst000066400000000000000000000002741376401056300175120ustar00rootroot00000000000000``primer-trim`` --------------- ``primer-trim`` trims an alignment to a region defined by a set of forward and reverse primers. Usage is as follows: .. literalinclude:: primer_trim.help seqmagick-0.8.4/docs/quality_filter.rst000066400000000000000000000004171376401056300202150ustar00rootroot00000000000000``quality-filter`` ------------------ ``quality-filter`` truncates and removes sequences that don't match a set of quality criteria. The subcommand takes a FASTA and quality score file, and writes the results to an output file: .. literalinclude:: quality_filter.help seqmagick-0.8.4/examples/000077500000000000000000000000001376401056300153125ustar00rootroot00000000000000seqmagick-0.8.4/examples/aligned.fasta000066400000000000000000004467661376401056300177640ustar00rootroot00000000000000>gi|66864576|gb|DQ027786.1| HIV-1 isolate QA013_2282M_C6 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACTTTAAACTGCATTGAATGGAAGAGTAATAGTAGCAATA--------------- -------------------ACGGCACTGAT--------------------------CAGG ACATGAATGAGAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAGCTTGATGTAGTACAGATAGATAATA---GTAATACTAGC TATAGATTAATAAATTGTAATACCT--GCCATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--TTGCAATTCTAAAATGTAACAAT AAGAAATTCAATGGGACGGGTCCATGCACAAACGTCAGCACAGT--AGTGTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--TA ATAATTAGATCTGAAAATTTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATAAG TCTGT--CAATTCATTGCACAAGACCCTACAACAATACAAGAAGAGGTGAACATAT---- --GGGACCAGGGCGAGCACTCT-----ACAGAAAAAATAGTTGGAAATATAAGACAAGCA TATTGTAACATTAGTGGAGGGGAATGGAATAAAG--TTACAGCAGGTAGCTGGCAAATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCCGCGAGG GGACCTAGAAATTACAACACACAGCTTTAATTGTAGAGGGGAATTTTTCTATTGTAATAC ATCA--CCTGTTTAACAGCACT---TGGGACAACAATACC---------CAGGA------ ---------ATCAAATGACACTATAATGAT-CCCATGCAGAAAAA--CAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGAC--ACATGTTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAGCTAATGGGAG---- ----------TTCGAATG--ACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864574|gb|DQ027785.1| HIV-1 isolate QA013_1790M_B6 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACGTTAAACTGCATTGAATGGATAAATAATAATAGCACTA--------------- -------------------ACGCCACTGGT--------------------------CAGG ACATGAATGAAAAACTGCTCTTTCAATATAGCCACAGAAGTAAGAGATAAGAAAAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTAATACTAGC TATAGATTAATAAATTGTAATACCT--GCCATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--TTGCAATTCTAAAATGTAATAAT AAGAAATTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGT--AGTGTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--TA ATAATTAGATCTGAAAATTTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--CAATTAGTTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACTCT-----ACAGAAAAAATAGTTGGAGATATAAGACAAGCA CATTGTAACATTAGTGGAAGGGAATGGAATAA--CGTTACAGCAGGTAGCTGACAAATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCTGCGAGG AGACCTAGAAATTACAACACACAGCTTTAATTGTCTAGGGGAATTTTTCTACTGCAACAC ATCAA--CTGTTTAATAATAGTAAATGGGAATCAAATAGT---AGTACAGGGGA---AAA TAA---------AAATGAAGATATAATCACTCCCATGCAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCC--TTGAAGGACACATCAGTTGTT CGTCAATTATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAACT--TCGGAG---- -------------TTCGGAGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ 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>gi|66864568|gb|DQ027782.1| HIV-1 isolate QA013_385M_C3 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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GTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTA--------------- -------------------ACGTCACTGAT--------------------------CAGG ACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTA---CCAGC TATAGATTAATAAATTGTAATACCTCTG--ATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--ATTCAATTCTAAAATGTAATGAT AAGAAGTTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACA--GTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--GA ATAATTAGATCTGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--ACCTTAATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACCCT-----TTAGAAAGAATAGTTGGAGATATAAGACAAGCA TATTGTAGCATTAGTGGAATGGGATGGAATAAAACTT--CAGCAGGTAGCTGACAAATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCCGCGGGG GGACCTAGAAATTACAACACACAGCTTTAATTGTGGAGGGGAATTTTTCTACTGCAACAC ATCAAGA--GTTTAATAATAGTGAATGGAAATCAAATAGT---AGTACAGGGGG------ ------------AAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAAGAAAAGCAATGTATGCCCCTCCCATTGAAGGAC--ATCAATTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAACTAATCAGAG---- ------------TGAATGAGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864564|gb|DQ027780.1| HIV-1 isolate QA013_105M_C2_1 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTA--------------- -------------------ACGTCACTGAT--------------------------CAGG ACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTA---CCAGC TATAGATTAATAAATTGTAATACCTCTG--ATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--ATTCAATTCTAAAATGTAATGAT AAGAAGTTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACA--GTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--GA ATAATTAGATCTGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--ACCTTAATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACTCT-----TTAGAAAGAATAGTTGGAGATATAAGACAAGCA TATTGTAGCATTAGTGGAATGGGATGGAATAAAACTT--CAGCAGGTAGCTGACAAATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCCGCGGGG GGACCTAGAAATTACAACACACAGCTTTAATTGTGGAGGGGAATTTTTCTACTGCAACAC ATCAAGA--GTTTAATAATAGTGAATGGAAATCAAATAGT---AGTACAGGGGG------ ------------AAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGAC--ATCAATTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAACTAATCAGAG---- ------------TGAAGGAGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTA--------------- -------------------ACGTCACTGAT--------------------------CAGG ACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTA---CCAGC TATAGATTAATAAATTGTAATACCTCTG--ATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--ATTCAATTCTAAAATGTAATGAT AAGAAGTTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACA--GTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--GA ATAATTAGATCTGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--ACCTTAATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACTCT-----TTAGAAAGAATAGTTGGAGATATAAGACAAGCA TATTGTAGCATTAGTGGAATGGGATGGAATAAAACTT--CAGCAGGTAGCTGACAGATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCCGCGGGG GGACCTAGAAATTACAACACACAGCTTTAATTGTGGAGGGGAATTTTTCTACTGCAACAC ATCAAGA--GTTTAATAATAGTGAATGGAAATCAAATAGT---AGTACAGGGGG------ ------------AAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGAC--ATCAATTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAACTAATCAGAG---- ------------TGAATGAGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864566|gb|DQ027781.1| HIV-1 isolate QA013_264M_A2 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTA--------------- -------------------ACGTCACTGAT--------------------------CAGG ACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTA---CCAGC TATAGATTAATAAATTGTAATACCTCTG--ATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--ATTCAATTCTAAAATGTAATGAT AAGAAGTTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACA--GTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--GA ATAATTAGATCTGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--ACCTTAATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACTCT-----TTAGAAAGAATAGTTGGAGATATAAGACAAGCA TATTGTAGCATTAGTGGAATGGGATGGAATAAAACTT--CAGCAGGTAGCTGACAAATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCCGCGGGG GGACCTAGAAATTACAACACACAGCTTTAATTGTGGAGGGGAATTTTTCTACTGCAACAC ATCAAGA--GTTTAATAATAGTGAATGGAAATCAAATAGT---AGTACAGGGGG------ ------------AAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGAC--ATCAATTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAACTAATCAGAG---- ------------TGAATGAGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864572|gb|DQ027784.1| HIV-1 isolate QA013_987M_C4 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACTTTAAACTGCACTGAATGGACGAATAATAGTAGCACTA--------------- -------------------ACGCCACTGAT--------------------------CAGG ACATGAATGAGAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTAATACTAGC TATAGATTAATAAATTGTAATACCT--GCCATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGG--TTGCAATTCTAAAATGTAATGAT AAGAAATTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGT--AGTGTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--TA ATAATTAGATCTGAAAATCTAGCAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--CAATTCATTGCACAAGACCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACTGT-----ACAGAAAAAATAGTTGGAGATATAAGACAAGCA TATTGTAGCATTAGTGGACTGGGATGGAATAAAACTA--CAGCAGGTAGCTGACAAATTA AGAAACCTTC------------TCAATACAACAACAATAATTTTTAAACCACCCGCGAGG GGACCTAGAAATTACAACACACAGCTTTAATTGTGGAGGGGAATTTTTCTACTGCAACAC ATCAA--CTGTTTAATAATAGTGAATGGAAATCAAATAGT---AGTACAGGGGG------ ------------AAATGAAAGTATAATCAAACTCCTGCAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAGACAC--ATCAGTTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAGCTAATCAGTT---- ------------CGAATGAGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864570|gb|DQ027783.1| HIV-1 isolate QA013_559M_C11 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------ACTCT GTGTCACTTTAAACTGCACTGAATGGAAGAATAATAGTAGCACTA--------------- -------------------ACGGCACTGAT--------------------------CAGG ACATGAATGAGAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGAAGCAA GTACAGGCAC--TTTTATAAACTTGATGTAGTACAGATAGATAATA---GTAGTACTAGC TATAGATTAATAAATTGTAATACCT--GCCATTACACAGGCATGTCCAAAGGTAACCTTT GAGCCAATTCCTATACATTATTGTGCCCCAGCTGG--TTGCAATTCTAAAATGTAATGAT AAGAAATTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGT--AGTGTACACATGGG ATTAGGCCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGA--TA ATAATTAGATCTGAAGATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAG TCTGT--CAATTAATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATAT---- --GGGACCAGGGCGAGCACTCT-----ACAGAAAAAATAGTTGGAGATATAAGACAAGCA TATTGTAGCATTAGTGGAATGGGATGGAATAAAA--TTACAGCAGGTAGCTGACAAATTA AGAAACCTTC------------TTAATAAAACAACAATAATTTTTAAACCACCCGCGAGG GGACCTAGAAATTACAACACACAGCTTTAATTGTAGAGGGGAATTTTTCTACTGCAACAC ATCAA--CTGTTTAATAATAGTGAATGGAAATCAAATAGT---AGTACAGGGGG------ ------------AAATGAAAGTATAATCATACTCCTGCAGAATAAAACAAATTATAAACA TGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAGACAC--ATCAGTTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTG-TAACTAATTCGTG---- ------------------AGACCTTCAGACCTGGGGGAGGAGAC---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >hxb2 TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACA CACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCAC TGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCA ACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGG AGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAG AGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCG CTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT CCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGA GCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCT TGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTC AGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAG CGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGG CAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGA AGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAA AAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCA AGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGT AGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCA TTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACC AAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAA GCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAAC ATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAA GTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAA GGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCC ATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCA GTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCA GGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCA GTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTAT AGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTA GACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATG ACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTG GGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGC CATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATG ATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAA GAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGA AAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC TGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCC CCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAG CCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCC TCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATG ATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAA TTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATA AAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGT TGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAA AATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAA TAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTG GGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAAT GGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTC AATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATG TGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTA CCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCAC AGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTT TTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGAT CTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGA GGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGG GTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACA GCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTT ACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAG AAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAA AAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGA AGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAA CAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGG CAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAAC TGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGA TTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGA AAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTA AATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTG ACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGAT TAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAG ATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGG TCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT TAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATG AACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTG TAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGC ATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAA AAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAG CAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAA AAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTT GGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAG TAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAAC ATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGA TTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTA AAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCA GAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAA TACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATT ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACA TGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTAT AGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGG GATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCAT TTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCT GAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATA AGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAAC AAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAG CCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACC AAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGA ATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATG AAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGC TGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGG AGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCA GCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTG TTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAG AGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGT AACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAAT AGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGA CAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGA AATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGA TGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGA AGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTAC ATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTAT TGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATG AGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCT GTGTTAGTTTAAAGTGCACTGATTTGAAG---AATGATACTAATA--------------- -------------------CCAATAGTAGT------AGCGGGAGAATGATAATGGAGAAA GGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAA GAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATG---ATACTACCAGC TATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTT GAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAAT AAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGA ATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTA GTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACA TCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAG AGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATA---GGAAATATGAGACAAGCA CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTA AGAGAACAATTTGGAA------ATAATAAAACAATAATCTTTAAGCAATCCTCAG-GAGG GGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTC AACACAACTGTTTAATAGTACT---TGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAA TAACACTGAAGGAAGTGACACAATCACCCT-CCCATGCAGAATAAAACAAATTATAAACA TGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTT CATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCA--ACAATG---- ------------AGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGA GAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCA AGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCC TTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTAC AGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTG AGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAA TCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTG GAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGG AACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAA GCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAAT TATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGT GGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTG CTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCC ACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGA GAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATC TGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGA GGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCC TACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCA TAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTA TTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGT GGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGA GCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCA ATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAG GAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAG GCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCAC TCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCT GATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGC TACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACC AGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAG TGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTAC TTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGG AGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCT GCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGG CTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGT GTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGT GTGGAAAATCTCTAGCA >gi|66864561|gb|DQ027778.1| HIV-1 isolate QA013_2282M_A10 from Kenya nonfunctional envelope glycoprotein (env) gene, partial sequence ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ -------------------------------------------------------TCTCT GCGTTACCTTAGATTGTCATCAT---------AATGTCACCACTGTCACCACTAACAATA CCAATGACACTGTATATCACCAATGCCACTATCACCAATGCCAATATCACCAAGGACGAT GCCGACATGAGAAACTGCTCTT--AATGTGACCACAGTAATAAGGGATAAGCAACAGAAA GTATACTCACTTTTTTATAGACTTGATCTAGCC--AACTGAAAGTAATGATAGTTATAGT TATAGATTAATAAATTGTAACACCTCCGTCATTAAACAGGC--GTCCAAAAGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAA--GTAAAGAT AAGAAGTTCAATGGAACAGGGCCATGCAGGAATGTCAGCACAGTACAATGCACACATGGG A--AAGCCAGTAGTATCAACTCAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTA AGAATTAGATC--AAAATATCACAAACAATGCCAAAAACATATTAGTACAATTGACCACA CCTGTAAGAATTAATTGTACCA--CCTAACAACAATACAAGAAAAAGTGTACATAT---- --AGGACCAGGACAAGCATTCTATGCAACAGGAGGAA--ATAGGAAATATAAGACAAGCA TATTGTAATGTTAGTAAAACACAATGGAATACAGCTTTGCAAAAGGT--CTAACAAATTA GAAGCATACTTTAACAAAACAATTAACAAAACAATAATCTTTACTCACTCATCAG---GA GGATACAGAAATTACAACACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATAC ATCAGGCC--TTTAATAGCACT---TAGGACAACGATACC---AACACACAGGA------ ---------ATCAAATGACACTATAATGAT-CCCATGCAG--TAAAGCAAATTATAAACA TGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAA--AGGTGTG ACTCAAATATTACAGGACTAATATTAACAAGAGATGGTAAGAATAATT--CTAA------ ------------TAACAGTGACCTTCAGACCTAGAGGAGGAGAT---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864559|gb|DQ027777.1| HIV-1 isolate QA013_1790M_C1 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------TCTCT GCGTTACCTTAGATTGTCATCAT---------AATGTCACCACTGTCACCACTAACAATA CCAATGACACTGCATATCACCAATGCCAAT---------------ATCACCAATGACAAG GCCGACATGAAAAACTGCTCTTACAATGTGACCACA--AATAAGGGATAAGCAACAGAAA GTATACTCACTTTTTTATAGACTTGATCTAGTACCAACTGAAAGTA---G-----ATAGT TATAGATTAATAAATTGTAACACCTCCGTCATTAAACAGGCTTGTCCAAAAGTAACCTTT GA--CAATTCCCATACATTATTGTGCCCCAGCTAGTTTTGCGATTCTAAAGTGTAAAGAT AAGGAGTTCAAT--AACAGGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGG ATCAAGCCAGTAGTATCAACTC--CTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTA AGAATTAGATCTGAAAATATCACAAACAATGC--AAAACATAATAGTACAATTGCCCACA CCTATAACAATTACTTGTACCAGACCCAACAACAATACAAGAAA--GTGTACATAT---- --AGGACCAGGACAAGCATTCTATGCAACAGGTGCAATAATAGGGGATATAAGACGAGC- -ATTGTAATGTTAATAAAACACAATGGAATACAGCTTTGCAAAAGGTAGCTAACAAATTA AAAACATA--------------TTAACAAAACAATAATCTTTACTCACTCATCAG-GAGG GGATATAGAAATTACAACACATAGTTTTAAT--TAGAGGAGAGTTTTTCTATTGTAATAC ATCAGGCCTGTTTAATAGCACT---TGGGTAAACAATACC---AACACAGGGGA--CAAC TAACACAGAATCAAATGACAATATAACGAT-CCCATGCAGAATAAAGCAAATTATAA--A TGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAATAAGGTGTG AATCAA--ATTACAGGACTAATATTAACAAAAGATAGTAAGAATAATG--CTAATA---- ------------GAACTGAAACCTTCAGACCTAGAG--AGAGAT---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864557|gb|DQ027776.1| HIV-1 isolate QA013_987M_B12 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------TCTCT GCGTTACTTTAGATTGTCAT------------AATGTCACCAATG--------------- -------------------ACACTGCCAGT------------------------------ ---ATCATGAAAAACTGCTCTT--AATGTGACCACAGTAATAAGGGATAAGCAACAGAAA GTATACTCACTTTTTTATAGACTTGATATAGTA--AACTGAAAGTA---ATA---CTAGT TATAGATTAATAAATTGTAACACCTCCGTCATTAAACAGGCTTGTCCAA--GTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTGTAAAG-- AAGGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGG ATCAAGCCA--AGTATCAACTCAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTA AGAATTAGATCTGAAAATA--ACAAACAATGCCAAAAACCTAATAGTACAATTGACCACA CCTATAAAAATTAATTGTACTAGACCTA--AACAATACAAGAAAAAGCGTACATAT---- --AGGACCAGGACAAGCATTCTATGCAACAGGTGAAATAATAGGG--TATAAGACAAGCA CATTGTAATGTTAATAAAACACAATGGGATAAAACTTTGCAAGAGGTAGCTAAC--ATTA AAAACATACT------------TTAACAAAACAATAATCTTTACTCACTCATCAG-GAGG GGATATAGAAATTACA--ACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATAC ATCAAGCCTGTTTAATAGCACT---TGGGGA--CAATACC---AACACACAGGAGTCAAA TAGCACAGAATCAAATGAAACTATAACGAT-CCCATGCAGAATAA--CAAATTATAAATA TGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAATAAG--GTG AATCAAATATTACAGGACTAATATTAACAAGAGATGGTGGGAATGATT--CTAGGG---- ------------AAAATGAAACC--CAGACCTGGAGGAGGAGAT---------------- ------------------------------------------------------------ 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------------------------------------------------------------ ----------------- >gi|66864555|gb|DQ027775.1| HIV-1 isolate QA013_765M_B1 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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-------------------------------------------------------TCTCT GCGTTACTTTAGATTGTCAT------------AATGTCACCAATG--------------- -------------------ACAATGCCAAT------------------------------ ---ATCATGAAAAACTGCTCTT--AATGTGACCACAGTAATAAGGGATAAGCAACAGAAA GTATACTCACTTTTTTATAGACTTGATATAGTA--AACTGAAAGTA---ATA---CTAGT TATAGATTAATAAATTGTAACACCTCCGTCATTAAACAGGCTTGTCCAA--GTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGACTCTAAAGTGTAAAG-- AAGGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAATGCGCACATGGG ATCAAGCCA--AGTATCAACTCAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTA AGAATTAGATCTGAAAATA--ACAAACAATGCCAAAAACCTAATAGTACAATTGACCACA CCTATAAAAATTAATTGTACCAGACCTA--AACAATACAAGAAAAAGTGTACATAT---- --AGGACCAGGACAAGCATTCTATGCAACAGGTGAAATAATAGGG--TATAAGACAAGCA CATTGTAATGTTAGTGAAACACAATGGCATAAAACTTTGCAAGAGGTAGCTAAC--ATTA AAAACATACT------------TTAACAAAACAATAATCTTTGATCACTCATCAG-GAGG GGATATAGAAATTACA--ACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATAC ATCAGGCCTGTTTAATAGCACT---TGGGAA--CGATGCC---AGCACACAGGAGTCAAA TAACACAGAATCAAATACCACTATAACGAT-CCCATGCAGAATAA--CAAGTTATAAATA TGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAATAAG--GTG AATCAAATATTACAGGACTAATATTAACAAGAGATGGTGGGGATAATT--CTAGGG---- ------------AAAATGAAACC--CAGACCTGGAGGAGGAGAT---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864553|gb|DQ027774.1| HIV-1 isolate QA013_559M_A1 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------TCTCT GCGTTACTTTAGATTGTCAT------------AATGTCACCACTG--------------- -------------------ACAATGCCAAT------------------------ATCACC ACCGACATGAAAAA--GCTCTTACAATGTGACCACAGTAATAAGGGATAAGCAACAGAAA GTATACTCACTTTTTTATAGACTT--TATAGTACCAACTGAAAGTA---ATA---CTAGT TATAGATTAATAAATTGTAACACCTCCGTCATTAAACAGG--TGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAA--GTAAAGAT AAGGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGG --CAAGCCAGTAGTATCAACTCAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTA AGAATTAGAT--GAAAATATCACAAACAATGCCAAAAACATAATAGTACAATTGACCACA CCTATAAAAATTAATTGTAT--GACCTAACAACAATACAAGAAAAAGTGTACATAT---- --AGGACCAGGACAAGCATTCTATGCAACAGGTGAAA--ATAGGGGATATAAGACAAGCA CATTGTAATGTTAGTAAAACACAATGGCATAAAACTTTGCAAGAGG--GCTAACAAATTA AAAACATACT------------TTAACAAAACAATAATCTTTAATCACTCATCAG-GAGG GGATATAG--ATTACAACACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATAC ATCAGGCCTGTTTAATAGCT-----TGGGGAAACCATGCC---AGCATACAGGAGTCCAA TAACACAGAATCAAATGACAATATAACGAT-CCCAT--AGAATAAAGCAAATTATAAATA TGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGTA--ATAAGGTGTG AATCAAATATTACAGGACTAATATTAACAAGAGATGGTGGGGATAATC--CTAGGGAATG AAACCTTCAGACAAAATGAAACCTTCAGACCTGGAGGAGGAGAT---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- >gi|66864614|gb|DQ027773.1| HIV-1 isolate QA013_385M_B5 from Kenya envelope glycoprotein (env) gene, partial cds ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ 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------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------------TCTCT GCGTTACTTTAGATTGTCAT------------AATGTCACCAATG--------------- -------------------ACAATGCCAAT------------------------ATCACC ACCGACATGAAAAA--GCTCTTACAATGTGACCACAGTAATAAGGGATAAGCAACAGAAA GTATACTCACTTTTTTATAGACTT--TATAGTACCAACTGAAAGTA---ATA---CTAGT TATAGATTAATAAATTGTAACACCTCCGTCATTAAACAGG--TGTCCAAAGGTAACCTTT GAGCCAATTCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAA--GTAAAGAT AAGGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGG --CAAGCCAGTAGTATCAACTCAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTA AGAATTAGAT--GAAAATATCACAAACAATGCCAAAAACATAATAGTACAATTGACCACA CCTATAAAAATTAATTGTAT--GACCTAACAACAATACAAGAAAAAGTGTACATAT---- --AGGACCAGGACAAGCATTCTATGCAACAGGTGAAA--ATAGGGGATATAAGACAAGCA CATTGTAATGTTAGTAAAACACAATGGAATAAAACTTTGCAAGAGG--GCTAACAAATTA AAAACATACT------------TTAACAAAACAATAATCTTTAATCACTCATCAG-GAGG GGATATAG--ATTACAATACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATAC ATCAGGCCTGTTTAATAGCT-----TGGGGAAACAATGCC---AGCACACAGGAGTCAAA TAACACAGAATCAAATGACACTATAACGAT-CCCAT--AGAATAAAGCAAATTATAAATA TGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGATA--ATAAGGTGTG AATCAAATATTACAGGACTAATATTAACAAGAGATGGTGGGGATAATC--CTAGGGAATG AAACCTTCAGACAAAATGAAACCTTCAGACCTGGAGGAGGAGAT---------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------- seqmagick-0.8.4/examples/apply-function/000077500000000000000000000000001376401056300202625ustar00rootroot00000000000000seqmagick-0.8.4/examples/apply-function/myfunctions.py000066400000000000000000000007431376401056300232160ustar00rootroot00000000000000""" A collection of functions to apply """ import hashlib def no_gaps(records): for record in records: if not '-' in str(record.seq): yield record def hash_starts_numeric(records): """ Very useful function that only accepts records with a numeric start to their sha-1 hash. """ for record in records: seq_hash = hashlib.sha1(str(record.seq).encode('utf-8')).hexdigest() if seq_hash[0].isdigit(): yield record seqmagick-0.8.4/examples/apply-function/run_filter.sh000077500000000000000000000003221376401056300227670ustar00rootroot00000000000000#!/bin/bash seqmagick convert --apply-function myfunctions.py:no_gaps \ ../aligned.fasta empty.fasta seqmagick convert --apply-function myfunctions.py:hash_starts_numeric \ ../aligned.fasta hashed.fasta seqmagick-0.8.4/examples/dewrapped.fasta000066400000000000000000001144141376401056300203120ustar00rootroot00000000000000>Ref_1_700 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BFKMA_3 AGTAGCATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BESA1_5 AGTAGTACCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BTN0L_2 AGTAGTATCAACTCAACTGCTGCTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CMG0I_4 AGTAGTATCAACTCAACTGCTGTTAAACGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01AKCZB_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGCCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01D21W0_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCGAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EJ82H_6 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAAAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGCATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01DHBXA_5 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAAAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EGZ72_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAAAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAGATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGCATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CR15A_6 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAAA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EOH19_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAAA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACGACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EEG9D_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---ATAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01D0V98_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCCCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BVKYZ_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATACCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EURR1_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGCGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EC9GP_3 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTAAAAATTAATTGTACAAGGCCTAATAATAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B9A6N_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTAAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGAGTATAAG >FTWCYXX01AH60X_10 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTAAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CDGOW_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAACTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01A3035_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTATACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BOFEE_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGCACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGACATAAG >FTWCYXX01D527F_6 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGCACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CEP6E_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAACAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B9M38_11 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAAAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01ATQR4_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAAAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CEBF5_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGCATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01APBT8_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGAACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B1JXC_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAAGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B3EQU_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGAGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CGWAF_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATCCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B0APB_7 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATAGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B6UVG_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACACAATAGGGGATATAAG >FTWCYXX01EDI76_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGAATATAAG >FTWCYXX01C5103_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGAGTATAAG >FTWCYXX01E5NP5_3 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAA >FTWCYXX01BR0C5_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAGTAGGGGATATAAG >FTWCYXX01AOC8L_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACGTAATAGGGGATATAAG >FTWCYXX01BK1NQ_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGATATAATAGGGGATATAAG >FTWCYXX01D30DM_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGG---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01ANS4X_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCGGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01DLI1O_3 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAGT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01D3HR3_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGGGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CWOZU_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACGATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CLMY5_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAGCAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EGLQ5_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAGTAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01C0BPR_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGTCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01AYW4L_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACGAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BWTVE_23 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTATAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01B15KV_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAGAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGAGGATATAAG >FTWCYXX01E4U9P_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATGGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BZ7KG_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATATTAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01DJM6W_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATGTAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01ERSZV_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCGCAAATAACGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EE0XE_2 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATGATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAGCAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATAGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CO8A3_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAGAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EEVDM_3 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGGAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BJF3C_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAGGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01EN1H7_1 AGTAGTATCAACTCAACTGCTGTTAAATGGTAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01BXB8X_1 AGTAATATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01D577V_1 GGTAGTATCAACTCAACTGCTGTTAAATGGCAGCCTAGCAGAAAAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGGCGAGCATTCTATGGA---------------AGTGACATAATAGGGGATATAAG >FTWCYXX01CKIMU_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAACAATGCCAAAATTATAATAGTACAACTTGTCCAACCTGTGACAATTAAGTGTATCAGACCTAACAACAATACAAGAAAAAGTATACGT------ATAGGACCAGGACAAGCATTCTATGCAACA------------GGTGACATAATAGGGGATATAAG >FTWCYXX01EFLKV_1 AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAAGA---GTAATAATTAGATCTCAAAATATCACAAATAATGCCAAAAATATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAGAGTATAAAT------ATAGGACCAGGACAAGCATTCTATGCAACA------------GGTGACATAATAGGGGATATAAG >FTWCYXX01AJ9L4_11 AGTAGTATCAACTCAATTGCTGTTGAATGGCAGTCTAGCAGAAAAAAAT---ATAACAATTAGATCTGAAAATATCACAAACAATGCCAAAATTATAATAGTACAACTTGTCCAACCTGTGACAATTAAGTGTATCAGACCTAACAACAATACAAGAAAAAGTATACGT------ATAGGACCAGGACAAGCATTCTATGCAACA------------GGTGACATAATAGGGGATATAAG >FTWCYXX01ATH85_1 AGTAGTATCAACTCAATTGCTGTTGAATGGCAGTCTAGCAGAAAAAAAT---ATAACAATTAGATCTGAAAATATCACAAACAATGCCAAAATTATAATAGTACAACTTGTCCAACCTGTGACAATTAAGTGTATCAGACCTAACAACAATACAAGAAAATGTATACGT------ATAGGACCAGGACAAGCATTCTATGCAACA------------GGTGACATAATAGGGGATATAAG >A1.AU.x.PS1044_Day0.DQ676872 -GTAGTAACAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAAATAGG---ACAATGATTAGATCTAAAAACATTACAGACAATAAAGAAAACATAATAGTACAGCTTACCGAGCCTGTAAACATTACTTGTATCAGACCTAACAACAATACAAGAAAAAGTGTACGT------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGTGAAATAATAGGGGATATTAG >A1.KE.94.Q23_17.AF004885 -GTAGTATCAACTCAATTGCTGTTGAATGGCAGTCTAGCAGAAAAAAAT---ATAACAATTAGATCTGAAAATATCACAAACAATGCCAAAATTATAATAGTACAACTTGTCCAACCTGTGACAATTAAGTGTATCAGACCTAACAACAATACAAGAAAAAGTATACGT------ATAGGACCAGGACAAGCATTCTATGCA------------ACAGGTGACATAATAGGGGATATAAG >A1.RW.92.92RW008.AB253421 -GTAGTGTCAACTCAACTGTTGTTAAATGGCAGTCTAGCAAAAGAAAAG---GTAATAATTAGATCTGAAAATATCACAAACAATGTCAAAACCATAATAGTACAACTTGTCAAGCCTGTGAAAATTAATTGTACCAGACCTAACAACAACACAAGAACAAGTATACGT------ATAGGACCAGGACAATCATTCCATGCA------------ACAGGTGACATAATAGGGGATATCAG >A1.UG.92.92UG037.AB253429 -GTAGTATCAACTCAACTGCTGTTAAATGGCAGTTTAGCAGAAGGAAAG---GTAATGATTAGATCTGAAAATATCACAAACAATGTCAAAAACATAATAGTACAACTTAACGAGTCTGTAACAATTAATTGTACCAGACCTAACAATAATACAAGAAGAAGTGTACGT------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGTGATATAATAGGGGATATAAG >A2.CD.97.97CDKS10.AF286241 -GTAGCATCAACTCAACTGCTGTTGAATGGCAGTCTAGCAGAAAAAGAG---GTGATGATTAGATCTGAAAATATTACAAACAATGCCAAAAACATAATAGTACAGTTTAATGAATCGGTACCAATTACTTGTATCAGACCCAACAACAATACGAGAAAAGGTATACCT------ATTGGACCAGGACAAGTCTTCTAT---------------ACAAGTGACATAATAGGGGATATAAG >A2.CD.97.97CDKTB48.AF286238 -GTAGCATCAACTCAACTGCTGCTGAATGGCAGTCTAGCAGAAGGAAAG---GTAATGATTAGATCTGAAAATATTACAGACAATGCCAAAAACATAATAGTACAGTTTAATAAACCTGTACCAATTAATTGTACCAGACCCAACAACAATACAAGAAAAAGTATACGC------TTTGGACCAGGACAGGCCTTCTATACA------------AATAATAACATAATAGGGGATATAAG >A2.CY.94.94CY017_41.AF286237 -GTAGCATCAACTCAACTGCTGTTGAATGGCAGTCTAGCAGAAGGAGGGAAAATAATGATTAGATCTGAAAATATTACAAACAATGCCAAAAACATAATAGTTCAGTTTACTAAGCCTGTACTAATTACTTGTATCAGACCCAACAACAATACAAGAAAAAGTATACGC------TTTGGACCAGGACAAGCCTTCTAT---------------ACAAATGAAATAATAGGGGACATAAG >B.FR.83.HXB2_LAI_IIIB_BRU.K034 -GTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAG---GTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACA------------ATAGGA---AAAATAGGAAATATGAG >B.NL.00.671_00T36.AY423387 -GTGGTGTCAACCCAATTACTGTTAAATGGCAGTCTAGCAGAAGAAGAT---GTAGTAATTAGATCTAAAAATTTCACAGACAATACCAAAACCATAATAGTACAGCTGAAGGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT------ATAGGACCAGGGAGAGCATTTTATGCA------------ACAGGAGAAATAATAGGAGATATAAG >B.TH.90.BK132.AY173951 -GTAGTATCAACTCAACTGCTGCTAAATGGCAGTCTAGCAGAAGAAGAG---GTAGTAATTAGATCTGAAAATTTTACAGACAATGCTAAAACCATAATAGTACAGCTGAAAGAACCTGTAGAAATTAATTGTACAAGACCTAACAACTATACAAGGAAAAGAATAACT------ATGGGACCAGGGAGAGTATATTATACA------------ACAGGAGAAATAATAGGAGATATAAG >B.US.98.1058_11.AY331295 -GTAGTATCTACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAT---GTAATAATCAGATCTGACAATTTCACGGACAATGCTAAAACCATAATAGTACAACTGAACGAAACTGTAGATATTCACTGTATAAGGCCCAACAATAATACAAGAAAACGTATAACT------ATGGGACCAGGGAAAGTATATTATACA------------ACAGGACAAATAATAGGAGATATAAG >B.US.98.15384_1.DQ853463 -GTAGTGTCAACTCAACTGCTGTTGAATGGCAGTCTAGCAGAAGAAGAG---ATAGTAATTAGATCACAAAATTTTACGGACAATGTTAAATCCATAATAGTACAGCTGAATGAAACTGTAAAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAGCTATACGT------ATAGGACGAGGGAGAGCAATTTATGCA------------ACAGATAGAATAATAGGAGATATAAG >C.BR.92.BR025_d.U52953 -GTAGTGTCAACTCAACTACTGTTAAATGGTAGTCTAGCAGAAGAAGAG---ATAATAATTAGATCTAAAAATCTAACAGACAATGTCAAAACAATAATAGTACATCTTAACGAATCTGTAGAGATTAATTGTACGAGACCCAACAATAATACAAGAAAAAGTATAAGG------ATAGGACCAGGACAAGCATTCTATGCA------------ACAGGAGAAATAATAGGAGATATAAG >C.ET.86.ETH2220.U46016 -GTGGTATCAACTCAACTATTGTTAAATGGTAGTATAGCAGAAGGTGAG---ACAATAATTAGATTTGAAAATCTGACAAACAATGCCAAAATAATAATAGTACAGCTTAATGAATCTGTAGAAATTACTTGTACGAGACCCAGCAATAATACAAGAGAAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGAGACATAATAGGAGATATAAG >C.IN.95.95IN21068.AF067155 -GTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGAGGG---ATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAACCTGTAGAAATTATGTGTACAAGACCCGACAATAATACAAGAAAAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGAGACATAATAGGAGACATAAG >C.ZA.04.SK164B1.AY772699 -GTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAG---ATAATAATTAGATCTGAAAATCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCAACAATAATACAAGGAAAAGTATAAGG------ATAGGACCAGGACAAGTATTCTAT---------------ACAAATGAAATAATAGGAAACATAAG >D.CD.83.ELI.K03454 -GTGGTGTCAACTCAACTGCTGTTGAATGGCAGTCTAGCAGAAGAAGAG---GTCATAATTAGATCCGAAAATCTCACAAACAATGCTAAAAACATAATAGCACATCTTAATGAATCTGTAAAAATTACCTGTGCAAGGCCCTATCAAAATACAAGACAAAGAACACCT------ATAGGACTAGGGCAATCACTCTATACT------------ACAAGATCA---AGATCAATAATAGG >D.CM.01.01CM_4412HAL.AY371157 -GTGGTATCAACTCAATTGCTGTTGAATGGCAGTCTAGCAGAAGAG------GTCATGGTTAGATCTGAAAATCTCACAGACAATGCTAAAAACATAATAGTCCAGCTTAATAATACTATAAACATTACTTGTGTAAGGCCGAACAGCAATACAAGAAAAAGTATAAAT------CTAGGACCAGGGCAGGCATTCTATGCAACATAT------GCAACAAATATAATAGGAAACATAAG >D.TZ.01.A280.AY253311 -GTGGTGTCAACTCAACTGCTGTTGAATGGCAGTTTAGCAGGAGAAGAG---ATAATAATTAGATCTGAAAATCTCACAAACAATGTTAAAACCATAATAGTACAGTTAAATGAGACTGTAAAAATTAATTGTACAAGGCCTAATAACAATACAAGAAAAGGTATACGT------ATAGGACCAGGGCAAACATTCTTTACA---------------GCAGAGGTAACAGGAGATATAAG >D.UG.94.94UG114.U88824 -GTAGTGTCAACTCAACTGTTGTTGAATGGCAGTCTAGCAGAAGAAGAA---ATAATAATTAGATCTGAAAATCTCACAAACAATGCTAAAATCATAATAGTACAGCTTAATGAGTCTGTACCAATTAATTGCATAAGGCCCTATAACAATACAAGACAAAGTACACGT------ATAGGACCAGGGCAAGCACTCTTTACA------------ACA---AAAGTAATAGGAGATATAAG >F1.BE.93.VI850.AF077336 -GTGGTATCAACTCAATTGTTGTTAAATGGCAGCCTAGCAGAAGAAGGT---ATAGTAATCAGATCTCAAAATATCTCAAATAATGCAAAAACCATAATAGTACACCTTAATGAATCTGTACAGATTAATTGTACAAGACCCAACAACAATACAAGGAAAGGTATACAT------TTAGGACCAGGACAAACATTCTATGCA------------ACAGGAGCAATAATAGGAGACATAAG >F1.BR.93.93BR020_1.AF005494 -GTGGTATCCACTCAATTGTTGTTAAATGGCAGCCTAGCAGAAGGAGAG---ATAGTAATCAGATCTCAAAATATCTCAGATAATGCAAAAACCATAATAGTGCACCTTAATGAATCTGTACAGATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATATCT------TTAGGACCAGGACGAGTATTTTATACA------------ACAGGAGAAATAATAGGAGACATCAG >F1.FI.93.FIN9363.AF075703 -GTGGTATCAACTCAATTGTTGTTAAATGGCAGCCTATCAGAAGGAGGT---ATAATAATCAGATCTCAAAATCTCTCAGATAATGCAAAAACTATAATAGTACACCTTAATGAATCTGTACAGATCAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACGT------ATAGGACCAGGACAATCATTTTATGCA------------ACAGGAGAAATAATAGGAGACATAAG >F1.FR.96.MP411.AJ249238 -GTGGTATCAACTCAATTGCTGTTAAATGGCAGCCTGGCAGAAGAAGAT---ATAATAATCAGATCTCAAAATATCTCAGATAATGCAAAAACCATAATAGTACACCTTAATGAAAGTGTACAGATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT------TTAGGACCAGGACAAGCATTCTATGCA------------ACAGGTGATATAATAGGAGATATAAA >F2.CM.02.02CM_0016BBY.AY371158 -GTGGTATCAACTCAACTACTGTTAAATGGCAGCTTAGCAGAAAAAAAT---ATAATAATTAGATCTGAAAATATCACAGATAATGCAAAAACCATAATAGTACAGTTTAATGAATCAGTAAAAATTAACTGTACAAGACCCAACAACAATACAAGAAAAAGTATACGT------ATAGGACCAGGACAAGTATTTTATGCA------------ACAGGTGAGATAATAGGAGACATAAG >F2.CM.95.MP255.AJ249236 -GTGGTATCAACTCAACTACTGCTAAATGGCAGCCTAGCACAAGAAGAT---ATAATAATTAGATCTAAAAATATCACAGATAATACAAAAAACATAATAGTACAGTTTAATAGATCTGTAATAATTGATTGTAGAAGACCCAACAACAATACAAGAAAAGGGATACGT------ATAGGACCAGGACAAACATTCTTTGCA------------ACAGGTGAAATAATAGGGGATATAAG >F2.CM.95.MP257.AJ249237 -GTGGTATCAACTCAACTACTGTTAAATGGCAGCCTAGCAGAAGAAAAG---ATGATAATTAGATCTGAAAATATCTCAGATAATACAAAAACCATAATAGTACAGTTTAAAAATCCTGTAAAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATACAT------ATAGGACCAGGACGAGCATTCTATGCA------------ACAGGTGAGATAATAGGAGATACAAG >F2.CM.97.CM53657.AF377956 -GTAGTGTCAACTCAACTACTGTTAAATGGCAGCCTAGCAGAAGGAGAT---ATAGTAATTAGATCTGAAAATATCTCAGATAATGCAAAAACCATAATAGTACAGTTTAATAGATCTGTAGCAATTAACTGTACAAGACCCACCAACATTACAAGAAGAAGTATGCGT------ATAGGACCAGGACGAGTATTTTATGCA------------ACAGGTACCGTACTAGGAGATATAAG >G.BE.96.DRCBL.AF084936 -GTAGTATCAACTCAACTACTGCTGAATGGCAGTTTAGCAGAAAAAGAT---ATCATAATTAGTTCTGAAAATATCTCAGACAATGCCAAAGTCATAATAGTGCACCTTAATAGGTCTGTAGAAATTAATTGTACCAGACCCAACAACAATACAAGAAGAAGTGTAGCA------ATTGGACCAGGACAAGCATTCTATACA------------ACAGGAGAAGTAATAGGAGACATAAG >G.KE.93.HH8793_12_1.AF061641 -GTGGTATCAACTCAACTACTGCTGAATGGCAGTTTAGCAGAAGGAGAA---ATAATAATTAAATCAGAAAACATCACAGACAATACCAAAGTCATAATAGTGCAGCTTAATGAAACTGTAGAAATTACGTGTGTCAGACCCAACAACAATACAAGAAAAAGTATACAC------CTCGGGCCAGGACAAGCGCTCTATGCA------------ACAGGGGACATAATAGGAAATATAAG >G.NG.92.92NG083.U88826 -GTGGTATCAACTCAACTACTGCTGAATGGCAGTTTAGCAGAAGAAGAT---ATAAGAATTAGATCTGAAAATTTCACAGACAATACCAAAGTCATAATAGTGCAGCTTAATAATAGTATAGAAATTAATTGTATCAGACCCAATAACAATACAAGAAAAAGTATACCA------ATCGGACCAGGACAAGCGTTCTATGCA------------ACAGGTGATATAATAGGAGACATAAG >G.PT.x.PT2695.AY612637 -GTGGTATCAACTCAATTGCTGCTGAACGGCAGTTTAGCAGAAGGGGAA---ATAATGATTAGATCTGAAAACATCACGAACAATGCCAAAAACATAATAGTACAGCTCAATGAAACTGTACCCATTACGTGTGCCAGACCCAGCAATAATACAAGAAAAAGTATAAGA------TTTGGACCAGGACAAGCGTTCTATGCA------------ACAGATGCCATAATAGGAGATATAAG >H.BE.93.VI991.AF190127 -GTGGTATCAACTCAACTGTTGTTAAATGGAAGCCTAGCAGAAGTGGAGGAGGTAATAATTAGATCTAAAAATATTACAGATAATACCAAAAACATAATAGTACAGTTAAATGAACCTGTACAAATTAACTGTACCAGAACAGGCAATAATACGAGAAAAAGTATACGT------ATAGGGCCAGGACAAGCATTCTATGCA------------ACAGGTGACATCATAGGAGATATAAG >H.BE.93.VI997.AF190128 -GTGGTATCAACTCAACTGCTATTAAATGGAAGCCTAGCAGAAGGACAG---GTCATAATTAGATCTAAAAATATCTCAGACAATACCAAAAACATAATAGTACAGCTTGATAGTCCTATAGAAATTACCTGTACCAGACCTAACAATAATACAAGAAAAGGTATACAT------TTCGGGCCAGGGCAAGCATTCTATGCA------------ACAGGTGATATCATAGGAAACATAAG >H.CF.90.056.AF005496 -GTGGTATCAACTCAACTGCTATTAAATGGAAGCCTAGCAGAAGAACAG---ATCATAATTAGAACTAAAAATATCTCAGACAATACCAAAAACATAATAGTACAGCTTAAGACACCAGTAAACATTACATGTACCAGGCCTAACAATAATACGAGAACAAGTATACAT------TTAGGGCCAGGACGAGCATTCTATGCA------------ACAGGTGACATCATAGGAGATATAAG >J.CD.97.J_97DC_KTB147.EF614151 -GTGGTGTCAACTCAACTACTGCTAAATGGTAGTATAGCGGAAAAAGAA---GTAATAATTAAATCCAAAAATATCTCAGACAATGCTAAGACCATAATAGTACAGCTTAACCAAACTGTAGAAATCAATTGTACCAGACCCGCCAACAATACAAGAAAGGGTATACCC------ATAGGACCAGGGCAAGTGCTATATGCA------------ACAGGTGCAGTAATAGGAAACATAAG >J.SE.93.SE7887.AF082394 -GTGGTATCAACTCAACTACTGCTAAATGGCAGTATAGCAGAAGGAGAC---ATAATAATTAGATCTGAAAACATCTCAGACAATGCCAAAAACATAATAGTACAACTTAATAAAACTGTAGAAATTGTGTGTTACAGACCTAATAACAATACAAGGAAAGGTATACAC------ATGGGACCAGGACAAGTGCTCTACGCA------------ACAGGAGAAATAATAGGAAATATAAG >J.SE.94.SE7022.AF082395 -GTGGTATCAACTCAACTACTGCTAAATGGCAGTGTAGCAGAAGGAGAC---ATAATAATTAGATCTGAAAATATCTCAGACAATGCTAAAAACATAATAGTACAACTTAATGACACTGTAGAAATTGTGTGTACCAGACCTAATAACAATACAAGAAAAGGTATACAC------ATGGGACCAGGACAAGTGCTCTACGCA------------ACAGGGGAAATAATAGGAGATATAAG >K.CD.97.EQTB11C.AJ249235 -GTGGTATCAACTCAATTGCTATTAAATGGCAGCCTAGCAGAAGAAGAG---ATAATTATTAGGTCTGAAGATATTACAAAGAATACAAAAAACATAATAGTACAGCTTAATGAAGCTGTAGAAATTAATTGTACAAGGCCAAGCAACAATACAAGAAAAAGTATACAT------ATAGGACCAGGAAGAGCATTCTATGCA------------ACAGGTGACATAATAGGAGATATAAG >K.CM.96.MP535.AJ249239 -GTGGTATCAACTCAACTGCTGTTAAATGGCAGCCTAGCAGAAGAAGAG---ATAATAATTAGGTCTGAAAATATTACAGATAATACAAAAAACATAATAGTACAGCTTAATGAAACTGTACAAATTAATTGTACAAGGCCAAACAACAATACAAGAAAAAGTATACAT------ATGGGACCAGGAAAAGCATTCTATACA------------ACAGGTGATATAATAGGAGATATAAG >01_AE.TH.90.CM240.U54771 -GTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAG---ATAATAATCAGATCTGAAGATCTCACAAACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACAAGTATAACT------ATAGGACCAGGACGAGTATTCTATAGA------------ACAGGAGATATAATAGGAAATATAAG >01_AE.TH.93.93TH051.AB220944 -GTGGTATCAACACAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAA---ATAATAATCAGATCTGAAAATCTCACAAACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATATAAGAACAAGTATAAGA------ATAGGACCAGGACGAGTATTCTATAAA------------ACAGGAGCTATAACAGGAGATATAAG >02_AG.CM.99.pBD6_15.AY271690 -GTAGTGTCAACTCAACTGCTACTAAATGGCAGTCTAGCAGAAGAAGAG---GTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAGCTGGTTACTCCTGTAAAAATTAATTGTACCAGACCTGGCAATCCTATAAGAAAAAGGGTAGGT------ATAGGACCAGGACAAGCATTCCATGCA------------ACAGGTAATATAATAGGAGACATAAG >02_AG.NG.x.IBNG.L39106 -GTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGGAGAA---GTAGTGATCAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAGTTGGCTAATCCTGTAAAAATTAATTGTACCAGACCTAACAACAATACAAGAAAAGGTGTACAT------ATAGGACCAGGGCAAGCATTCTATGCA------------ACAGGTGACATAATAGGGGATATAAG >03_AB.BY.00.98BY10443.AF414006 -GTAGTGTCAACTCAACTGCTGTTAAATGGTAGCCTAGCAGAAAAAGAG---GTAGTAATTAGATCTGTCAATTTCACGGACAATACTAAAACCATAATAGTACAGCTGAAAGAACCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAGGTATTCAT------ATGGGACCAGGGAGAGCATTTTATGCA------------ACAGGAGACATAATAGGAGACATAAG >04_cpx.GR.91.97PVCH.AF119820 -GTGGTATCAACTCAATTGCTGTTAAATGGAAGCTTAGCAACAGGAGGG---GTAGTAATTAGATCTAAAAATTTCACAGACAATCCCAAAAATATAATAGTACAGCTTGACAAGGCTGTAAAAATTAATTGTACCGGCCTTAACAACAATACAGGAGGAAGTGAACGTATCGGTATAGGGCCAGGACACACATGGTATGCA------------ACAGGTAACATAGTAGGAGATATAAG >04_cpx.GR.97.97PVMY.AF119819 -GTAGTATCAACTCAATTGCTGTTAAATGGAAGCTTATCAACAGAAGGG---GTAGTACTTAGATCTAAAAACTTCACAGACAATACCAAAAATATAATAGTACAGCTTGCAGAGGCTGTAAAAATTAATTGTACCAGACCTAACAACAATACAAGAAAAGGTGTACAT------ATAGGACCAGGAAAAACATGGTTTGCA------------ACAGGGGAAGTAATAGGAGACATAAG >05_DF.BE.x.VI1310.AF193253 -GTGGTATCAACTCAGTTGCTGTTAAATGGCAGCCTAGCAAAAGAAGGT---ATAATAATCAGATCTCAAAATATCTCAGATAATGCAAAAAACATAATAGTACACCTTAATGAATCTGTACATATTAATTGTACAAGGCCCAACAACAATACAAGAAAAAGTATACAT------TTAGGACCAGGACAAGCATTCTATGCA------------ACAGGTGACATAATAGGAGACATAAG >06_cpx.EE.01.EE0359.AY535659 -GTGGTATCAACTCGATTACTGCTAAATGGTAGTTTAGCAGAAGAAAGT---ATAATAATTAGATCTGAAAACATCACAGACAATGCCAAAAACATAATAGTGCAGCTTAATAAATCTGTAGAAATTATATGTACCAGACCCTATAATAATACAAGAAAAAGTATACAC------TTTGGACCAGGGCAAGCGCTTTTTGCA------------ACAGGTGAAATAATAGGAGATATAAG >06_cpx.GH.03.03GH173_06.AB2868 -GTGGTGTCAACTCAATTACTGCTGAATGGTAGTTTAGCAGAAAAAGAA---ATAATAATTAGATCTGAAAATCTCACAGACAATACCAAAAACATAATAGTGCAGCTTAATAGCACTGTACAAATTACATGCAATAGACCCAATAACAATACAAGAAGAGGTATACAC------CTTGGACCAGGGCAAGTGTTCTTTGCA------------ACAGGTGACATAATAGGAGATATAAG >06_cpx.ML.95.95ML127.AJ288982 -GTGGTATCAACTCAGTTACTGCTGAATGGCAGTTTAGCAGAAGAAGAA---ATAATAATTAAATCTAAAAACCTCACAGACAATACCAAAATCATAATAGTGCAGCTTAATAAATCTGTAGAAATTAGTTGTTCCAGACCCAATAACAATACAAGAAAAAGTATACAC------ATTGGACCAGGGCAAGCGTTCTATGCA------------ACAGGTGAAATAATAGGAAATATAAG >06_cpx.ML.95.95ML84.AJ245481 -GTGGTATCAACTCAGTTACTGCTGAATGGCAGTTTAGCAGAAGATGAA---ATAATAATTAAATCTGAAAACCACACAAACAATGCCAAGATCATAATAGTGCAGCTTAATAAAACTGTACAAATTAGGTGTACCAGACCCAGTAACAATACAAGGAAAAGTATACCC------CTTGGACCAGGGCAAGCGTTCTATGCA------------ACAGGTGACATAATAGGAGATATAAG >06_cpx.RU.05.04RU001.DQ400856 -GTAGTATCAACTCAATTACTGCTAAATGGCAGTTTAGCAGAAGAAAAT---GTAATAATTAGATCTGAAAACATCACAGACAATACCAAAACCATAATAGTGCATCTTAATAAATCTGTAGAAATTACATGTACCAGACCCAATAATAATACAAGAAAAGGTATACAC------TTTGGACCAGGGCAAGTGTTTTTTGCA------------ACAGGTGACATAATAGGAGATATAAG >06_cpx.SN.97.97SE1078.AJ288981 -GTGGTATCAACTCAATTACTACTGAATGGCAGTTTAGCAGAAGAGGAA---ATAATAATTAAAACTGAAAACCTCACAGACAATAGCAAGAACATAATAGTACAGCTTAATAAATCTATAGAAATTAAGTGTACCAGACCCAATAACAATACAAGAAAAAGTATATCC------TTTGCACCAGGGCAAGCGTTCTATGCA------------ACAGGTGACATAATAGGAGATATAAG >07_BC.CN.97.97CN001.AF286226 -GTGGTATCAACTCAACTACTTGTTAATGGTAGCCTAGCAGAAGGAGAA---ATAATAATTAGGTCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCGGCAATAATACAAGAAAAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGAGACATAATAGGAGACATAAG >08_BC.CN.98.98CN006.AF286229 -GTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGAGAG---ATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCAACAATAATACAAGAAAGAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGAGACATCATAGGAGACATAAG >09_cpx.CI.00.00IC_10092.AJ8665 -GTAGTATCAACTCAATTACTGCTGAATGGCAGCTTAGCAGAAGGAGAT---ATAATGATTAGATCTGAGAATATCACAGACAATGCCAAAGACATAATAGTACAATTGAAGGAGCCTGTAAATATTACTTGTATCAGACCTAGCAACAATACAAGGGAAAGTGTACGT------ATAGGACCAGGACAAACTTTCTTTGCA------------ACAGGTGATATAATAGGAGACATAAG >10_CD.TZ.96.96TZ_BF061.AF28954 -GTAGTGTCAACTCAACTGTTATTGAATGGCAGTCTAGCAGAAGAAGAG---ATAATAATTAGATCTGAAAATCTCACAGATAATGCTAAAAATATAATAGTGCAGCTTAATGAGTCTGTAACAATTAATTGCGTGAGACCCAACAATAATACAAGAAGAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCA------------ACA---GACATAATAGGAAACATAAG >11_cpx.CM.95.1816.AF492624 -GTAGTATCAACTCAATTACTGTTAAATGGCAGTCTAGCAGAAGGAGAG---GTAAGAATTAGATCTAAAAACATCACAGACAATGCTAAAACCATAATAGTACAATTTGACAGTCCTGTACACATTAATTGTACCAGACCTAACAACAATACAAGAAAAAGTATACGG------ATAGGACCAGGACAAGCTTTCTATGCA------------ACAGGTGCTATAATAGGGGATATAAG >12_BF.AR.97.A32879.AF408629 -GTGGTATCAACTCAATTGTTGTTAAATGGCAGCCTAGCAGAAGAAGAG---ATAATAATCAGCTCTCAAAATATCTCAGATAATGCAAAAAACATAATAGTACACCTTAAGGAACCTGTATGGATTAATTGTACAAGACCCAACAATAATACAAGAAAAAGTATACAT------TTAGGACCAGGACAAGCATTTTATGCA------------ACAGGAGATATAATAGGAGACATCAG >12_BF.AR.97.A32989.AF408630 -GTGGTATCAACTCAATTGTTGTTAAATGGCAGTCTACCAGAAGGAGAG---ATAATAATCAGATCTCAAAATATTTCACATAATACAAAAACCATAATAGTACACCTTAATGAATCTGTACAGATTACTTGTATAAGACCCAACAATAATACAAGAAAAAGTATACAT------ATAGGACCAGGAAGAGCATTTTATGCA------------ACAGGAGACATAATAGGAGACATGAG >12_BF.AR.99.ARMA159.AF385936 -GTGGTATCAACTCAATTGTTGTTAAATGGCAGCCTAGCAGAAGAAGAT---ATAATAATTAGATCTCAAAACATCTCAGATAATACAAAAACCATAATAGTTCATCTTAATGAATCTGTACAGATTAACTGTACAAGACCCAACAATAATACAAGAAAAAGTATACAG------TTAGGACCAGGACGGGCATTTTATGCA------------ACAGGAGACATAATAGGGGACATTAG >13_cpx.CM.02.02CM_A1394.DQ8453 -GTAGTATCAACTCAACTACTGTTAAATGGCAGCCTAGCAGAAGGAGGAGAGATAAAGATTAGATCTGAAAACATCTCAAACAATGCTAAAACCATAATAGTACAGCTTAAAGATCCTGTGAGAATTAATTGTACTAGACCTAACAACAATACAAGAAAAAGTATAAGG------ATAGGACCAGGACAAACATTCTATGCA------------ACAGGTGATATAATAGGGGATATAAG >14_BG.DE.01.9196_01.AY882421 -GTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAAAAGAG---GTAATAATTAGGTCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTAAATAAATCTGTAGTAATTAATTGYTCAAGACCCAACAACAATACAAGAAAAAGTATACCT------ATAGGACCAGGGAGAGCATTTTATGCA------------ACAGGACAAATAATAGGAGACATAAG >15_01B.TH.99.99TH_MU2079.AF516 -GTAGTATCAACTCAACTGCTGTTAAATGGCAGTTTAGCAGAAGAAGAG---GTAATAATCAGATCTAGCAACTTCACGAACAATGCTAAAATCATAATAGTACAGCTAAATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT------ATAGGTCCAGGGAGATCATGGTATACA------------ACAGGAGAAATAATAGGAGATATAAG >16_A2D.KR.97.97KR004.AF286239 -GTGGCATCTACTCAATTGCTGCTGAATGGCAGTCTAGCAGAAGGAAATAAAACAATAATTAGATCTGCAAATATTACAGACAATACTAAAAACATAATAGTACAGTTTACTAAGCCTGTACAAATTAATTGTACCAGACCCGACGTCGGTCAAAGAAGGAGTGTACGC------ATTGGACCAGGACGAGCCTTCTATACAAGGCAAACATATACAAGGCAAGCAAAAGGGGATATAAG >18_cpx.CU.99.CU76.AY586540 -GTGGTATCAACTCAATTGCTGTTAAATGGAAGTCTAGCAACAGAAAAG---GTAATGATCAGATCTGAAAATATCACAGACAATACCAAGAACATAATAGTACAGCTTACGACGCCTGTAAACATTACCTGTACCAGACCCAGCAATAACACGAGAAGAAGTATACAT------ATAGGACCAGGACAAGCATTCTATGCA------------ACAGGTGACATAATAGGAGATATAAG >19_cpx.CU.99.CU29.AY588971 -GTAGTGTCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAGGAG---ATAGTAATTAGTTCTGAAAATATCACAAACAATGCCAAAATCATAATAGTACAGCTTAAGAAGCCTGTACAAATTAATTGTACCCGACCTAACAACAATACAAGACAAGGTGTACAT------ATAGGACCAGGAGCAGTATTCTATAGA------------ACAGGTGATATAATAGGGGATATAAG >20_BG.ES.99.R77.AY586544 -GTGGTATCAACTCAATTACTGCTGAATGGCAGCTTAGCAGAAAAGGAA---ATAATGATTAGATCTGAAAACCTCACAAACAATGCCAAAGTCATAATAGTGCAGCTTAATAAAAGTATAGAAATTAATTGTACCAGACCCAACAACAATACAAGAAAGAGTATAAGA------TTTGGACCAGGACAAGCGTTCTATGCA------------ACAGGTGACATAATAGGAGATATAAG >21_A2D.KE.91.KNH1254.AY945737 -GTGGTGTCAACTCAACTGCTGTTGAATGGCAGTTTAGCAGAGGAAGAG---ATCATAATTAGAACTGAAAATATCAGCAGGAATGAAAAAAGCATAATAGTACAGCTTAATGAGTCTGTAACAATTAATTGTACAAGGCCCAATAACAATACAAGAAGAGGTATACAT------ATAGGACCAGGGCAAGCAATATATGCA------------ACCGGTAAGATAATAGGAAACATAAG >23_BG.CU.03.CB118.AY900571 -GTGGTATCAACTCAATTACTGCTGAATGGCAGCTTAGCAGAAAAGGAA---ATAATGATTAGATCTGAAAACCTCACAAACAATGCCAAAGTTATAATAGTGCAGCTTAATAGCAGTATAACAATTAATTGTACCAGACCCAACAACAATACAAGAAAGAGTATAACA------TTTGGACCAGGACAAGCATTCTATGCA------------ACAGGTGACATAATAGGAAATATAAG >24_BG.CU.03.CB378.AY900574 -GTGGTATCAACTCAATTACTGCTGAATGGCAGCTTAGCAGACAAGGGA---ATAATGATTAGATCTGAAAACCTCACAAACAATGCCAAAGTCATAATAGTGCAGTTTAATAAAAGTATAGATATTAATTGTACCAGACCTGGCAACAATACAAGAAAGAGTATAAGA------TTTGGACCAGGACAAGCGTTCTATGCA------------ACAGGTGCCATAATAGGCGATATAAG >25_cpx.CM.01.101BA.DQ826726 -GTAGTGTCAACACAACTGTTGCTAAATGGCAGCTTAGCAGAAGAAGAG---ATAGTAATTAGATCTGAAAATATTTCAAACAATGCCAAAAGCATAATAGTGCATTTTAATGAGACTGTAACAATTAATTGTATCAGACCTAACAACAATACAAGAAAAAGTGTACGT------ATAGGGCCAGGACAAACATTCTATGCA------------ACAGGTGATATAATAGGAGATATAAG >27_cpx.FR.04.04CD_FR_KZS.AM851 -GTGGTATCAACTCACTTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAG---ATAATAATTAAATCTGAAAATCTCACAGACAATACCAAAACCATAATAGTACACCTTAATGAATCTGTAAAAATTAATTGTACCAGACCCTTCAACAATACAAGGAAAAGTGTAAGT------CTAGGACCAGGATCCGTATGGTATAGA------------CCAGGAGAAGTAATAGGAGATATAAG >28_BF.BR.99.BREPM12313.DQ08587 -GTAGTGTCAACTCAACTGCTATTAAATGGCAGTCTGGCAGAAGAAGAA---ATAATAATTAGATCTGAAAATTTCACAAACAATGCTAAAATTATAATAGTACAGCTGAATAGGACTGTAGACATTAATTGTACAAGACCCGGCAACAATACAAGAAAAAGTATACAT------ATAGCACCGGGAAGAGCATTTTATGCA------------ACAGGAGACATAATAGGAGATATAAG >29_BF.BR.99.BREPM11948.DQ08587 -GTAGTGTCAACACAACTACTGTTAAATGGCAGTCTAGCAGAAGAAGAT---ATAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAACCATAATAGTACAGTTGAACGAAACTGTACGAATTAATTGTACAAGACCCAACAATAATACAAGAAGAAGTATGCAT------CTAGGACCAGGGAGAGCATTATTTCAT------------GCAACAGATATAATAGGAGATATAAG >31_BC.BR.02.110PA.EF091932 -GTAATATCAACTCAACTACTGTTAAATGGTAGTCTAGCAGAAGATGAG---ATAATAATTAGATCTAAAAATATAACAGACAATGTCCAAACAATAATAGTACAGCTTAAGGAACCTGTAGAAATTAATTGTACGAGACCCAACAATAATACAAGAGAAAGTATAAGA------ATAGGTCCAGGACAAACATTCTATGCA------------ACAGGAGACATAATAGGAGATATAAG >33_01B.MY.05.05MYKL045_1.DQ366 -GCGGTATCAACTCAATTGCTGTTAAATGGTAGTTTAGCAGAAGAAGAG---ATAATAATCAGATCTGCAAATCTCACAGACAATACCAAAACCATAATAGTGAATCTTAATACACCTGTAGAAATCAATTGTACCAGACCCTCTGAAAAGAAAAGAATGCGTATGACT------ACGGGACCAGGACACGTATTCTATAAA------------ACAAACGAAATAACAGGAGATATAAG >34_01B.TH.99.OUR2478P.EF165541 -GTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAG---ATAATAATCAGATCTGAAAATATCACAAACAATGCAAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACAAGTGTACAT------ATAGGACCAGGACAAGCATTCTATAAA------------ATAGGAGACATAATAGGAGATATAAG >35_AD.AF.05.05AF026.EF158043 -GTGGTATCAACTCAACTATTGTTGAATGGCAGTCTAGCAGAAGGAGAG---ATAATAATTAGATCTGAAAATATCTCAGACAATGCTAAAACCATAATAGTACAGCTTAATGAGACTGTAACAATTAATTGTACCAGACCTGGCAACAATACAAGAAAAAGTATACAT------ATAGGACCAGGACAAGCATTCTATGCA------------ACAGGTGATATAATAGGGGATATAAG >36_cpx.CM.00.00CMNYU830.EF0879 -GTGGTATCAACTCAATTACTGTTAAATGGCAGTCTAGCAAAAAATGAA---ACAATAATCAGATCTGAAAATATCACAAACAATGCCAAGACCATAATAATACAGTTGGTCAAGCCTGTAAATATTACTTGTGTCAGGCCTAACAACAATACAAGAAAAGGTACACCT------ATAGGACCAGGACAAGCTTTCTATGCA------------AGAAATGATGTAATAGGGGACATAAG >37_cpx.CM.00.00CMNYU926.EF1165 -GTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGGAAAG---GTAATGATTAGATCTGAAAATATCACAAACAACGCCAAAACCATAATAGTACAATTTAATGAGACTGTAGAAATTAATTGTACCAGGTTTAACAACAACACAAGAAAAAGTGTACGC------ATAGGACCAGGACAAACATTCTTTGCA------------ACAGGTGACATAATAGGGGACATAAG >42_BF.LU.03.luBF_05_03.EU17015 -GTAGTGTCAACTCAACTGCTGTTAAATGGCAGCYTAGCAGAAGAAGAT---ATAATAATCAGATCTCAAAATATYTCAGACAATGCAAAAACCATAATAGTACACCTTAATGAATCTGTACAGATTAATTGCACGAGACCCAACAATAATACAAGAAAAAGTATACAT------ATAGCACCAGGACGAGCATTTTATGCA------------ACAGGAGACATAATAGGAGACATCAG seqmagick-0.8.4/examples/dewrapped.phy000066400000000000000000002154701376401056300200200ustar00rootroot00000000000000 134 500 Ref.A1.KE.94.Q23_17.AF004885 GGGTTATGCAAGAATGTCAGCACAGTCCAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAATTGCTGTTG---AATGGCAGTCTAGCAGAAAAAA---ATATAACAATTAGATCTGAAAATATCACAAACAATGCCAAAATTATAATAGTACAACTTGTCCAACCTGTGACAATTAAGTGTATCAGACCTA------ACAACAATACAAGAAAAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGACAAGCACATTGTAATGTCACTAGATCAAG-ATGGAATAAGACTTTACAAGAGGTAGCTGAAAAATTAAGAACATACT------------TTGGG------------AACAAAACAATAA---------T---ATTTGCTAAC-----------TCCTCAGGAGGGGATCTAGAGATCACAACACATAGT-TTT Ref.A1.SE.94.SE7253.AF069670 GGGCCATGCAACAATGTAAGCACAGTACAGTGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAA---AGATAATGATTAGATCTGAAAATATCTCAGACAATGCCAAAACCATAATAGTACAACTTACCGAGCCTGTAACAATTAATTGTACCAGACCTA------GCAACAATACAAGAACAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAACAGGGGATATAAGACAAGCACATTGTAATGTCAGTAGATCAAG-CTGGAATAAAACTCTACAAGACATAGTTACACAATTAAGAGTATACT------------GGAAT-A--------------GAACAATAA---------T---CTTTAATAGC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT Ref.A1.UG.85.U455.M62320 GGGCCATGCAGGAATGTCAGCACAGTACAATGTACACATGGAATCAAGCCAGTGGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAAGAG---AAATAAGGATTAGATCTGAAAATTTCACAAACAATGCAAAAACCATAATAGTACAGCTTGTCAATCCTGTAAAAATCAATTGTTCCAGACCTT---------ACAATACAAGAAAAAATATACGTAGGTATAG-TATAGGATCAGGACAAGCATTCTATGTAACA---------------GGTAAAATAATAGGGGATATAAGACAAGCACATTGTAATGTCAGTAGAAGGGA-CTGGAATAGAACTATACAACAGGTAGCTGAACAATTAAAGAAAAAGT------------TTAAT------------AACAAAACAATAA---------T---CTTTGCTAGC-----------TCCTCAGGAGGGGATATAGAAATTACAACACATAGC-TTT Ref.A1.UG.92.92UG037.U51190 GGGCTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAGGCCAGTAGTGTCAACTCAACTGCTGTTA---AATGGCAGTTTAGCAGAAGGAA---AGGTAATGATTAGATCTGAAAATATCACAAACAATGTCAAAAACATAATAGTACAACTTAACGAGTCTGTAACAATTAATTGTACCAGACCTA------ACAATAATACAAGAAGAAGTGTAC----------GTATAGGACCAGGACAAACATTCTATGCAACA---------------GGTGATATAATAGGGGATATAAGACAAGCACATTGTAATGTCAGTGGGTCACA-ATGGAATAAAACTTTACACCAGGTAGTTGAACAATTAAGAAAATATT------------GGAAC------------AACAATACAATAA---------T---CTTTAATAGC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT Ref.A2.CD.97.97CDKS10.AF286241 GGACCATGCAATAATGTTAGCTCAGTACAATGTACACATGGAATTATGCCAGTAGCATCAACTCAACTGCTGTTG---AATGGCAGTCTAGCAGAAAAAG---AGGTGATGATTAGATCTGAAAATATTACAAACAATGCCAAAAACATAATAGTACAGTTTAATGAATCGGTACCAATTACTTGTATCAGACCCA------ACAACAATACGAGAAAAGGTATAC----------CTATTGGACCAGGACAAGTCTTCTATACAAGT---------------G---ACATAATAGGGGATATAAGACAAGCATATTGTAGTATCAACAAAACAAA-ATGGGATGCCTCTTTACAAAAGGTAGCTGAACAATTAAGAAAACACT------------TCCCT------------AATAAAACAATAA------------ATTTTACCAAA-----------CCCTCAGGAGGGGATCTAGAAATTACAACACATAGT-TTT Ref.A2.CD.97.97CDKTB48.AF286238 GGGTCATGCAGTAATGTTAGCTCAGTACAATGTGCACATGGAATTAGGCCAGTAGCATCAACTCAACTGCTGCTG---AATGGCAGTCTAGCAGAAGGAA---AGGTAATGATTAGATCTGAAAATATTACAGACAATGCCAAAAACATAATAGTACAGTTTAATAAACCTGTACCAATTAATTGTACCAGACCCA------ACAACAATACAAGAAAAAGTATAC----------GCTTTGGACCAGGACAGGCCTTCTATACAAAT---------------AATAACATAATAGGGGATATAAGACAAGCACATTGTAATATCAGCATAACAGA-ATGGAATGCCACTCTAAAAAAGGTAGTTGAACAATTAAGAGAACACT------------TCCCT------------AATAAAACAATAA---------T---CTTTAATAGC-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGT-TTT Ref.A2.CY.94.94CY017_41.AF286237 GGGTCATGCAAGAATGTTAGCTCAGTACAATGTACACATGGAATTAAACCAGTAGCATCAACTCAACTGCTGTTG---AATGGCAGTCTAGCAGAAGGAGGGAAAATAATGATTAGATCTGAAAATATTACAAACAATGCCAAAAACATAATAGTTCAGTTTACTAAGCCTGTACTAATTACTTGTATCAGACCCA------ACAACAATACAAGAAAAAGTATAC----------GCTTTGGACCAGGACAAGCCTTCTATACAAAT---------------G---AAATAATAGGGGACATAAGACAAGCACATTGTAATATCAACAAAACATT-ATGGAATGACACTTTACAAAAGGTAGCTGAACAATTAAGAGAGAAAT------------TCCCT------------AAGAAAACCATAA---------T---CTTTACTAAC-----------TCCTCAGGAGGGGACCCAGAAATTACAACACTTAGT-TTT Ref.B.FR.83.HXB2-LAI-IIIB-BRU.K03455 GGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACA------ATACAAGAAAAAGAATCCGTATC---C-AGAGAGGACCAGGGAGAGCATTTGTTACAATA---------------G---GAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAA-ATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAAT------------TTGGAA-AT---A-----ATAAAACAATAA---------T---CTTTAAGCAA-----------TCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGT-TTT Ref.B.US.83.RF.M17451 GGACCATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTGTCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAGTAATTAGATCTGAAAATTTCACGGACAATGTTAAAACCATAATAGTACAGCTGAATGCATCTGTACAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGTATAA----------CTAAGGGACCAGGGAGAGTAATTTATGCAACA---------------GGACAAATAATAGGAGATATAAGAAAAGCACATTGTAACCTTAGTAGAGCACA-ATGGAATAACACTTTAAAACAGGTAGTTACAAAATTAAGAGAACAAT------------TTGAC------------AATAAAACAATAG---------T---CTTTACGTCA-----------TCCTCAGGAGGGGACCCAGAAATTGTACTTCACAGT-TTT Ref.B.US.86.JRFL.U63632 GGACCATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAGTAATTAGATCTGACAATTTCACGAACAATGCTAAAACCATAATAGTACAGCTGAAAGAATCTGTAGAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGTATAC----------ATATAGGACCAGGGAGAGCATTTTATACTACA---------------GGAGAAATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTAGAGCAAA-ATGGAATGACACTTTAAAACAGATAGTTATAAAATTAAGAGAACAAT------------TTGAG------------AATAAAACAATAG---------T---CTTTAATCAC-----------TCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGT-TTT Ref.B.US.90.WEAU160.U21135 GGACCCTGTAAAAATGTCAGCACAGTACAATGTACACACGGAATTAGACCAGTAGTGTCAACCCAATTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---ACATAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAAACATAATAGTACAGCTGAATGTATCCATAGAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAAAATAA----------CTTTAGGACCAGGGAGAGTACTTTATACAACA---------------GGAGAAATAATAGGAGATATAAGACGAGCACATTGTAACCTTAGTAGAACAAG-TTGGAATAACACTTTAAAACAGATAGTTGAAAAATTAAGAG------AAATAAAACAATTTAAG------------AATAAAACAATAG---------T---TTTTAAACAA-----------TCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGT-TTT Ref.C.BR.92.BR025-d.U52953 GGACCATGCAATAATGTCAGCACAATACAGTGTACACATGGAACTAAGCCAGTAGTGTCAACTCAACTACTGTTA---AATGGTAGTCTAGCAGAAGAAG---AGATAATAATTAGATCTAAAAATCTAACAGACAATGTCAAAACAATAATAGTACATCTTAACGAATCTGTAGAGATTAATTGTACGAGACCCA------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAGCATTCTATGCAACA---------------GGAGAAATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTAGAACAGC-ATGGAACAAAACTTTACAAGAGGTAGGTAAAAAATTAGCAGAGCACT------------TCCCT------------AATAAAGCAATAA---------A---ATTTGCAAAG-----------CACTCAGGAGGAGACCTAGAAATTACAACACATAGC-TTT Ref.C.BW.96.96BW0502.AF110967 GGACCATGCAATAATGTCAGCTCAGTACAATGTGCACATGGAATTAAGCCAGTGGTATCAACTCAGCTACTGTTA---AATGGTAGCGTAGCAAAAGGAG---AGATAATAATTAGATCTGAAAATCTGACAAACAATGCCAAAATAATAATAGTACAACTTAATAAACCTGTAAAAATTGTGTGTGTAAGGCCTA------ACAATAATACAAGAAAAAGTGTAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGAAATAATAGGAGACATAAGACAAGCATATTGTATCATTAATAAAACTGA-ATGGAATAGCACTTTACAAGGGGTAAGTAAAAAATTAGAAGAACACT------------TCTCT------------AAAAAAGCAATAA---------A---ATGTGAACCG-----------TCATCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.C.ET.86.ETH2220.U46016 GGACCATGCCATAATGTCAGCACAGTACAATGCACACATGGAATTAAACCAGTGGTATCAACTCAACTATTGTTA---AATGGTAGTATAGCAGAAGGTG---AGACAATAATTAGATTTGAAAATCTGACAAACAATGCCAAAATAATAATAGTACAGCTTAATGAATCTGTAGAAATTACTTGTACGAGACCCA------GCAATAATACAAGAGAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTGAAGAAAA-ATGGAATAAAACTCTACAAAAGGTAAAGGAAAAATTACAAAAGCACT------------TCCCT------------AATAAAACAATAG---------A---ATTTAAGCCA-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.C.IN.95.95IN21068.AF067155 GGACCATGCCATAATGTCAGCACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAGGAG---GGATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAACCTGTAGAAATTATGTGTACAAGACCCG------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTGAAGATAA-GTGGAATGAAACTTTACAAAATGTAAGTAAAAAGTTAGCAGAACACT------------TCCCT------------AATAAAACAATAA---------T---ATTTAATTCA-----------TCATCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.D.CD.83.ELI.K03454 GGCCCATGCACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTGGTGTCAACTCAACTGCTGTTG---AATGGCAGTCTAGCAGAAGAAG---AGGTCATAATTAGATCCGAAAATCTCACAAACAATGCTAAAAACATAATAGCACATCTTAATGAATCTGTAAAAATTACCTGTGCAAGGCCCT------ATCAAAATACAAGACAAAGAACAC----------CTATAGGACTAGGGCAATCACTCTATACTACA---------------A---GATCAAGATCAATAATAGGACAAGCACATTGTAATATTAGTAGAGCACA-ATGGAGTAAAACTTTACAACAAGTAGCTAGAAAATTAGGAACCCTTC------------TTAAC------------AAAACAATAAT------------AAAGTTTAAACCA-----------TCCTCAGGAGGGGACCCAGAAATTACAACACACAGT-TTT Ref.D.CD.83.NDK.M27323 GGCCCATGCTCAAATGTCAGCACAGTACAATGTACACATGGAATTAGACCAGTGGTGTCAACTCAACTGCTGTTG---AATGGCAGTCTAGCAGAAGAAG---AGATCATAATTAGATCTGAAAATCTCACAAACAATGTTAAAACCATAATAGTACAGCTTAATGCATCTATAGTAATTAATTGTACAAGGCCCT------ACAAATATACAAGGCAAAGGACAT----------CGATAGGACTAAGGCAATCACTCTATACAATAACAGGAAAAAAGAAG------AAAACAGGATACATAGGACAAGCACATTGTAAAATTAGCAGAGCAGA-ATGGAATAAAGCTTTACAACAGGTAGCTACAAAACTAGGAAACCTTC------------TTAAC------------AAAACAACAATAA---------C---TTTTAAGCCA-----------TCCTCAGGAGGGGACCCAGAAATTACATCACACATG-CTT Ref.D.CD.84.84ZR085.U88822 GGCCCATGCAAAAATGTCAGCTCAGTACAATGTACACATGGAATTAGGCCAGTGGTGTCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGATCGTAATAAGATCTGAAAATCTCACAAACAATGCTAAAATCATAATAGTACATCTTAATCAATCTGTAGAAATTAATTGTACAAGGCCCT------ACAAAAAGGAAAGACAAAGGACAC----------CTATAGGACAAGGGCAAGCGCTCTATACAACA---------------AGGTATACAACAAGGATAATAGGACAAGCATATTGTAATATTAGTGGAGTAAA-ATGGAATAACACCTTACGACAGGTAGCTAGAAAATTAGGAAACCTTT------------TGAAC------------CAAACAAAAATAA---------T---TTTTAAACCA-----------TCCTCAGGAGGGGATCCAGAAATTACAACACACAGT-TTT Ref.D.UG.94.94UG114.U88824 GGTCCATGCAAAAATGTCAGCACAGTACAGTGTACACATGGGATTAAGCCAGTAGTGTCAACTCAACTGTTGTTG---AATGGCAGTCTAGCAGAAGAAG---AAATAATAATTAGATCTGAAAATCTCACAAACAATGCTAAAATCATAATAGTACAGCTTAATGAGTCTGTACCAATTAATTGCATAAGGCCCT------ATAACAATACAAGACAAAGTACAC----------GTATAGGACCAGGGCAAGCACTCTTTACAACA---------------A---AAGTAATAGGAGATATAAGACAAGCACATTGTAACATTAGTGGAGCAGG-ATGGAATAAAACTTTACAACAGGTAGCTGAAAAATTAGGAAACCTTC------------TTAAC------------CAGACAACAATAA---------T---TTTTAAACCA-----------TCCTCGGGAGGGGACCCAGAAATTACAACACACAGC-TTT Ref.F1.BE.93.VI850.AF077336 GGGCCATGCAAGAATGTCAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAATTGTTGTTA---AATGGCAGCCTAGCAGAAGAAG---GTATAGTAATCAGATCTCAAAATATCTCAAATAATGCAAAAACCATAATAGTACACCTTAATGAATCTGTACAGATTAATTGTACAAGACCCA------ACAACAATACAAGGAAAGGTATAC----------ATTTAGGACCAGGACAAACATTCTATGCAACA---------------GGAGCAATAATAGGAGACATAAGAAAGGCACATTGTAACATTAGTGGAACACA-ATGGAATAACACTCTGGAGTATGTAAAGGCAGAATTAAAGTCGCATT------------TCCCTA-AT---A-----ATACAGCAATAA---------A---ATTTAACCAA-----------TCCTCAGGAGGGGACCTAGAAATTACAATGCATAGT-TTT Ref.F1.BR.93.93BR020_1.AF005494 GGGTCATGCAAGAATGTCAGTACAGTACAATGTACACATGGAATTAAACCAGTGGTATCCACTCAATTGTTGTTA---AATGGCAGCCTAGCAGAAGGAG---AGATAGTAATCAGATCTCAAAATATCTCAGATAATGCAAAAACCATAATAGTGCACCTTAATGAATCTGTACAGATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGAATAT----------CTTTAGGACCAGGACGAGTATTTTATACAACA---------------GGAGAAATAATAGGAGACATCAGAAAGGCACATTGTAACGTTAGTGGAACACA-ATGGAGGAACACGTTAGCAAAGGTAAAGGCAAAGTTAGGGTCTTATT------------TCCCT------------AATGCAACAATAA---------A---ATTTAACTCA-----------TCCTCAGGAGGGGACCTAGAAATTACAAGGCATAAT-TTT Ref.F1.FI.93.FIN9363.AF075703 GGGCCATGTAGGAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTGGTATCAACTCAATTGTTGTTA---AATGGCAGCCTATCAGAAGGAG---GTATAATAATCAGATCTCAAAATCTCTCAGATAATGCAAAAACTATAATAGTACACCTTAATGAATCTGTACAGATCAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGTATAC----------GTATAGGACCAGGACAATCATTTTATGCAACA---------------GGAGAAATAATAGGAGACATAAGAAAGGCACATTGTAACATTAGTGGAGAACA-ATGGAATAAAACTTTAGACCGAGTAAAGGCAGAGTTAAAGCTTCATT------------TTAAT-A--------------AAACAATAC---------A---ATTTAACTCA-----------TCCTCAGGAGGGGACCTAGAAATTACAATGCATAGT-TTT Ref.F1.FR.96.MP411.AJ249238 GGGCCATGCAAGAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTGGTATCAACTCAATTGCTGTTA---AATGGCAGCCTGGCAGAAGAAG---ATATAATAATCAGATCTCAAAATATCTCAGATAATGCAAAAACCATAATAGTACACCTTAATGAAAGTGTACAGATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGTATAC----------ATTTAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGATATAATAGGAGATATAAAAAAGGCATATTGTGAAATTAATGGAACACA-ATGGAGTAAAACTAAAACACAGGTACAAGAAAAGTTACGGGCTCTTT------------TTAAT-A--------------AAACAATAA---------A---ATTTAACCAA-----------TCCTCAGGAGGGGACCTAGAAATTACAATGCATAGT-TTT Ref.F2.CM.95.MP255.AJ249236 GGGCCATGCGAAAAGGTCAGCACAGTACAATGTACACATGGAATTAGACCAGTGGTATCAACTCAACTACTGCTA---AATGGCAGCCTAGCACAAGAAG---ATATAATAATTAGATCTAAAAATATCACAGATAATACAAAAAACATAATAGTACAGTTTAATAGATCTGTAATAATTGATTGTAGAAGACCCA------ACAACAATACAAGAAAAGGGATAC----------GTATAGGACCAGGACAAACATTCTTTGCAACA---------------GGTGAAATAATAGGGGATATAAGAAAGGCATATTGTAACATTAATAGAACACT-GTGGAATGAAACTTTAAAAAATGTAAGTGGAGAGTTCAAAAAACACT------------TCAAC-T--------------TCTCAGTAG---------C---CTTTAATTCA-----------TCCTCAGGAGGGGATGTAGAAATTACAACGCATAGT-TTT Ref.F2.CM.95.MP257.AJ249237 GGATTATGCAGGAATGTTAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAACTACTGTTA---AATGGCAGCCTAGCAGAAGAAA---AGATGATAATTAGATCTGAAAATATCTCAGATAATACAAAAACCATAATAGTACAGTTTAAAAATCCTGTAAAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAGAAGTATAC----------ATATAGGACCAGGACGAGCATTCTATGCAACA---------------GGTGAGATAATAGGAGATACAAGAAAGGCACATTGTAACATTAGTGAAAAACA-GTGGTATGACACTTTAATAAAGATAGCTACAGAGTTCAAAGACCAAT------------ATAAT-A--------------AAACAGTAG---------G---GTTTCAACCA-----------TCAGCAGGAGGGGATCTAGAAATTACAACACATAGT-TTT Ref.G.BE.96.DRCBL.AF084936 GGAACATGTAACAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTAGTATCAACTCAACTACTGCTG---AATGGCAGTTTAGCAGAAAAAG---ATATCATAATTAGTTCTGAAAATATCTCAGACAATGCCAAAGTCATAATAGTGCACCTTAATAGGTCTGTAGAAATTAATTGTACCAGACCCA------ACAACAATACAAGAAGAAGTGTAG----------CAATTGGACCAGGACAAGCATTCTATACAACA---------------GGAGAAGTAATAGGAGACATAAGAAAGGCACATTGTAATGTTAGTTGGACAAA-ATGGAATGAGACGCTAAGGGATGTCCAGGCAAAACTACAGGAATACT------------TTATT------------AATAAGAGCATAG---------A---ATTTAACTCA-----------TCTTCAGGAGGGGACCTAGAAATTACAACACATAGT-TTC Ref.G.KE.93.HH8793_12_1.AF061641 GGACCATGTCAAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTGCTG---AATGGCAGTTTAGCAGAAGGAG---AAATAATAATTAAATCAGAAAACATCACAGACAATACCAAAGTCATAATAGTGCAGCTTAATGAAACTGTAGAAATTACGTGTGTCAGACCCA------ACAACAATACAAGAAAAAGTATAC----------ACCTCGGGCCAGGACAAGCGCTCTATGCAACA---------------GGGGACATAATAGGAAATATAAGACAGGCACATTGTGATGTTAGTGGAAGAAA-TTGGAGTAACATGATAGAGAAGGTAAAAGCACAACTAAGAAAAATCT------------TTAAC-A--------------AGACCATAA---------C---CTTTGACTCA-----------TCTGCAGGAGGGGACCTAGAAATTACAACACATAGT-TTT Ref.G.NG.92.92NG083.U88826 GGACCATGTAAAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTGCTG---AATGGCAGTTTAGCAGAAGAAG---ATATAAGAATTAGATCTGAAAATTTCACAGACAATACCAAAGTCATAATAGTGCAGCTTAATAATAGTATAGAAATTAATTGTATCAGACCCA------ATAACAATACAAGAAAAAGTATAC----------CAATCGGACCAGGACAAGCGTTCTATGCAACA---------------GGTGATATAATAGGAGACATAAGACAAGCACATTGTAATGTTAGTAGAATAAA-ATGGAGGGAGATGTTAAAGAATGTCACAGCACAGCTAAGGAAAATCT------------ATAAT------------AATAAGAACATAA---------C---CTTTAACTCA-----------TCTGCAGGAGGGGACCTAGAAATTACAACACATAGT-TTC Ref.G.SE.93.SE6165.AF061642 GGACCATGTAAAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTACTG---AATGGCAGTTTAGCAGAAGGAA---AAATAAAAGTTAGATCTGAAAATTTCACAGACAATACCAAAGTCATAATAGTACAGCTTAATAAAACTGTAGAAATTAATTGTACCAGACCCA------ACAACAATACAATGAAAAGGATAAGAATG---G-GAATTGGACCAGGACAAACGTTCTATGCAACA---------------GGTGCCATAATAGGAGACATAAGACAAGCACATTGTAATGTTACTAAAAGAAA-ATGGAAAGAGGCCTTACAGAATGTCGCTGCAGAACTAGGGAAAATCT------------TTAAT----AAGAGCAG--CGAGAACATAA---------C---CTTTAACTCA-----------TCTGCAGGAGGGGACCTAGAAATTACAACACATAGT-TTC Ref.H.BE.93.VI991.AF190127 GGACCATGCACAAATGTCAGCACAGTACAATGCACACATGGAATTAGGCCAGTGGTATCAACTCAACTGTTGTTA---AATGGAAGCCTAGCAGAAGTGGAGGAGGTAATAATTAGATCTAAAAATATTACAGATAATACCAAAAACATAATAGTACAGTTAAATGAACCTGTACAAATTAACTGTACCAGAACAG------GCAATAATACGAGAAAAAGTATAC----------GTATAGGGCCAGGACAAGCATTCTATGCAACA---------------GGTGACATCATAGGAGATATAAGACGAGCATATTGTAATATTAGTGGAAAACA-ATGGAATGAGACCTTACACAAGGTAATCACCAAATTAGGAAGCTACT------------TTGAC------------AATAAAACAATAA---------T---TTTACAACCA-----------CCCGCAGGAGGGGATATAGAGATTATAACACATAGT-TTT Ref.H.BE.93.VI997.AF190128 GGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTGCTATTA---AATGGAAGCCTAGCAGAAGGAC---AGGTCATAATTAGATCTAAAAATATCTCAGACAATACCAAAAACATAATAGTACAGCTTGATAGTCCTATAGAAATTACCTGTACCAGACCTA------ACAATAATACAAGAAAAGGTATAC----------ATTTCGGGCCAGGGCAAGCATTCTATGCAACA---------------GGTGATATCATAGGAAACATAAGACAAGCACATTGTAATGTTAGTGAAGAGAA-ATGGAATAAGACTTTACAACAGATAGCTACACAATTAAGTAAATACT------------TTGTC------------AATAGAACATTAA---------T---TTTTAAACCA-----------CACTCAGGAGGGGACCTGGAAGTTACAACACATAGT-TTT Ref.H.CF.90.056.AF005496 GGATTATGTACAAATGTCAGTACAGTACAATGTACACATGGAATTAGACCAGTGGTATCAACTCAACTGCTATTA---AATGGAAGCCTAGCAGAAGAAC---AGATCATAATTAGAACTAAAAATATCTCAGACAATACCAAAAACATAATAGTACAGCTTAAGACACCAGTAAACATTACATGTACCAGGCCTA------ACAATAATACGAGAACAAGTATAC----------ATTTAGGGCCAGGACGAGCATTCTATGCAACA---------------GGTGACATCATAGGAGATATAAGACAAGCACATTGTAATATTAGTAGAACAGA-CTGGAATAAGACTTTACACCAGGTAGTTACACAATTAGGAATACACT------------TGAAC------------AATAGAACAATAA---------G---CTTTAAGCCA-----------AACTCAGGAGGGGACATGGAAGTTAGAACACATAGT-TTT Ref.J.SE.93.SE7887.AF082394 GGATCATGCAAAAATGTCAGTACAGTACAATGTACACACGGAATTAAGCCAGTGGTATCAACTCAACTACTGCTA---AATGGCAGTATAGCAGAAGGAG---ACATAATAATTAGATCTGAAAACATCTCAGACAATGCCAAAAACATAATAGTACAACTTAATAAAACTGTAGAAATTGTGTGTTACAGACCTA------ATAACAATACAAGGAAAGGTATAC----------ACATGGGACCAGGACAAGTGCTCTACGCAACA---------------GGAGAAATAATAGGAAATATAAGAGAAACACATTGTAACATTAGTGAAAGAGA-TTGGAGTAACACTTTACGTAGAGTAGCTACAAAACTAAGAGAACACT------------TTAAT-A--------------AAACAATAA---------A---CTTTACATCA-----------CCCTCAGGAGGGGATATAGAAATTGTGACACATAGT-TTT Ref.J.SE.94.SE7022.AF082395 GGACCATGCAAAAATGTCAGTACAGTACAATGTACACACGGAATTAAGCCAGTGGTATCAACTCAACTACTGCTA---AATGGCAGTGTAGCAGAAGGAG---ACATAATAATTAGATCTGAAAATATCTCAGACAATGCTAAAAACATAATAGTACAACTTAATGACACTGTAGAAATTGTGTGTACCAGACCTA------ATAACAATACAAGAAAAGGTATAC----------ACATGGGACCAGGACAAGTGCTCTACGCAACA---------------GGGGAAATAATAGGAGATATAAGGAAAGCATATTGTAACATTAGTAGAAAAGA-TTGGAATAACACTTTACGTAGAGTAGCTAAAAAACTAAGAGAACACT------------TTAAT-A--------------AAACAATAG---------A---CTTTACATCA-----------CCCTCAGGAGGGGACATAGAAATTACAACACATAGT-TTT Ref.K.CD.97.EQTB11C.AJ249235 GGGCCATGCACAAATGTCAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAATTGCTATTA---AATGGCAGCCTAGCAGAAGAAG---AGATAATTATTAGGTCTGAAGATATTACAAAGAATACAAAAAACATAATAGTACAGCTTAATGAAGCTGTAGAAATTAATTGTACAAGGCCAA------GCAACAATACAAGAAAAAGTATAC----------ATATAGGACCAGGAAGAGCATTCTATGCAACA---------------GGTGACATAATAGGAGATATAAGGCAGGCGCATTGTAACATTAGCGGAGGACA-GTGGAATAAAACTGTAAACCAAGTAAAGAAAGAATTAGGAAAACACT------------TTAAC-A--------------AAACAATAA---------TA---TTTCAACCA-----------TCCTCAGGAGGGGACCCACAAGTCACAAGGCACATT-TTT Ref.K.CM.96.MP535.AJ249239 GGACCATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAACTGCTGTTA---AATGGCAGCCTAGCAGAAGAAG---AGATAATAATTAGGTCTGAAAATATTACAGATAATACAAAAAACATAATAGTACAGCTTAATGAAACTGTACAAATTAATTGTACAAGGCCAA------ACAACAATACAAGAAAAAGTATAC----------ATATGGGACCAGGAAAAGCATTCTATACAACA---------------GGTGATATAATAGGAGATATAAGACAGGCACATTGCAACATTAGTGGAGAAAA-ATGGAACATGACTTTAAGCAGAGTAAAGGAAAAGCTAAAAGAACATT------------TTAAG------------AATGGAACAATA------------ACATTTAAACCA-CCA-------AACCCAGGAGGAGACCCAGAAATTCTAACGCACATG-TTT Ref.U.CD.83.83CD003.AF286236 GGACCATGCAAAAATGTCAGCACAGTACAATGCACACATGGAATTAGGCCAGTGGTGTCAACTCAATTACTATTA---AATGGCAGTTTATCAGAAGAAG---AGGTAATAATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAGCTTAATGAGACTGTAAAAATTAATTGTACCAGACCCGGATCCGACAAGAAGATAAGACAAAGTATA---------C-GTATAGGACCAGGAAAAGTATTCTATGCAAAA---------------GGTGGAATAACAG---------GACAAGCACATTGTAACATTACAGATGGGGA-ATGGAGGAATACTTTACAACAGGTAGCTATCGCATTAAGAAGACAAT------------TTAAT------------AATAAATCAATAA---------T---ATTTAACTCA-----------TCCTCAGGAGGGGACATAGAGATTACAACACATACT-TTT Ref.U.CD.90.90CD121E12.AF457101 GGACCATGCAGAAATGTCAGCACAGTACAATGCACACATGGAATTAGGCCAGTGGTGTCAACTCAATTACTATTA---AATGGCAGTTTATCAGAAAAAG---AGGTAATAATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAGTTTAATGAGACTGTAAAAATTAATTGTAGCAGACCCA------ATAATAATACAAGGCAAGGTATAC----------ATATAGGACCAGGACGAGTATTCTATGCAACA---------------AGTAACATAATAGGAGATATAAGACAAGCACATTGTAACCTTACAAAATGGCA-ATGGAAGAGAGCTTTACAACAGGTAGCTGATGCATTAAGAAGACACT------------TTAAT-AAA---A-----------CAATAG---------T---ATTTAACTCA-----------TCCTCAGGAGGGGACTTAGAAATTACAACACATAGC-TTT Ref.U.GR.99.GR303.AY046058 GGGCCATGCAAAAATGTCAGTTCAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAAAAGGAG---AGGTAATAATTAGATCTGAAAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTTAATGAGTCTGTATCAATTAATTGTACCAGACCTA------GCAACAATACAAGAAAAAGTATAC----------ATATAGGACCAGGACAAGCGTTCTTTGCAACA---------------G---ACATAATAGGAGATATAAGACAAGCACATTGTAATGTTTCAGGAGCAAC-ATGGAACAACACTCTAAAAAGGGTAGTTGCAAAACTAAGAGAACAGT------------TTGGG------------AACAAAACAATAA---------T---CTTTAATTCA-----------TCTACAGGAGGGGATTTAGAAATTACAACACATAGT-TTA Ref.01_AE.CF.90.90CF11697.AF197340 GGGCCATGCAAAAATGTCAGCTCAGTACAATGCACACATGGAATTAAGCCAGTGGTGTCAACTCAATTGTTGTTA---AATGGCAGTCTAGCAGAAGAAG---ACATAATAATCAGATCTGAAAATCTCACAAACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCT------TCAAAAATATGAGAACAAGTGCAC----------GTATAGGACCAGGACAAGTATTCTATAAAACA---------------GGAAGCATAACAGGAGACATAAGAAAAGCATATTGTGAGATTAATGGAACAAA-ATGGAATGAAACTTTAAAACAGGTAACAAAAAAATTAAGAGAGCACT------------TTAAG------------AATAAGACAATAA---------T---CTTTCAACCA-----------TCCTCAGGAGGAGATCCAGAAATTACAATGCATCAT-TTT Ref.01_AE.CF.90.90CF402.U51188 GGGCCATGCAAAAATGTCAGCTCAGTACAATGCACACATGGAATTAAGCCAGTGGTATCAACTCAATTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGATAATAATCAGATCTGAAGATCTCACAGACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTATAGAAATCAATTGTACCAGACCCT------TCAAGAAAGTAAGAATAAGTGCAA----------GGATAGGACCAGGACGAGTATTCCATACAACA---------------GGAAACATAAATGGTGATATAAGAAAAGCATATTGTGAAATTAATAAAACAAA-ATGGAAAGAAACTTTAAAACAGGTAACAAGAAAATTAAGAGAGCACC------------TTAATG-GG---A-----CAATGACAATAA---------G---CTTTCGACCA-----------TCCTCAGGAGGAGATCCAGAAATCACAATGCATCAT-TTT Ref.01_AE.CF.90.90CF4071.AF197341 GGGCCATGTAAAAAGGTAAGCTCAGTACAATGCACACATGGAATTAAGCCAGTGGTATCAACTCAATTGCTGTTA---AACGGTAGTCTAGCAGAAGAAG---AAATAATAATTAGATCTGAAAATCTCACAAACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCTT------TCAAAAAGATGAGAACAAGTGTAA----------GAATAGGACCAGGGCGAGTATTCTATAAAACA---------------GGATCCATAACAGGAGATATAAGAAAAGCATATTGTGAGATTAATGGAACAAA-ATGGAATGAAACTTTACAACAGATAATTAGAAAATTAGAAGAGCACT------------TTAAT------------AATAAGACAATA------------CAATTTAAACCA-CCA-------TACTCAGGAGGAGATCTAGAAATTACAATGCACCAT-TTT Ref.01_AE.TH.90.CM240.U54771 GGGCCATGTAAAAATGTCAGCTCAGTACAATGCACACATGGAATTAAGCCAGTGGTATCAACTCAATTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGATAATAATCAGATCTGAAGATCTCACAAACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCT------CCAACAATACAAGAACAAGTATAA----------CTATAGGACCAGGACGAGTATTCTATAGAACA---------------GGAGATATAATAGGAAATATAAGAAAAGCATATTGTGAGATTAATGGAACAAA-ATGGAATAAAGTTTTAAAACAGGTAACTGAAAAATTAAAAGAGCACT------------TTAAT-A--------------AGACAATAA---------T---CTTTCAACCA-----------CCCTCAGGAGGAGATCTAGAAATTACAATGCATCAT-TTT Ref.02_AG.CM.97.97CM_MP807.AJ286133 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAACCAGTAGTATCAACCCAACTGCTACTA---AATGGCAGTCTAGCAGAAGAAA---AGGTAAGGATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAGTTGGTTAAGCCTGTAAAAATTAATTGTACCAGACCTA------ACAACAATACAAGGAAAGGTGTAC----------GTATAGGACCAGGACAAACATTCTATGCAACA---------------GGGGAAATAATAGGGGATATAAGACAAGCATATTGTAATGTCAGTAGAACAAA-ATGGAATAACACTTTACAACAGGTAGTTACACAATTAAGGGAGTACT------------TTGGGA-AA---A-----ACAAAACAATAA---------A---ATTTGCTAAC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT Ref.02_AG.FR.91.DJ264.AF063224 GGGCCATGCAAGAATGTTAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAGTGATTAGATCTGAAAATATCACAAACAATGCCAAAAACATAATAGTGCAGTTGGTGACGCCTGTAAGAATCAATTGTACTAGACCTA------ACAACAATACAAGAAAGAGTGTGC----------GTATAGGACCAGGGCAAACATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGAAAAGCACATTGTAATGTCAGTAGATCAAA-ATGGAATAACACTTTACAACAGGTGGCTATACAATTAAGGAAGCACT------------TTAAC-A--------------CAACAATAA---------T---CTTTGCTAAC-----------CCCTCAGGAGGGGATATAGAAATTACAACACATAGT-TTT Ref.02_AG.NG.-.IBNG.L39106 GGGCCATGCAAAAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAG---AAGTAGTGATCAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAGTTGGCTAATCCTGTAAAAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAGGTGTAC----------ATATAGGACCAGGGCAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGACAAGCACATTGTAATGTCAGTAAAACAGA-ATGGAATAAAACTTTACATCAGGTAGTTACACAATTAAAGACGTACT------------TTAAG------------AACACCACAATAA---------T---CTTTGCTAAC-----------CCCTTAGGAGGGGATGTAGAAATTACAACACATAGT-TTT Ref.02_AG.SE.94.SE7812.AF107770 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGTTATTA---AATGGCAGCCTAGCAGAAGAAG---AGATAGTGATTAGATCTGAAAATTTTACAAACAATGCCAAAATCATAATAGTACAGTTGCATGAATCTGTAAAAATTAATTGTACCAGACCTG------GCAACAATACAAGAAAAAGTGTAC----------GTATAGGACCAGGGCAAACATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGACAAGCACATTGTAATGTCAGCTGGCAACA-ATGGAACAAAACTTTACACGATGTGGCTACAAAATTAAGGGAGTATT------------TTAAT------------AATACCACAATAA---------T---CTTTGATGAA-----------CCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT Ref.03_AB.RU.97.KAL153_2.AF193276 GGGCCATGTACAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGTAGTCTAGCAGAAGAAG---AGGTAGTAATTAGATCTGTCAATTTCACGGACAATACTAAAACCATAATAGTACAGCTGAAAGAACCTGTGGAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAGGTATTC----------ATATAGGACCAGGGAGAGCATTTTATGCAACA---------------GGAGACATAACAGGAGATATAAGACAAGCACATTGTAACATTAGTATAACAAA-ATGGAATAACACATTAAAACAGATAGTTATCAAATTAAGAAAACAAT------------TTGGG------------AATAAAACAATAG---------T---CTTTAATCAA-----------TCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGT-TTT Ref.03_AB.RU.98.RU98001.AF193277 GGGCCATGTACAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTAGTGTCAACTCAACTGCTGTTA---AATGGTAGCCTAGCAGAAGAAG---AGGTAGTAATTAGATCTGTCAATTTCACGGACAATACTAAAACCATAATAGTACAGCTGAAAGAACCTGTAGAAATTAATTGTACGAGACCCA------ACAACAATACAAGAAAAGGTATTC----------ATATAGGACCAGGGAGAGCATTTTATGCAACA---------------GGAGACATAATAGGAGATATAAGACAAGCATATTGTAACATTAGTAGAACAAA-ATGGAATAACACATTAGAACAGATAGTTAGCAAATTAAGAAAACAAT------------TTAGG------------AATAAAACAATAG---------T---CTTTAATCAA-----------TCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGT-TTT Ref.04_CPX.CY.94.CY032.AF049337 GGGCCATGCACAAATGTCAGCTCGGTACGATGCACTCATGGAATTAAGCCAGTGGTATCAACTCAATTGCTGTTA---AATGGAAGCTTAGCAACGGAAG---AGGTAGTAATTAGATCTAAAAATATCACAGACAATACCAAAAATATAATAGTACAGCTTGCAAAGGCTGTAAAAATTAATTGTACCAGACCTG------GCAACAATACAAGAAAAAGTGTAC----------ATATAGGGCCAGGACTAACATGGTATGCAACA---------------GGTGAAATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTGGAAATGA-TTGGAATGACACCTTAAAAGTGATAAGTGAAGAATTGAAAAGACTCT------------TCCCT------------AATAAAACAATAA---------A---ATTTGCTCCA-----------CCCGTAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.04_CPX.GR.91.97PVCH.AF119820 GGGTCATGCACAAATGTCAGCCCGGTACAATGCACTCATGGAATTAAGCCAGTGGTATCAACTCAATTGCTGTTA---AATGGAAGCTTAGCAACAGGAG---GGGTAGTAATTAGATCTAAAAATTTCACAGACAATCCCAAAAATATAATAGTACAGCTTGACAAGGCTGTAAAAATTAATTGTACCGGCCTTA------ACAACAATACAGGAGGAAGTGAACGTATC---G-GTATAGGGCCAGGACACACATGGTATGCAACA---------------GGTAACATAGTAGGAGATATAAGACAAGCACACTGTAACATTAGTGGAAGTGA-TTGGAATGAAGCTTTACAGAAGGTAGTTGTAAAATTAAGAGAACACT------------TCCCT------------AATAAAACAATAA---------T---ATTTAATCAA-----------TCCTCAGGAGGGGACCTAGAGATTACAACACATAGC-TTT Ref.04_CPX.GR.97.97PVMY.AF119819 GGTCCATGCAAAAATGTCAGCTCGGTGCAATGCACTCATGGAATTAAGCCAGTAGTATCAACTCAATTGCTGTTA---AATGGAAGCTTATCAACAGAAG---GGGTAGTACTTAGATCTAAAAACTTCACAGACAATACCAAAAATATAATAGTACAGCTTGCAGAGGCTGTAAAAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAGGTGTAC----------ATATAGGACCAGGAAAAACATGGTTTGCAACA---------------GGGGAAGTAATAGGAGACATAAGAAAAGCACATTGTAACATTAGTGAAAAAGA-TTGGAATACAACTTTACAAAAGATAGTTGATGAATTAAGAAAACACT------------TCCCT------------AATAAAAACATAA---------C---ATTTGCTCCA-----------TCAGCAGGAGGGGACGTAGAAATTACAACACATAGT-TTT Ref.05_DF.BE.-.VI1310.AF193253 GGACCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATTAAGCCAGTGGTATCAACTCAGTTGCTGTTA---AATGGCAGCCTAGCAAAAGAAG---GTATAATAATCAGATCTCAAAATATCTCAGATAATGCAAAAAACATAATAGTACACCTTAATGAATCTGTACATATTAATTGTACAAGGCCCA------ACAACAATACAAGAAAAAGTATAC----------ATTTAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGAGACATAAGAAAGGCACATTGTAACGTTAGTAGGGAACA-ATGGAATAAAACCTTAATCCAGGTAGCGAAAGAGTTACAGTCTCACT------------TCCCT------------AATAAAACAATAA---------A---ATTTAACTCA-----------TCCTCAGGAGGGGACCTAGAAATTACAATGCATAGT-TTT Ref.05_DF.BE.93.VI961.AF076998 GGGCCATGCAAGAATGTCAGCACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAATTGCTATTA---AATGGCAGTCTAGCAGAAGAAA---GTATAATAATCAGATCTCAAAATATCTTAGATAATACAAAAACCATAATAGTACACCTTAATGAATCTGTACAGATTAATTGTACAAGGCCCA------ACAACAATACAAGAAAAAGTATAC----------CTTTAGGACCAGGACAAGCATTCTATACAACA---------------GGGGACATAATAGGAGACATAAGAAAGGCACATTGTAACGTTAGTGGAGCACA-ATGGAATAAAACTTTAGAACAGGTAAAGGAAGAGCTAAGGGCTC---ATATAAAGGACA----------TAGGC--AATAAAACAATAG---------T---ATTTAACTCA-----------TCCGCAGGAGGGGACCTAGAAATTACAAGCCATATT-TTT Ref.06_CPX.AU.96.BFP90.AF064699 GGACCATGTAAAAATGTCAGTACAGTACAATGTACACATGGGATTAAGCCAGTGGTATCAACTCAATTACTGCTG---AATGGCAGTTTAGCAGAAGGAA---ACATAACAATTAAAACTGAAAACATCACAGACAATACCAAAAATATAATAGTGCAGCTTAATCAGCCTGTAGAAATTAGGTGTACCAGACCCG------GTAACAATACAAGAAAAAGTATAT----------CCTTTGGACCAGGACAAGCGTTCATTGCAACA---------------GGTGACATAATAGGAGATATAAGACAAGCTCATTGTAATGTTAGTAGAGCAAA-TTGGACAGATATACTAGGAGAAGTGAAGGTAAAACTAGAAGAAGTTT------------TTAAT------------AACACACACATAA---------C---CTTTAAGTCA-----------TCTGCAGGAGGGGACCTAGAAATTACAACACATAGT-TTT Ref.06_CPX.ML.95.95ML127.AJ288982 GGACCATGTAAAAATGTTAGTACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAGTTACTGCTG---AATGGCAGTTTAGCAGAAGAAG---AAATAATAATTAAATCTAAAAACCTCACAGACAATACCAAAATCATAATAGTGCAGCTTAATAAATCTGTAGAAATTAGTTGTTCCAGACCCA------ATAACAATACAAGAAAAAGTATAC----------ACATTGGACCAGGGCAAGCGTTCTATGCAACA---------------GGTGAAATAATAGGAAATATAAGAAAAGCTCATTGTAATGTTAGTAGAAAAGC-TTGGAATAGTATGTTACAGAATGTGACTGCAAAACTAAAAGAACTCT------------TTAAT------------AATAAGAATATAA---------C---CTTCAATTCA-----------TCAGCAGGAGGGGACCTAGAAGTTACAACACATAGT-TTT Ref.06_CPX.ML.95.95ML84.AJ245481 GGACCATGTAAAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAGTTACTGCTG---AATGGCAGTTTAGCAGAAGATG---AAATAATAATTAAATCTGAAAACCACACAAACAATGCCAAGATCATAATAGTGCAGCTTAATAAAACTGTACAAATTAGGTGTACCAGACCCA------GTAACAATACAAGGAAAAGTATAC----------CCCTTGGACCAGGGCAAGCGTTCTATGCAACA---------------GGTGACATAATAGGAGATATAAGACAAGCTCATTGTAATGTTAGTAGAACAGC-ATGGAAGGAGACGTTACAGAATGTGACTGAAAAACTAAAACAACTCC------------TTAAT-A--------------CGAACATAA---------C---CTTTAATCCA-----------TCTGCAGGAGGGGACCTAGAAATTACAACACATAGT-TTT Ref.06_CPX.SN.97.97SE1078.AJ288981 GGAGCATGTAAAAATGTCAGTACAGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAATTACTACTG---AATGGCAGTTTAGCAGAAGAGG---AAATAATAATTAAAACTGAAAACCTCACAGACAATAGCAAGAACATAATAGTACAGCTTAATAAATCTATAGAAATTAAGTGTACCAGACCCA------ATAACAATACAAGAAAAAGTATAT----------CCTTTGCACCAGGGCAAGCGTTCTATGCAACA---------------GGTGACATAATAGGAGATATAAGACAAGCTCATTGTAATGTTAGTAGAACAGA-TTGGAATAATATGTTAAAGAATGTGACTACAAAACTAATAGAAGTCT------------TTAAA-A--------------AGAACATAA---------C---CTTTAATTCA-----------TCTGCAGGAGGGGATCTAGAAATTACAACACATAGT-TTT Ref.07_BC.CN.97.97CN001.AF286226 GGACCATGCCATAATGTTAGCACAGTACAATGTACACATGGGATTAAGCCAGTGGTATCAACTCAACTACTTGTT---AATGGTAGCCTAGCAGAAGGAG---AAATAATAATTAGGTCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCG------GCAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTGAAGATAA-ATGGAATGAAACTTTACAAAGGGTAAGTAAAAAATTAGCAGAACACT------------TCCAG------------AATAAAACAATAA---------A---ATTTGCATCA-----------TCCTCAGGAGGGGACCTAGAAGTTACAACACATAGC-TTT Ref.07_BC.CN.97.C54A.AX149647 GGACCATGCCATAATGTTAGCACAGTACAATGTACACATGGGATTAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAGGAG---AAATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCG------GCAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTGAAGATAA-ATGGAATGAAACTTTACAAAGGGTAAGTAAAAAATTAGCAGAACACT------------TCCAG------------AATAAAACAATAA---------A---ATTTGCATCA-----------TCCTCAGGAGGGGACCTAGAAGTTACAACACATAGC-TTT Ref.07_BC.CN.98.98CN009.AF286230 GGACCATGCCATAATGTTAGCACAGTACAATGTACACATGGGATTAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAGAAG---AAATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCG------GCAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGAAATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTGAAGATAA-ATGGAATAAAACTCTACAAGGGGTAAGTGAAAAATTAGCAGAACACT------------TCCAG------------AATAAAACAATAA---------A---ATTTGCATCA-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.08_BC.CN.97.97CNGX_6F.AY008715 GGACAATGCCATAATGTTAGCACGGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAAGAG---AGATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCA------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATCATAGGAGACATAAGACAAGCACATTGTAACATTAGTAAAGATGC-ATGGTATGAAACTTTACAGAGGGTAAGTAAAAAATTAGCAGAACACT------------TCCCT------------AATAAAACAATAA---------A---ATTCGCATCA-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.08_BC.CN.97.97CNGX_7F.AY008716 GGACAATGCCATAATGTTAGCACGGTACAATGTACACATGGAATCAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAAGAG---AGATAATAATTAAATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCA------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATCATAGGAGACATAAGACAAGCACATTGTAACATTAGTAAAGATGA-ATGGTATGAAACTTTACAGAGGGTAAGTAAAAAATTAGCAGAACACT------------TCCCT------------AATAAAACAATAA---------A---ATTTGCATCA-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.08_BC.CN.97.97CNGX_9F.AY008717 GGACAATGCCATAATGTTAGCACGGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAAGAG---AGATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCA------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATCATAGGAGACATAAGACAAGCACATTGTAACATTAGTAAAGATAA-ATGGTATGAAACTTTACAGGGGGTAAGTAAAAAATTAGCAGAACACT------------TCCCT------------AATAAAACAATAA---------A---ATTTGCATCA-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.08_BC.CN.98.98CN006.AF286229 GGACAATGCAATAATGTTAGCACGGTACAATGTACACATGGAATTAAGCCAGTGGTATCAACTCAACTACTGTTA---AATGGTAGCCTAGCAGAAGGAG---AGATAATAATTAGATCTGAAAATCTGACAAACAATGTCAAAACAATAATAGTACATCTTAATCAATCTGTAGAAATTGTATGTACAAGACCCA------ACAATAATACAAGAAAGAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATCATAGGAGACATAAGACAAGCACATTGTAACATTAGTAAAAATAA-ATGGAACGAAACTATACAGAGGGTAAGTGAAAAATTAGCAGAACACT------------TCCCT------------AATAAAACAATAA---------C---ATTTGCACCA-----------TCCTCAGGAGGGGACCTAGAAATTACAACACATAGC-TTT Ref.10_CD.TZ.96.96TZ_BF061.AF289548 GGACCATGCAAAAACATCAGTACAGTACAGTGTACACATGGGATTAAACCAGTAGTGTCAACTCAACTGTTATTG---AATGGCAGTCTAGCAGAAGAAG---AGATAATAATTAGATCTGAAAATCTCACAGATAATGCTAAAAATATAATAGTGCAGCTTAATGAGTCTGTAACAATTAATTGCGTGAGACCCA------ACAATAATACAAGAAGAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------G---ACATAATAGGAAACATAAGACAAGCATATTATAACATTAGTGGAACAGA-ATGGAATAAAACTTTACAACAAGTAGCTAAAAAATTAGGAGACCTTT------------TTAAC------------CGACCAACAATAA---------T---TTTTAAACCA-----------TCCTCAGGAGGGGACCCAGAAATTACAACACACACC-TTT Ref.10_CD.TZ.96.96TZ_BF071.AF289549 GGTCCATGCGACAATGTCAGTACAGTACAATGTATACATGGGATTAAGCCAGTAGTGTCAACTCAACTGTTATTG---AATGGCAGTCTAGCAGAAGAAG---AGATAATAATTAGATCTGAAAATATCACAAGTAGTCTTAAAACTATAATAGTACAGCTTAATGAGTCTGTAACAATTAATTGCACGAGACCCA------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAGACATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTGGAACAGA-ATGGAATAAAACTTTACAACAGGTAGCTAAAAAACTAAGAGACCTTC------------TTAAC------------AAAACAAAAATAA---------T---TTTTAAACCT-----------TCTTCGGGAGGGGACCCAGAAGTTACAACACACACC-TTT Ref.10_CD.TZ.96.96TZ_BF110.AF289550 GGACCCTGTAAAAACGTCAGTACAGTACAGTGCACACATGGGATTAGGCCAGTAGTGTCAACTCAGCTGTTATTG---AATGGCAGTCTAGCAGAAGAAG---AGATAATAATTAGATCTGAGAATCTCACAGATAATGCTAAAACTATAATAGTACATCTTAATGAGTCTGTAACAATTAATTGCACGAGACCCA------ACAATAATACAAGAAAAAGTATAA----------GGATAGGACCAGGACAAACATTCTATGCAACA---------------GGAAACATAATAGGCAATATAAGGCAAGCATATTGTGAAATTAATGGGACAGA-ATGGAATAAAACTTTACAACAGGTAGCTAACAAATTAGGAAAACTTC------------TTAAC-A-----------AAACAACAATAC------------ATTTTCGACCA-----------TCCTCGGGAGGAGACCCAGAGATTACAGAACATACC-TTT Ref.11_CPX.CM.97.MP818.AJ291718 GGACCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAGAAA---AGGTAAAGATTAGATCTGAAAACTTCACAAACAATGCTAAAACCATAATAGTACAGTTTAACAATACTGTAAGAATTAATTGTACCAGACCTG------GCAACAATACAAGAAAAAGTATAC----------ATTTAGGACCAGGACACGCTTTCTATGCCACA---------------GGTGCTATAATAGGGGATATAAGACAAGCACATTGTAAAGTCAGTAAAGCAGA-ATGGCTCAACACTTTACAACAGGTAGCTACACAATTACGAGGAAAGT------------TTAAC-A--------------AAACAATAA---------T---CTTTGATAAC-CCC-------TCCCCAGGAGGGGATATAGAAATTACATCACATAGC-TTT Ref.11_CPX.FR.99.MP1298.AJ291719 GAGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAATAGTATCAACTCAACTACTGATA---AATGGCAGTCTAGCAAAAGGGG---AGGTAAAGATTAGATCTGAAAACTTCACAGACAATGCTAAAACCATAATAGTTCAGCTAAACAGTTCTGTAATGATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAGGGATAC----------AGATAGGACCAGGACGAACTGTCTATGCAACA---------------GGGGCTATAATAGGGGACATAAGGAAAGCACATTGTAATATCAGTG-------GATGGAAAAACACGTTAGAACAGGTAGCTATGCAATTAAGAAAACAGT------------TTAAC-A-----------AAACAAACATAA---------T---CTTTAATAGT-----------ACCTCAGGAGGGGATATAGAAATTACAACACATAGC-TTT Ref.11_CPX.FR.99.MP1307.AJ291720 GGACCGTGCAACAATGTCAGCACAGTACAATGCACACATGGGATTAAACCAGTAGTATCAACTAAACTACTGCTAAATAATGGCAGTCTAGCAGAAGGAG---AGGTAAAGATTAGATCTGACAACTTCACAGACAATGCTAAAACCATAATAGTACAGCTTAACGAAACTGTAAAAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAGGTATAC----------ATACAGGACCAGGACAAGCTCTCTATACAACA---------------GGTGCTATAATAGGAGATATAAGACAAGCATATTGTAACATCAGTGGAAAAGC-CTGGAATAACACACTAAAACAGGTAGCTACACAATTATGGAGGAAGT------------TTAAC-A--------------AAACAATAG---------T---CTTTACTAAC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGC-TTT Ref.11_CPX.GR.-.GR17.AF179368 GGACCATGCAAAAATGTCAGCACAGTACAATGTACACATGGAATCAAGCCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAGGAG---AGGTAAGGATTAGATCTGAAAACCTCACAAACAATGCTAAAACCATAATAGTACAGCTTAACAGTACTGTAAGAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAGGGTATAC----------ATATAGGACCAGGACAAGCTTTTTATGCAACA---------------GGTGATATAATAGGGGATATAAAACAAGCACATTGTAACGTCAGTAGAGCAGA-CTGGAATAACACTTTACAACAGGTAGCTGAACAATTACATAATAACT------------TTAAC-A--------------AAACAATAG---------T---ATTTAATGAG-----------CATTCAGGAGGGGATTTAGAAGTTACAACACATAGT-TTT Ref.12_BF.AR.97.A32989.AF408630 GGGCCATGCAAGAATGTCAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAATTGTTGTTA---AATGGCAGTCTACCAGAAGGAG---AGATAATAATCAGATCTCAAAATATTTCACATAATACAAAAACCATAATAGTACACCTTAATGAATCTGTACAGATTACTTGTATAAGACCCA------ACAATAATACAAGAAAAAGTATAC----------ATATAGGACCAGGAAGAGCATTTTATGCAACA---------------GGAGACATAATAGGAGACATGAGAAAGGCATATTGTAGCGTTAATGGAACACA-ATGGAATAAAACGTTAGAACGGGTAAGGGAAAAGCTAAGGTCTTATT------------TGCCT------------AATACAACAATAA---------A---ATTTAACTCA-----------TCCTCAGGAGGAGACCCAGAAATTACAACACATAGT-TTC Ref.12_BF.AR.99.ARMA159.AF385936 GGGCCATGCCAGAATGTCAGCACAGTACAATGTACACATGGGATTAAACCAGTGGTATCAACTCAATTGTTGTTA---AATGGCAGCCTAGCAGAAGAAG---ATATAATAATTAGATCTCAAAACATCTCAGATAATACAAAAACCATAATAGTTCATCTTAATGAATCTGTACAGATTAACTGTACAAGACCCA------ACAATAATACAAGAAAAAGTATAC----------AGTTAGGACCAGGACGGGCATTTTATGCAACA---------------GGAGACATAATAGGGGACATTAGAAAGGCACATTGTAATGTTAGTGGAGCACA-ATGGAGTAAAACGGTAGAACAGGTAAAGGCAAAGTTAAGATCTCAAT------------TCAAT-A--------------AAACAATAA---------A---ATTTAACTCA-----------TCCTCAGGAGGGGACCCAGAAATTACAATGCATAGT-TTC Ref.12_BF.UY.99.URTR23.AF385934 GGGCCATGCAAGAATGTCAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAATTGTTGTTA---AACGGCAGCCTAGCAGAAGAAG---ATATAGTAATCAGATCTCAAAATTTCTCAGATAATGCAAAAATCATAATAGTACACCTTAATGACTCTGTACAGATTAATTGTACAAGGCCCA------ACAATAATACAAGAAAAGGTATAC----------ATATAGGACCAGGACAAGCATTTTATGCAACA---------------GGGGACATAATAGGAGACATCAGAAAGGCACATTGTAACGTTAGTGGAGCAAA-ATGGAATGAAACATTAGAACGGGTAAAGACAAAATTAAGGTCTTATT------------TCTCTA-AT---A-----CAACATCAATAA---------C---ATTTAACTCA-----------TCCTCAGGAGGGGACCCAGAAATTACAATGCATAGT-TTC Ref.12_BF.UY.99.URTR35.AF385935 GGGCTATGCCAAAATGTCAGCACAGTACAATGTACACATGGAATTAAACCAGTGGTATCAACTCAATTGTTGTTA---AATGGCAGCCTAGCAGAAGAAG---ATATAGTAATCAGATCTCAAAATATCTCAGATAATGTGAAAACAATAATAGTACACCTTAATGAATCTGTACAGATTAATTGTATAAGACCTA------ACAATAATACAAGAAAAAGTATAC----------AGCTGGGACCAGGACGAGCATTTTATGCAACA---------------GGAGACATAATAGGAGACATCAGACAGGCACATTGTAACGTTGATGGAAAACA-ATGGCATAAAAAGTTAGAAGAGGTGAGGAAAGAGTTAAAGTCTCATT------------TCTCT------------GATGCAGAAATAA---------A---ATTTAACTCA-----------TCCTCAGGAGGGGACCTAGAAATTGCAATGCATAGT-TTC Ref.13_CPX.CM.96.1849.AF460972 GGGCCATGCAGGAATGTCAGCTCAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGCCTAGCAGAAGGAG---AAATAAAGATTAGAGCTAAAAACTTCTCAGACAATGTTGGAAACATAATAGTACAGCTTGCTACGCCTGTAAGAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAAGTATAC----------GGATAGGACCAGGACAAGCATTCTATGCAACA---------------GGGGATATAATAGGAGATATAAGACAGGCACATTGTAACATCAGTAGACAAAA-ATGGAATAACACCTTACAACAGGTAGCTGCACAGTTAAGAAAATATT------------TGAAAG-AT---A-----ATACAACAATAA---------T---CTTTGCTAAT-----------CCCTCAGGAGGGGATTTAGAAGTTACAACACATAGT-TTT Ref.13_CPX.CM.96.4164.AF460974 GGGCCATGCAAGAATGTCAGCTCAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGCCTAGCAGAAGAAG---AAGTAATGATTAGATCTGAAAACTTCTCAGACAATGTTAAAACCATAATAGTACAGCTTGCTAAGCCTATAAGAATTAATTGTACCAGACCTA------ACAACAATACAAGGAAAAGTATAC----------GGATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGGAATAATAGGGGATATAAGACAAGCATATTGTAACATAAGTAAAAAAGA-ATGGAATAACACGTTACAAGAGGTAGCTAAACAATTAAGAGAACACC------------TTAACA-AT---AAGAC--AGC---------AACAATAGT---CTTTGCTAAT-----------CACTCAGGAGGGGATATAGAAATTACAACACATAGT-TTT Ref.14_BG.ES.00.X475.AF423758 GGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAGAAGAAA---AAATAGTAATTAGGTCTAAAAACTTCACGGACAATACTAAAACCATAATAGTACAGCTGAAAGACCCTATAGAAATTAATTGTACAAGACCCA------ACAACAATACAAGAARAGGAATAA----------CTATGGGACCAGGGAGAGTATGGTATACAACA---------------GGACAAATAATAGGAGATATAAGAAAAGCACATTGTAACATTAGCAAARCAAA-ATGGAATAACACTTTAGGACAGATAGCTGAAAAATTAAGAGAACAAT------------TCATG------------AATAAAACAATAG---------T---CTTTMAGCGT-----------TCCTCAGGAGGAGACCCAGAAATTGTAATGCACAGT-TTC Ref.14_BG.ES.00.X477.AF423759 GGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAGAAGAAG---AAATAGTAATTAGGTCTAAAAACTTCACRGACAATGCTAAAACCATAATAGTACAGCTGAAAGAACCTATAGAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGTATAC----------CTATGGGACCAGGGAGAGCATTGTATGCAACA---------------GGACAAATAATAGGAGATATAAGACAAGCACATTGTAACATTAGCAAAACAAA-ATGGAATAACACTTTAGGACAGATAGTTAATAAATTAAGAGAACAAT------------TCAGG------------AATAAAACAATAA---------T---CTTTCAGCAT-----------TCCTCAGGAGGAGACCCAGAAATTGAAATGCACAGT-TTC Ref.14_BG.ES.00.X623.AF450097 GGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---ACATAGTAATTAGGTCTAAAAACTTCTCGGACAATGCTAAAACCATAATAGTACAGCTGAAGGAGCCTATASAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAGAAGCATAA----------CTATGGGACCAGGGAAAGTATTGTATACAACA---------------GGACAAATAATAGGAAATATAAGAAGTGCACATTGTAACCTTAGCACAGAAAG-ATGGAATACCACTTTAAGACAAATAGTTGGAAAATTAAGAGAACAAT------------TCGGG------------AATAAAACAATAG---------T---CTTTAATCAT-----------TCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGT-TTC Ref.14_BG.ES.99.X397.AF423756 GGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAGAAGAAG---AAATAGTAATTAGGTCTAAAAACTTGAGTGACAATACTAAAACCATAATAGTACAGCTGAAAGACCCTATAGAAATTAATTGTACAAGACCCA------ACAACAATACAAGAAAAAGAATAA----------CTATGGGACCAGGGAGAGTATTGTATACAACA---------------GGACAAATAATAGGAGATATAAGAAAAGCACATTGTAACATTAGCAAAACAAA-ATGGAATAACACTTTAGGACAGATAGTTAGAAAATTAAGAAAACAAT------------TCATG------------AATAAAACAATAG---------T---CTTTCAGCGT-----------TCCTCAGGAGGAGACCCAGAAATTGTAATGCACAGT-TTC Ref.N.CM.95.YBF30.AJ006022 GGAAGCTGTACAAATGTGAGTACTGTACAATGCACACATGGAATAAAGCCAGTGATATCCACTCAGTTAATCCTA---AATGGAAGCTTAAATACAGATG---GAATTGTTATTAGAAATGATA------------GTCACAGTAATCTGTTGGTGCAATGGAATGAGACAGTGCCAATAAATTGTACAAGGCCAG------GAAATAATACAGGAGGACAGGTGC----------AGATAGGACCTGCTATGACATTTTATAACATA---------------GAAAAAATAGTAGGAGACATTAGACAAGCATACTGTAATGTCTCTAAAGAACT-ATGGGAACCAATGTGGAATAGAACAAGAGAGGAAATAAAGAAAATCC------TGG------G----GAAAAAC--------AACATAACCTTCAGGG-------------CTCGAGAGAGGA----ATGAAGGAGACCTAGAAGTGACA-CACTTAATGTTC Ref.N.CM.97.YBF106.AJ271370 GGAAGCTGTACAAATGTGAGTACTGTACAATGCACACATGGAATAAAGCCAGTGATATCCACTCAGTTAATCCTA---AATGGAAGCTTAGATACAGATG---ATATTGTTATTAGACATCATG------------G---GGGTAATCTGTTGGTGCAATGGAATGAGACAGTGTCAATAAATTGTACAAGGCCAG------GAAATAATACAGGAGGACAGGTGC----------AGATAGGACCTGCTATGACATTTTATAATATA---------------GAAAAAATAGTAGGAGACGTTAGACAAGCATACTGTAATGTCTCTGAAG----AATGGGGATCAATGTGGAATAAAACAAAAAAGAAGATAAAAAGACTCC------T------GGGAA-AC---A-----ACAC------AACTTTCAAAG-------------CTCAGGATAAAA----ATGGAGGAGACCTAGAAGTAACA-CACTTAATGTTC A1.UA.1997.ukr970063 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAGAAAG---AGGTAATGATTAGATCTGAAAATATCACAGACAATAGCAAAATCATAATAGTACAGCTTACTGAGCCTGTAAACATCACTTGTATCAGACCTG------GCAACAATACAAGAACAAGTATAC----------GTATAGGACCAGGACAAACCTTCTATGCAACA---------------GGTGATGTAATAGGGGACATAAGAAAAGCATATTGTAATGTCAGCAGAGCAGC-ATGGAATAGCACTTTACAAAAGATAAGTACACAATTAAGAAGATACT------------TTAAT------------AACAAAACAATAA---------T---CTTTAAGAAC-----------TCCCCAGGAGGGGATTTAGAAGTTACAACACATAGT-TTC A1.FI.1991.FIN91121 GGGCCATGCACGAATGTTAGCACAGTACAGTGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTGGCAAAAGAAG---AGGTAAGAATTAGATCTGAAAATATCACAAATAATGTCAAAACTATAATAGTACAACTTGTCAAGCCTGTAAACATTACCTGTATCAGACCTA------ACAATAATACAAGAAAGAGTATAC----------ATTTAGGACCAGGACGAGCATTCTATGCAACA---------------GGTGACATAATAGGGAATATAAGAAAAGCACATTGTATTGTCAATGAATCAGA-ATGGAATGAAGCTTTACAACAGGTAGCTACACAATTAGGAAAATACT------------TTGAG------------AACAAAACGATAA---------A---TTTTACTAGC-----------CCCTCAGGAGGGGATCTAGAAGTCACAACACATAGT-TTT A1.FI.1991.FIN9199 GGGCCACGCAAGAATGTCAGCACAGTACAATACACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAAAAGAAA---AGGTAAAAATTAGATGTGAAAATATCACAAACAATGCCAAAACTATAATAGTACAACTGGTCGAGCCTGTGCAAATTAATTGTACCAGACCTA------ACAACAATACAAGAAGAAGTGTAC----------GTATAGGACCAGGACAGGCATTTTATACAACA---------------G---ACATAATAGGGGATATAAGACAAGCCCATTGTAATGTCAGTAGATCAGC-ATAGAATAAAACTTTACAAAAGGTAGCTGAGCAATTAGGAGGATACT------------TTGGG------------AACAAAACAATAA---------T---ATTTGCTAAC-----------GCCTCAGGAGGGGATCTAGAAATCACAACACATAGT-TTT A1.KE.1995.Q168-a2_PNS32d GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGGTAATGATTAGATCTGAAAATTTCACAAACAACGCCAAAAACATACTAGTACAATTTAAAGAGCCTGTAAAAATTAATTGTACCAGACCTG------ACAACAATACAAGAACAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------G---GTATAATAGGGGATATAAGACAAGCATATTGTACTGTCAATGGATCAGA-ATGGAATAAAGCGTTACAAAAGGTAGTTGAACAATTAAGAAGCTCCT------------TCGAG------------AACAAAACAATAA---------T---ATTTGCTAAC-----------TCCTCAGGAGGGGATCTAGAAATCACAACACATAGT-TTT A1.KE.1994.Q259-w6_PNS59d GGGCCATGCAAGAATGTTAGCTCAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAA---AAGTAAGAATTAGATCTGAGAATATCACAGACAATGGCAAAAACATAATAGTACAACTTAAAACACCTGTAAACATTAGTTGTACCAGACCTA------ACAACAATACAAGAAAAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GATGACATAATAGGGAATATAAGACAAGCATATTGTACTGTTAATAGAACACA-ATGGGATGACACTTTGCAAGAGGTAGCCAACCAATTAAGAATATACT------------TTAAC-A--------------AAACAATAA---------T---TTTTAATAAC-----------TCAGCAGGAGGGGATCTAGAAATTACAACACATAGT-TTT A1.KE.1995.Q461 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTTTAGCAGAAAGAA---AGGTAATGATTAGATCTGAAAATATTACAAACAATGCCAAAAACATAATAGTACAATTTACCAAGCCTGTGAATATTACTTGTATCAGACCTG------GCAACAATACAAGAAAAAGTGTAC----------GCATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAACAGGGGACATAAGAAACGCACATTGTGTTGTCAATAGAACAGA-GTGGAATAACACTTTACAAAAGGTAGTTGAACAATTAAGAGAATACT------------TCCCT------------AATAAAACAATAA---------T---CTTTACTAAC-----------TCCTCAGGAGGGGACATAGAAATTACAACACATAGT-TTT A1.KE.1996.Q769-b9_PNS79d GGGCTATGCAAAAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTGTCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAGGAA---AGGTAATGGTCAGATCTGAAAATATCACAAACAATGCCAAGAACATAATAGTACAATTTAACAATTCTGTACAAATTAATTGTATCAGACCTG------GCAACAATACAAGAAAAAGTATAC----------ATTTAGGACCAGGAAAAGTATTCTATGCAACA---------------A---ATATAATAGGGGATATAAGAAAAGCACATTGTAATGTCAATAGACAACA-ATGGAATAAAGCTTTGCAAGATGTAGCCACACAATTAAGAACACACT------------TTAGA------------AACAGAACAATAA---------T---CTTTAATAAT-----------TCCTTAGGAGGAGATCTAGAAATAACAACACATAGT-TTT A1.KE.1994.Q842-d12_PNS70d GGGCCATGCAAGAATGTCAGCACAGTCCAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGGTAAAAATTAGATGTGAAAATATCACAAACAATGCTAAAACTATAATAGTACAACTTGTCAATCCTGTGAAAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAAGTATAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGACAAGCACATTGTAATGTCAACAGGACAGA-ATGGAACAACACTTTGCACCAGGTAGTCGAACAATTAAGAAAACACT------------TTAAC-A--------------AAACAATAA---------A---CTTTGCTAAC-----------TCCACAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A.CD.1997.KCC2 GGGCCATGCAAAAATGTCAGCACAGTACAATGTACACATGGAATTAAACCTGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTTTAGCAGAAGGAG---GAATAAAGATTAGATCTGCAAATATCTCATACAATGCCAAAAACATAATAGTACAGCTTGACATACCTGTAAAAATTAATTGTAGTAGGCCCA------ACAACAATACAAGAACAAGTGTGC----------GTATAGGACCAGGGCAAACATTTTATGCAACA---------------GGTGATATAATAGGGAATATAAGACAAGCACACTGCAACCTTAGTAGAACAGC-ATGGAACGATACTTTATACAATGTATCTAAAGCCTTAAGAGAACACT------------TCCCA------------AATAAAACAATAA---------T---CTTTAATAAA-----------TCATCAGGAGGGGACCTAGAAGTGACACAACATATG-TTT A.CD.1997.KMST91 GGGACATGCAACAATGTCAGCCCAGTGCAATGCACACATGGGATTAAGCCAGTGGTGTCCACTCAGCTGTTGCTA---AATGGCAGTCTACCAGAAGGAG---GGGTAATAATTAGATCTGAAAATATCACAAACAATGCCAAAACAATAATAGTACAGCTTGATGAGCCTGTAAGAATCAATTGTACCAGACCCA------ACAACAACACAAGAAAAGGTATAC----------ATATAGGACCGGGAGGAGCATTCTACGCAACA---------------GGAGAAGTAGTAGGAAACATAAGACATGCATGGTGTGAAGTTAATGGAACAGC-CTGGAAAGAAGCTTTAAAGAAAGTAGTTACAAAATTAAAAGAACACT------------TCAAA------------AATAAAACAATAG---------C---CTTTCAGCCA-----------TCATCAGGAGGGGACCTAGAAATTACAACACACAGT-TTT A.CM.1997.97CM_MP582 GGACCATGCACGAATGTCAGCACAGTACAATGCACACATGGAATCAGGCCAGTAATATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAG---AGGTACGAATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAACTTGATGAGGGTGTACATATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAAGTGTAC----------ATATAGCACCAGGACAGGCATTCTATGCAACA---------------GGGGCCATAATAGGGGACATAAGAAGAGCATATTGTCAGATCAATGGAACAAG-ATGGAATGAAACTTTGCACAAGATAGTCAAACAATTAAGAAAACACT------------TTAAC------------AACAGAACAATAA---------T---CTTTAATAGT-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTC A.CM.1997.97CM_MP812 GGGCCATGTAAGAATGTCAGTACAGTACAATGCACACATGGAATCATGCCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGCCTAGCAGAAGGAA---AGACAATGATTAGATCTAAAAATTTCACAAACAATGCCAAAATCATAATAGTACAGTTTAACCAGTCTGTAGAAATTAATTGTACTAGACCTT------ATAAGAATATAAGAAGGAGGATAC----------ATATAGGACCAGGACGAGCATTCTATGCAACA---------------AGTGGCATAGAAGGGGGTATAAGGCAAGCATATTGTAATGTCAATGCAACAGC-ATGGAATAAAACTTTACACATGGTAGCTGAACAATTAAAAACACAGT------------TTAAT-A--------------AAACAATAA---------T---CTTTGATAAC-----------TCTTCAGGAGGGGATATAGAAATTACAACACATAGT-TTT A.CM.1999.99CM_MP1370 GGGCCATGCAAGAATGTCAGTACAGTACAATGTACACATGGAATCAAACCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAG---AGGTARTCATTAGATCTGAAAATATTACAAACAATGYCAAAAACATCATAGTACAGTTTGTCAAGCCTGTAAAAATTAATTGTACAAGACCTA------ATAATAATACAAGAACAGGTATAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGAAATAATAGGGGATATAAGACAAGCACATTGTARTATCAGTAAAAGAGA-ATGGTATGAAGCTTTAAACCAGACACAAACACAATTTAAGAAACACT------------TTAAC-A--------------GAACAATAA---------A---ATTTAATAAC-----------TCCTCAGGAGGGGACTTAGAAATTACAACACATAGT-TTT A.CM.1999.99CM_MP1433 GGGCTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTGGTATCAACTCAATTGCTGTTA---AATGGTAGTCTAGCAGAAGGAG---AAATAAAGGTTAGATCTGAGAATTTCACAAACAATGCTAAAACTATAATAGTACAGCTTGACCAGCCTGTAATAATTAATTGTACCAGACCTA------ACAACAATACAAGAAGAAGTGTAC----------GTATAGGACCAGGACAAGCATACTATGCAACA---------------GGAGAAATAATAGGGGATATAAGAAAAGCATATTGTACTGTCAATAAAACAGC-ATGGAATGAAACAAAACACAAGGTAATGGAAAAATTAAGAGGAATAT------------ACCAC-A--------------GACCAATAA---------A---GTTTAATAGC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATATG-TTT A.CM.1998.98CM_MP1014 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTG---AATGGCAGTCTAGCAGAAGGAA---ATGTAAYGATTAGATCTGAGAATCTCACAAAYAATGCCAAAACCATAATAGTACAGCTTGCTGATCCTGTAAACATTACTTGTATCAGACCCA------ACAACAATACAAGAAAAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGACAAGCACATTGTAATGTCAGWAGARAAAA-WTGGAATAACACTTTACACAAGGTAGCTGAACAGTTAAGACAGTACT------------TTAWC------------AACAAAACAATAG---------C---ATTCAATAAA-----------TCATCAGGAGGGGATTTAGAAATTACAACACATAGC-TTT A.CM.1997.97CM_MP640 GGGCAATGCAATGATGTCAGCTCAGTACAATGCACACATGGAATCAGACCAGTAGTATCAACYCAATTGCTGTTA---AATGGCAGTCTAGCAAAAGGAA---AGGTAAAGATTAGAWCTGAAAGTCTCACAAACAATGCCAAAACCATAATAGTACAATTTAATGAGACTGTAAGAATTAATTGTACCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------ATATGGGACCAGGAAAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGACATAAGAAAAGCACACTGTAATGTCAGTAGAGCAAA-ATGGAAGGACACTTTACAAGAGGTAGCCAGACAATTAAGTGAACACT------------TTAAT------------AAAACAGAAATAA---------C---CTTTAAGAAC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT A.KE.2000.00KE_KER2018 GGGTTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCGGTAGTGTCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGATAAGAATTAAATCTGAAAACATCTCAGACAATGCTAAAACCATAATTGTACAACTTACCAAGCCTGTACTAATCAATTGTGCCAGACCTA------GCAACAATACAAGAAAAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGCTATAACAGGAGATATAAGACAAGCATATTGTGTAGTCAATAGAACACA-ATGGAATGACACTTTAGGACAGGTAGCGATACAATTAAGAAAACACT------------GGAAC-A--------------CAACAATAA---------T---CTTTAATGAA-----------CCCTCAGGAGGGGATTTGGAAATTACAACACATAGT-TTT A.KE.-.MS208w6BMCB1_gp160 GGGCCATGCGAGAATGTCAGTACAGTACAATGTACACATGGAATCAAGCCAGTAGTGTCAACTCAATTGCTATTA---AATGGCAGTCTAGCAGAAGAAC---ATGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAAATATACTAGTACAACTTAACGAGTCTGTAGAAATTTATTGTATTAGACCTA------GTAACAATACAAGAAAAAGTGTAC----------GTATAGGACCAGGACAAACATTCTATGCAACA---------------GGTGAAATAATGGGGGATATTAGACAAGCACATTGTAATGTCAGTGGGTCAAA-ATGGAATAAAACTTTACAACAGGTAGCCAACCAATTAAGAAAACACT------------TTAAC------------ACCACAACAATAA---------T---CTTTGCTAAC-----------CCCTCAGGAGGGGATCTAGAAATTACAACACATAGT-TTT A.KE.-.MJ613_W1M_ENV_A2 GGGCTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAA---AGGTAATGATCAGATCTGAAAATATCACAAACAATGCCAAAAACATAATAGTACAATTTACCAGTCCTGTAGAAATTAAGTGTATCAGACCTA------ACAACAATACAAGAAAAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGAATATAAGACAAGCACATTGTAATGTCAGTAGAACAGA-ATGGAATAAAACTTTGCAACAAGTAGCCACCCAATTAAGAACATACT------------TTGGA------------AACAAGACAATAA---------T---CTTTGCTAAC-----------TCCACAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A.KE.-.BJ613_W6M_ENV_A1 GGACTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAACCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAGGAA---AGGTAATGATCAGATCTGAAAATCTCACAAACAATGCCAAAAACATAATAGTACAATTTAACGAGTCTGTAAAAATTGATTGTATCAGGCCTA------ACAACAATACAAGAAAAAGTATAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGCCATATTAGGGGATATAAGACAAGCACATTGTAAAGTTAATAAAACAGA-ATGGAATAAAGCTTTGCAAAAGGTAGTCACCCAATTAGGAACATACT------------TTAAG------------GACAAAGCAATAA---------C---CTTTGATAAC-----------TCCACAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A.KE.-.MG505_W0M_ENV_A2 GGGCCATGCCCAAAGGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAAACATACTAGTACAATTTAACACGCCTGTGCAAATTAATTGTACCAGACCTA------ACAACAATACAAGGAAAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGGGACATAATAGGGGATATAAGACAAGCACATTGTACTGTCAGTAAAGCAAC-ATGGAATGAAACTTTGGAAAAGGTAGTCAAACAATTAAGAAAACACT------------TTGGGA-AC---A-----ACAAAACAATAA---------T---ATTTGCTAAC-----------TCCTCAGGAGGGGATCTAGAAGTCACAACACATAGT-TTT A.KE.-.BG505_W6M_ENV_A5 AGGCCATGCCCAAGTGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAAACATACTAGTACAATTTAACACGCCTGTGCAAATTAATTGTACCAGACCTA------ACAACAATACAAGGAAAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGGGACATAATAGGGGATATAAGACAAGCACATTGTACTGTCAGTAAAGCAAC-ATGGAATGAAACTTTGGGAAAGGTGGTCAAACAATTAAGAAAACACT------------TTAGGA-AC---A-----ACACAATAATAA---------G---ATTTGCTAAT-----------TCCTCAGGAGGGGATCTAGAAGTCACAACACATAGT-TTT A.KE.-.MI206_W0M_ENV_A1 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGTTGTTA---AATGGCAGTCTAGCAGAAA------AGGTAAAAATTAGATCTGAAAATACCACAAACAATGCCAAAATTATAATAGTACAACTTGACGAGCCTGTGACAATTAATTGTACCAGACCCA------ACAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGCCATAATAGGGAACATAAGACAAGCACATTGTAATGTCAGTAGATCAGC-ATGGAATCAAACTTTACAAAAGGTAGTTACACAATTAAGAACATACT------------TTGGG------------AACAAAACAATAA---------T---ATTTGCTAAC-----------TCCTCAGGAGGGGATCTAGAAGTCACAACACATAGT-TTT A.KE.-.BI206_W6P_ENV_A1 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAACGA---AGGTAAAAATTAGATCTGAAAATATCACAAACAATGCCAAAATTATAATAGTACAACTTGACAATCCTGTGACAATTAATTGTACCAGACCCA------ACAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGCCATAATAGGGAACATAAGACAAGCACATTGTAATGTCAGTAGATCAGC-ATGGAATCAAACTTTACAAAAGGTAGTTACACAATTAAGAACATACT------------TTGGG------------AACAAAACAATAA---------T---ATTTGCTAAC-----------TCCTCAGGAGGGGATCTAGAAATCACAACACATAGT-TTT A.KE.-.ML274_W0M_ENV_A1 GGACCATGCAAAGATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAA---AGGTAATAATTAGATCTGAAAATATCACAAACAATGCCAAAAACATAATGGTGCAATTTAACGAGTCTGTAACAATTAATTGCACCAGACCTC------ACAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCGTTCTATGCAACA---------------GGTGCCATAACAGGGGATATAAGACAAGCACATTGTAATGTCAGTAAAACAGA-ATGGGATAAAACTTTGCAAAAGGTAGCCACACAATTGGAAACATACT------------TTAAG------------AACAAAACAATAA---------C---ATTTGCTAAA-----------CCCACAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A.KE.-.BL274_W6M_ENV_A3 GGACCATGCAAAAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTGGCAGAAAAAA---AGGTAATGATTAGATCTGCAAATATCACAAACAATGCCAAAAACATAATAGTACAACTGACCGAGTCTGTAAAAATTAATTGCACCAGACCTC------ATAATAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGCTATAACAGGGGATATAAGACAAGCACATTGTAATGTCAGTAGACCAGC-ATGGAATAAAGCTTTGCAAGAGGTAGCCACACAATTGAAAACATACT------------TTAAC-A--------------AAACAATAA---------T---ATTTGATAAA-----------CCCACAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A.CM.2000.NYU1423 GGGGAATGCAAGAATGTCAGTACAGTACAATGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTATTA---AATGGCAGCCTAGCAAAGGAGC---AGGTAATGATTAGATCTAAAAATTTCACGAACAATGCCAAAACCATAATAGTACAACTTAACCAGTCCATATCAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAAGTATAC----------ACATAGGACCTGGACAAGCGTTCTATGCAACA---------------GGTGACATAATAGGAAATATAAGACAAGCACATTGTAATGTGTCTAGAGCTGA-ATGGAATGAAGCTTTAAAGCGGGTATCTGCAAAATTAAGGGAACAGT------------TTAAG------------AACAAAACAATAG---------T---TTTTAATTCA-----------TCTACAGGAGGTGATCCAGAAATTACAACACATAGT-TTT A1.BE.-.VI2809 GGACCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGATAAGGATTAGATTTGAAAATATCACAGACAATGCCAAAGCTATAATAGTACAATTTAATCAGTCGGTAGAAATTAATTGTACCAGGCCTA------ACAACAATACAAGAACAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGACATAAGAAATGCACATTGTAATGTCAGTAGAAAGAA-TTGGACTGAGGCTTTATACAGGGTAGCCACACAATTAAGAAAACACT------------TTAAC-A--------------GAACAATAA---------A---CTTTACTAGT-----------GCCTCAGGGGGGGATTTAGAACTTACAACACATACT-TTT A1.UG.1997.pt185 GGGCCATGCAAGAATGTTAGCACAGTACAATGCACACATGGAATCAGGCCAGTAGTAACAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAA---AGGTAATAATTAGAGCTGAAAATATCACAAACAATGCCAAAAACATAATAGTACAATTAAGCGAGCCTGTARATATTACTTGTACCAGACCTG------GCAACAATACAAGGAGAGGTATAC----------GTATAGGACCAGGACGAAAATTCTATGCAGCA---------------GATAAAATAATAGGGGATATAAGACAAGCATATTGTACTGTCAGTAGAGCAAA-ATGGAACGAAACTTTGCAAAAGGTAGCCAACCAATTAAAAACACACT------------TCAACA-CA---N-----NNNNNACAATAG---------T---CTTTGATAGC-----------CCCATAGGAGGGGATCTAGAAATAACAACACATACT-TTT A1.UG.1998.120MPC12 GGGCTATGCAAGAATGTTAGCACAGTACAATGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAG---AAGTAATGATTAGATCTGAAAATATCATAAACAATGCCAAAAACATAATAATACAATTTAACCAGTCTGTACCAATTAATTGTACCAGACCTG------GCAACAATACAAGAAAAGGTATAC----------ATATAGGACCAGGACAGGCATTCTATGCAACA---------------GGTGCCATAATAGGGGATATAAGACAAGCACATTGCACTGTCAATAGAACAGA-ATGGAATAACACTTTGCAAAAGGTAGTCAAAAAATTAAGAACACACT------------TTGGG------------AACAAAACAATAA---------T---CTTTAATAAC-----------TCCGCAGGAGGGGATCTGGAAATAACAACACATAGT-TTT A1.UG.1998.120FIc01 GGGCTATGCAAGAATGTTAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTGTCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAG---AGGTAATGATTAGATCTGAAAATATCACAGACAATACCAAAAACATAATAGTACAATTTAACCAGTCTGTACAAATTATTTGTACCAGACCTA------ACAACAATACAAGAGAAAGTATAC----------ATATAGGACCAGGACAGGCATTCTATGCAACA---------------GGTGAAATAATAGGGAATATAAGACAAGCACATTGCAATGTCAGTGGAACAAG-ATGGAATAAAACTTTGCAAGAGGTAGCCAACAAATTAAGAATACACT------------TTGGG------------AACACAACAATAA---------A---CTTTACTAGC-----------CCCGCAGGAGGGGATCCAGAAATAACAACACATAGT-TTC A1.UG.1999.601MPC7 GGGCTATGCCAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAGAAGGGA---CGGTAAAAATTAGATCTGAAAACATCACAAACAATGTCAAAACCATAATAGTACACCTTAACGAGTCTGTGGAAATTAATTGTACCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------G---ACATAATAGGAGATATAAGGAAGGCATATTGTAAAGTCAATCGCTCAGA-ATGGCATAAAGCTTTACAAAAGGTAGTCGAGCAATTAAGAAAACACT------------TTAAG------------AACAAAACAATAA---------T---CTTTGCTAGC-----------TCCTCAGGAGGGGATCTAGAAATCACAACACATAGT-TTT A1.UG.1999.601FIC3 GGGCTATGCCAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGCTA---AATGGCAGTCTAGCAGAAGGGG---AGGTAAAAATTAGATCTGAAAACATCACAAACAATGTCAAAACCATAATAGTACACCTTAACGAGTCTGTGAAAATTAATTGTACCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------G---ACATAATAGGAAATATAAGGAAGGCATTTTGTACAGTCAATAGCTCAGA-ATGGCATAGAGCTTTACAAAAGGTAGTCGAGCAATTAAGAAAACACT------------TTAAG------------AACAAAACAATAA---------T---CTTTGCTAGC-----------TCCTCAGGAGGGGATCTAGAAATCACAACACATAGT-TTT A1.UG.1997.368MPc02 GGGCTATGCCAGAATGTCAGCACAGTACAATGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAA---ACATAACAATTAAATCTGAAAATATCACAAATAATGCTAAAACCATAATAGTGCAACTTACCAAGCCTGTAATAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAGGTGTAC----------ACATAGGACCAGGACAAGCATTCTTTGCAGCA---------------GGTGACATAATAGGAAACATAAGGCAAGCATATTGTACGGTCAATGCATCAGA-ATGGAATAACACTTTACAACAGGTAGCTGAACAATTAAGGAAACATT------------GGAAC-A--------------CAACAATAA---------T---CTTCACTAAC-----------TCCTCAGGAGGGGATGTAGAAATTACAACACATAGT-TTT A1.UG.1997.368FIc01 GGGCTATGCCAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAA---ACATAACAATTAAATCTGAAAATATCACAAATAATGCTAAAACCATAATAGTGCAACTTACCAAGCCTGTAATAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAGGTGTAC----------ACATAGGACCAGGACAAGCATTCTTTGCAACA---------------GGTGACATAATAGGAGACATAAGACAAGCATATTGTACGGTCAATGCATCAGA-ATGGAATAACACTTTACAACAGGTAGCTGAACAATTAAGGAAACATT------------GGAAC-A--------------CAACAATAA---------T---CTTCACTAAC-----------TCCTCAGGAGGGGATGTAGAAATTACAACACATAGT-TTT A1.KE.1998.QA413_1007M_ENV_A4 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATTAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAA---AGGTAATAATTAGATCTGAAAATATCACAGACAATACCAAAAATATAATAGTACAATTTGCTGATTCTGTGAACATTACTTGTATCAGACCCA------ATAACAATACAAGAAAAAGTATAC----------ATATAGGACCAGGACAGGCATTCTATGCAACA---------------GGTGACATAATAGGGGATGTAAGACAAGCACATTGTAATGTCAGTAGATCAAA-ATGGAATAAAACTTTAGAACAGGTAGTTGAGCAATTAAGCCAATACT------------TTAAG------------AACAAAACAATAA---------G---ATTTGCTAAC-----------CCCTCAGGAGGGGATCCAGAAATCACAACACATAGT-TTT A1.KE.1998.QB726_1165M_ENV_A3 GGGTCATGCAAGAATGTCAGTACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAA---AGGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAATTTAACAAGTCTGTAGAAATTAACTGTACCAGACCCA------CCAACAATACAAGAAAAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGCCATAATAGGGGATATAAGGAAAGCACATTGTAATGTCAGTAGAACAAA-ATGGAATCAAACTTTGCAAGAGGTAGTCAACCAATTAAGAACACACT------------TTGGG------------ACCGAAACAATAG---------T---CTTTGATAAA-----------CCCATAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A1.BE.-.PIC771_12 GGACCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAACAAG---ACATAAGGATTAGATCTGAAAATATCTCACAAAATCACAAAACCATAATAGTACAATTTAATCAGTCGGTAGCAATTAATTGTACCAGACTTA------GAAACAATACAAGAAGAAGTATAC----------ATATAGGACCAGGACAAGCATTCTATGCAGCA---------------GGAGCAATAATAGGGGACATAAGAAGTGCACATTGTAATATCAGTAGCAAAGC-TTGGAATAAGACTTTACACAGGGTAGCCACACAGTTAAGAAAACACT------------TTAAC-G--------------GAACAATAA---------T---CTTTACTAAT-----------GCCTCAGGGGGGGATTTAGAAATTACAACACATAGT-TTT A1.BE.-.PIC13072_1 GGACCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAACAAG---ACATAAGGATTAGATCTGAAAATATCTCACAAAATCACAAAACCATAATAGTACAATTTAATGAGTCGGTAGCAATTAATTGTACCAGAGTTA------GAAACAATACAAGAAGAAGTATTC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGAGAAATAATAGGGGACATAAGGAGTGCACATTGTAATATCAGTAGCAAAGC-TTGGAATAAGACTTTATACAGGGTAGCCACACAATTAAGAAAACACT------------TTACC------------GGAACAACAATAA---------T---CTTTACTAAT-----------GCCTCAGGGGGGGATTTAGAAATTACAACACATAGT-TTT A1.BE.-.VI2992_2 GGACCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCGGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAACAAG---ACATAAGGATTAGAGCTGAAAATATCTCAGCAAATCACAAAATCATAATAGTACAATTTAATCAGTCGGTAGAAATTAATTGTTCCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGACATAAGAGCTGCACATTGTAATGTCAGTAAACATAA-TTGGACTGAGGCTTTATACAGGGTAGCCACACAATTAAGAAAACACT------------TTGAA------------AACAAAACAATAA---------A---CTTTACTAGT-----------GCCTCAGGAGGGGATTTAGAACTTACAACACATACT-TTT A1.BE.-.VI3050_25 GGACCATGCAACAATGTTAGCACAGTACAATGCACACATGGAATCAAGCCGGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGATAAGGGTTAGATTTGAAAATATCTCAGACAATGCCAAAGCTATAATAGTACAATTTAATCATTCGGTAGAAATTAATTGTTCCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGACATAAGAGCTGCACATTGTAATGTCAGTAAACATAA-TTGGACTGAGACTTTATACAGGGTAGCCACACAATTAAGAAAACACT------------TTGAA------------AACAAAACAATAA---------A---CTTTACTAGT-----------GCCTCAGGGGGAGATTTAGAACTTACAACACATACT-TTT A1.BE.-.VI3196_10 GGACCATGCAACAATGTTAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTACTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGATAAGGGTTAGATTTGAAAATATCTCAGACAATGCCAAAGCTATAATAGTACAATTTAATTATTCGGTAGAAATTAATTGTTCCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------ATATAGGACCAGGACAAGCATTCTATGCAACA---------------GGGGACATAATAGGGGACATAAGAGCTGCACATTGTAATGTCAGTAAACATAA-TTGGACTGAGACTTTATACAGGGTAGCCACACAATTAAGAAAACACT------------TTGGA------------AACAAAACAATAA---------A---ATTTACTAAT-----------GCCTCAGGGGGAGATTTAGAACTTACAACACATACT-TTT A1.BE.-.VI1383_20 GGACTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAAAAG---AGGTAAGGATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAACTTGATCAGCCTGTAAATATTACTTGTATGAGACCTA------ACAACAATACAAGAAAAAGTGTAC----------ATATAGGACCAGGACAAGCATTTTATGCAACA---------------GGTGACATAATAGGGAACATAAGAGAAGCACATTGTAATGTCAGTAGAGAAGA-TTGGAACAATACTTTACAAAAGGTAGCCACACAATTAAGAAAACACT------------TTGGG------------AACAAAACAATAA---------T---CTTTGCTAAG-----------TCCTCAGGGGGGGATTTAGAAATTACAACACATAGT-TTT A.RW.-.PVPI GGGCCATGCAAAAATGTCAGCTCAGTACAATGCACACATGGAATCAGGCCAGTAATATCAACTCAACTGTTGTTA---AATGGCAGTCTAGCAGAAGAAAAAGATGTACAGATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAATTTACCAAGGCTGTAAAAATTAATTGTACCAGACCTA------ACAAAACTACAAGAAAAGGTGTGC----------GTATAGGACCAGGACAAGCATGGTATGCAAGA---------------GGTAACATGATAGGAGATATAAGAAAAGCATATTGTAATGTCAGTAGAACAGA-ATGGAATCAAACATTACAAAAGGTAGCCACACAATTAGGAAAACACT------------TTAAC-A--------------AAACAATAA---------C---CTTTACTAAA-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT A.KE.1990.K89 GGGCCATGCACGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAG---AGGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAAATATAATAGTACAATTTGCCGAGCCTGTAAAAATTAATTGTACCAGACCTA------ACAACAATACAAGAATGAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGAACATAAGACAAGCACATTGTAATGTCAGTAGAGCAGA-ATGGAATACAACTTTGCAAAAGGTAGTCACAAAATTAAGGGAATACT------------TTGGGA-AC---A-----ACAAAACAATAA---------A---ATTTGCTAAC-----------TCCTCAGGAGGGGATCTAGAAATCACAACACATAGT-TTT A1.UG.1990.UG275A GGGATATGTAATAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAGCTGCTGTTA---AATGGCAGTTTAGCAGAAGGAA---AGGTAAAGATTAGATCTGAAAATATCACAAACAATGCCAAAAATATACTGGTATAACTTACCACGCCTGTAACAATTAATTGTACCAGACCTA------ACAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAATCATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAAACAAGCACATTGTAATATCAGTAGAGCAGA-ATGGAATGAAACTTTACAAAAGGTAGTCAGCCAATTAAGAACACACT------------TTGGC------------AACAAAACAATAA---------T---CTTTGGTAAC-----------TCCTCAGGAGGGGATATAGAAATAACAACACATAGT-TTT A1.UG.1990.UG273A GGGCTATGCAAGAATGTCAGCTCAGTACAATGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAACAG---AGGTAAAAATTAAATCTGAAAATATCTCAGACAATGCTAAAACCCTAATAGTACAACTTACCACGCCTGTAAAAATTAATTGTACTAGACCTG------GCAACAATACAAGAACAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGATATAATAGGAGATATAAGACAAGCACATTGTAATGTCAGTAGATCAGA-ATGGAAGGAAACTTTGCAAAAGGTAGTCAAACAATTAAGAACACACT------------GGAAC-A--------------AAACAATAA---------T---CTTTACAAAC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT A.RW.-.SF1703 GGGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAGGCCAGTAATATCAACCCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGGAA---GGGTAAAGATTAGATCTGAAAATATCACAAACAATGCCAAAACCATAATAGTACAACTTAACAAGACTGTAGAAATTAATTGTACCAGACCTA------ACAACAATACAAGAAAAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGACATAATAGGGGATATAAGACAAGCATATTGTAATGTCAGTAGAGCAGA-CTGGAATAAAACTTTACAAGGGGTAGCCAACCAATTAAAAAGTTACT------------TTAGT------------AACAAAACAATAA---------T---CTTTGCTAGC-----------TCCTCAGGAGGGGATTTAGAAATTACAACACATAGT-TTT A.GB.-.MC108 GGGCCATGCACGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTA---AATGGCAGTCTAGCAGAAGAAG---AGGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAAACATAATAGTACAATTTACCACGTCTGTAAAAATTAATTGTACCAGATTTA------ACAACAATACAAGAAGAAGTATAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------AATGACATAATAGGGAATATAAGACAAGCACAATGTGATGTCAATAGAACAGA-ATGGAATAAAGCTTTGCAAGGGGTAGTCAAACAATTACAAAAATACT------------TTGGG------------AACAAAACAATAA---------T---CTTTACTAAC-----------TCCTCAGGAGGGGATCTAGAAATAACAACACATAGT-TTT A.GB.-.MA246 GGGCTATGCAAGAATGTCAGCACAGTACAATGCACACATGGAATCAAGCCAGTAGTATCAACCCAACTGCTGTTA---AATGGCAGTCTAGCAGAAAGCA---AGGTAATGATTAGATCTGAAAATATCACAAACAATGCCAAAAACATACTAGTACAACTTACCAGTCCTGTAAACATTAGTTGTATCAGACCTA------ACAACAATACAAGAAAAAGTGTAC----------GTATAGGACCAGGACAAGCATTCTATGCAACA---------------GGTGAAATCATAGGGAATATAAGACAAGCATATTGTAATGTCAATAGATCAGA-ATGGAATGAAGCTCTGCGGGAGGTAGTCAAACAATTAAGAACATACT------------TTAAC-A--------------AAACAATAA---------T---CTTTGATAAC-----------TCCTCAGGAGGGGATCTAGAAATAACAACACATAGT-TTT seqmagick-0.8.4/examples/include-from-file/000077500000000000000000000000001376401056300206135ustar00rootroot00000000000000seqmagick-0.8.4/examples/include-from-file/do_filter.sh000077500000000000000000000001451376401056300231210ustar00rootroot00000000000000#!/bin/bash seqmagick convert --include-from-file selection.txt \ ../aligned.fasta filtered.fasta seqmagick-0.8.4/examples/include-from-file/selection.txt000066400000000000000000000000731376401056300233410ustar00rootroot00000000000000gi|66864576|gb|DQ027786.1| hxb2 gi|66864553|gb|DQ027774.1| seqmagick-0.8.4/examples/quality-filter/000077500000000000000000000000001376401056300202655ustar00rootroot00000000000000seqmagick-0.8.4/examples/quality-filter/sample.barcodes.csv000066400000000000000000000000171376401056300240420ustar00rootroot00000000000000Sample1,AAAAAA seqmagick-0.8.4/examples/quality-filter/sample.fna000066400000000000000000000020061376401056300222320ustar00rootroot00000000000000>s1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA >s2 CCCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA >s3 GGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >s4 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAA >s5 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA seqmagick-0.8.4/examples/quality-filter/sample.qual000066400000000000000000000056611376401056300224420ustar00rootroot00000000000000>s1 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 17 17 17 18 30 35 37 40 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 38 39 40 39 37 38 38 35 40 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 34 32 32 30 30 31 27 25 19 19 14 14 22 22 24 22 22 20 20 21 25 >s2 22 27 31 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 32 32 33 40 40 40 40 40 40 28 29 29 29 39 40 40 40 40 40 40 40 40 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 38 38 35 35 32 32 32 36 37 37 37 37 37 37 35 36 36 37 37 38 38 39 37 39 35 32 32 32 29 29 29 29 21 21 13 13 22 24 27 24 23 22 22 22 25 >s3 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 36 36 39 40 40 40 40 34 34 34 40 23 23 23 23 24 33 37 37 33 33 33 33 30 30 30 30 30 33 30 22 22 22 26 26 20 20 29 30 35 33 37 34 34 34 34 >s4 34 36 36 40 37 37 37 36 32 27 31 32 37 37 37 37 32 36 32 35 36 39 38 33 36 36 36 34 32 32 16 16 16 14 18 24 24 35 35 31 31 29 28 28 30 33 32 32 32 40 40 32 32 32 36 38 40 36 36 32 32 38 38 40 38 40 40 40 37 40 38 36 34 36 36 37 38 38 40 40 37 37 37 37 40 40 38 38 36 35 36 36 40 37 37 37 37 37 37 38 38 38 38 38 38 38 40 38 38 38 38 38 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 37 37 34 32 31 35 37 27 25 17 17 16 20 27 34 37 38 38 34 34 34 37 38 38 40 40 39 39 38 38 37 29 29 28 29 29 29 27 16 16 13 20 21 27 27 27 24 24 24 25 >s5 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 30 30 18 18 18 33 35 33 38 38 38 34 33 26 29 29 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 29 28 28 31 31 31 39 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 35 35 35 35 40 38 38 40 30 31 30 28 37 33 23 35 35 37 37 37 32 28 28 28 28 35 25 40 38 38 40 39 39 40 40 39 35 35 35 35 40 36 36 33 33 38 37 24 38 38 37 37 34 34 32 35 30 31 16 14 14 20 16 16 19 19 20 18 16 13 13 13 13 17 20 30 30 20 20 16 16 17 16 14 14 14 16 12 12 12 16 19 23 26 27 27 24 24 27 29 29 27 27 24 26 30 24 23 23 23 18 17 14 14 14 13 13 13 17 16 16 16 17 14 16 20 20 seqmagick-0.8.4/examples/range.fasta000066400000000000000000000004771376401056300174360ustar00rootroot00000000000000>456442|refseq_protein.39.micro/1-331 ---MINVGVLGATGAVGQRFVELLSDHP-------------------------------- ----------------------------------------------------------- >368407|refseq_protein.39.micro/1-331 ---MINVGVLGATGAVGQRFVQLLADHP-------------------------------- ----------------------------------------------------------- seqmagick-0.8.4/examples/test.fasta000066400000000000000000000620261376401056300173170ustar00rootroot00000000000000>gi|66864576|gb|DQ027786.1| HIV-1 isolate QA013_2282M_C6 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCATTGAATGGAAGAGTAATAGTAGCAATAACGGCACTGA TCAGGACATGAATGAGAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAGCTTGATGTAGTACAGATAGATAATAGTAATACTAGC TATAGATTAATAAATTGTAATACCTGCCATTACACAGGCATGTCCAAAGGTAACCTTTGA GCCAATTCCCATACATTATTGTGCCCCAGCTGGTTGCAATTCTAAAATGTAACAATAAGA AATTCAATGGGACGGGTCCATGCACAAACGTCAGCACAGTAGTGTACACATGGGATTAGG CCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGATAATAATTAG ATCTGAAAATTTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATAAGTCTGTCAA TTCATTGCACAAGACCCTACAACAATACAAGAAGAGGTGAACATATGGGACCAGGGCGAG CACTCTACAGAAAAAATAGTTGGAAATATAAGACAAGCATATTGTAACATTAGTGGAGGG GAATGGAATAAAGTTACAGCAGGTAGCTGGCAAATTAAGAAACCTTCTTAATAAAACAAC AATAATTTTTAAACCACCCGCGAGGGGACCTAGAAATTACAACACACAGCTTTAATTGTA GAGGGGAATTTTTCTATTGTAATACATCACCTGTTTAACAGCACTTGGGACAACAATACC CAGGAATCAAATGACACTATAATGATCCCATGCAGAAAAACAAATTATAAACATGTGGCA GGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGACACATGTTGTTCATCAAATA TTACAGGACTATTGTTGACAAGAGATGGTGGTGTAGCTAATGGGAGTTCGAATGACCTTC AGACCTGGGGGAGGAGAC >gi|66864574|gb|DQ027785.1| HIV-1 isolate QA013_1790M_B6 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACGTTAAACTGCATTGAATGGATAAATAATAATAGCACTAACGCCACTGG TCAGGACATGAATGAAAAACTGCTCTTTCAATATAGCCACAGAAGTAAGAGATAAGAAAA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTAATACTAGC TATAGATTAATAAATTGTAATACCTGCCATTACACAGGCATGTCCAAAGGTAACCTTTGA GCCAATTCCCATACATTATTGTGCCCCAGCTGGTTGCAATTCTAAAATGTAATAATAAGA AATTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTAGTGTACACATGGGATTAGG CCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGATAATAATTAG ATCTGAAAATTTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTCAA TTAGTTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAG CACTCTACAGAAAAAATAGTTGGAGATATAAGACAAGCACATTGTAACATTAGTGGAAGG GAATGGAATAACGTTACAGCAGGTAGCTGACAAATTAAGAAACCTTCTTAATAAAACAAC AATAATTTTTAAACCACCTGCGAGGAGACCTAGAAATTACAACACACAGCTTTAATTGTC TAGGGGAATTTTTCTACTGCAACACATCAACTGTTTAATAATAGTAAATGGGAATCAAAT AGTAGTACAGGGGAAAATAAAAATGAAGATATAATCACTCCCATGCAGAATAAAACAAAT TATAAACATGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCTTGAAGGACACATCA GTTGTTCGTCAATTATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAACTTCGGAGT TCGGAGACCTTCAGACCTGGGGGAGGAGAC >gi|66864568|gb|DQ027782.1| HIV-1 isolate QA013_385M_C3 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTAACGTCACTGA TCAGGACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTACCAGCTAT AGATTAATAAATTGTAATACCTCTGATTACACAGGCATGTCCAAAGGTAACCTTTGAGCC AATTCCCATACATTATTGTGCCCCAGCTGGATTCAATTCTAAAATGTAATGATAAGAAGT TCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACAGTACACATGGGATTAGGCCA GTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGAGAATAATTAGATC TGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTACCTTA ATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAGCAC CCTTTAGAAAGAATAGTTGGAGATATAAGACAAGCATATTGTAGCATTAGTGGAATGGGA TGGAATAAAACTTCAGCAGGTAGCTGACAAATTAAGAAACCTTCTTAATAAAACAACAAT AATTTTTAAACCACCCGCGGGGGGACCTAGAAATTACAACACACAGCTTTAATTGTGGAG GGGAATTTTTCTACTGCAACACATCAAGAGTTTAATAATAGTGAATGGAAATCAAATAGT AGTACAGGGGGAAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACAT GTGGCAGGGAGTAAGAAAAGCAATGTATGCCCCTCCCATTGAAGGACATCAATTGTTCAT CAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAACTAATCAGAGTGAATGAG ACCTTCAGACCTGGGGGAGGAGAC >gi|66864564|gb|DQ027780.1| HIV-1 isolate QA013_105M_C2_1 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTAACGTCACTGA TCAGGACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTACCAGCTAT AGATTAATAAATTGTAATACCTCTGATTACACAGGCATGTCCAAAGGTAACCTTTGAGCC AATTCCCATACATTATTGTGCCCCAGCTGGATTCAATTCTAAAATGTAATGATAAGAAGT TCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACAGTACACATGGGATTAGGCCA GTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGAGAATAATTAGATC TGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTACCTTA ATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAGCAC TCTTTAGAAAGAATAGTTGGAGATATAAGACAAGCATATTGTAGCATTAGTGGAATGGGA TGGAATAAAACTTCAGCAGGTAGCTGACAAATTAAGAAACCTTCTTAATAAAACAACAAT AATTTTTAAACCACCCGCGGGGGGACCTAGAAATTACAACACACAGCTTTAATTGTGGAG GGGAATTTTTCTACTGCAACACATCAAGAGTTTAATAATAGTGAATGGAAATCAAATAGT AGTACAGGGGGAAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACAT GTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGACATCAATTGTTCAT CAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAACTAATCAGAGTGAAGGAG ACCTTCAGACCTGGGGGAGGAGAC >gi|66864562|gb|DQ027779.1| HIV-1 isolate QA013_70M_B1 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTAACGTCACTGA TCAGGACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTACCAGCTAT AGATTAATAAATTGTAATACCTCTGATTACACAGGCATGTCCAAAGGTAACCTTTGAGCC AATTCCCATACATTATTGTGCCCCAGCTGGATTCAATTCTAAAATGTAATGATAAGAAGT TCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACAGTACACATGGGATTAGGCCA GTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGAGAATAATTAGATC TGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTACCTTA ATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAGCAC TCTTTAGAAAGAATAGTTGGAGATATAAGACAAGCATATTGTAGCATTAGTGGAATGGGA TGGAATAAAACTTCAGCAGGTAGCTGACAGATTAAGAAACCTTCTTAATAAAACAACAAT AATTTTTAAACCACCCGCGGGGGGACCTAGAAATTACAACACACAGCTTTAATTGTGGAG GGGAATTTTTCTACTGCAACACATCAAGAGTTTAATAATAGTGAATGGAAATCAAATAGT AGTACAGGGGGAAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACAT GTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGACATCAATTGTTCAT CAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAACTAATCAGAGTGAATGAG ACCTTCAGACCTGGGGGAGGAGAC >gi|66864566|gb|DQ027781.1| HIV-1 isolate QA013_264M_A2 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCACTGAATGGAAGAATAATGGTAGCACTAACGTCACTGA TCAGGACATGAATGAAAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTACCAGCTAT AGATTAATAAATTGTAATACCTCTGATTACACAGGCATGTCCAAAGGTAACCTTTGAGCC AATTCCCATACATTATTGTGCCCCAGCTGGATTCAATTCTAAAATGTAATGATAAGAAGT TCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTACAGTACACATGGGATTAGGCCA GTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGAGAATAATTAGATC TGAAAATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTACCTTA ATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAGCAC TCTTTAGAAAGAATAGTTGGAGATATAAGACAAGCATATTGTAGCATTAGTGGAATGGGA TGGAATAAAACTTCAGCAGGTAGCTGACAAATTAAGAAACCTTCTTAATAAAACAACAAT AATTTTTAAACCACCCGCGGGGGGACCTAGAAATTACAACACACAGCTTTAATTGTGGAG GGGAATTTTTCTACTGCAACACATCAAGAGTTTAATAATAGTGAATGGAAATCAAATAGT AGTACAGGGGGAAATGAAAGTATAATCATACTCCCATAGAATAAAACAAATTATAAACAT GTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAAGGACATCAATTGTTCAT CAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAACTAATCAGAGTGAATGAG ACCTTCAGACCTGGGGGAGGAGAC >gi|66864572|gb|DQ027784.1| HIV-1 isolate QA013_987M_C4 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCACTGAATGGACGAATAATAGTAGCACTAACGCCACTGA TCAGGACATGAATGAGAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTAATACTAGC TATAGATTAATAAATTGTAATACCTGCCATTACACAGGCATGTCCAAAGGTAACCTTTGA GCCAATTCCCATACATTATTGTGCCCCAGCTGGTTGCAATTCTAAAATGTAATGATAAGA AATTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTAGTGTACACATGGGATTAGG CCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGATAATAATTAG ATCTGAAAATCTAGCAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTCAA TTCATTGCACAAGACCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAG CACTGTACAGAAAAAATAGTTGGAGATATAAGACAAGCATATTGTAGCATTAGTGGACTG GGATGGAATAAAACTACAGCAGGTAGCTGACAAATTAAGAAACCTTCTCAATACAACAAC AATAATTTTTAAACCACCCGCGAGGGGACCTAGAAATTACAACACACAGCTTTAATTGTG GAGGGGAATTTTTCTACTGCAACACATCAACTGTTTAATAATAGTGAATGGAAATCAAAT AGTAGTACAGGGGGAAATGAAAGTATAATCAAACTCCTGCAGAATAAAACAAATTATAAA CATGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAGACACATCAGTTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAGCTAATCAGTTCGAAT GAGACCTTCAGACCTGGGGGAGGAGAC >gi|66864570|gb|DQ027783.1| HIV-1 isolate QA013_559M_C11 from Kenya envelope glycoprotein (env) gene, partial cds ACTCTGTGTCACTTTAAACTGCACTGAATGGAAGAATAATAGTAGCACTAACGGCACTGA TCAGGACATGAATGAGAAACTGCTCTTTCAATATAACCACAGAAGTAAGAGATAAGAAGA AGCAAGTACAGGCACTTTTATAAACTTGATGTAGTACAGATAGATAATAGTAGTACTAGC TATAGATTAATAAATTGTAATACCTGCCATTACACAGGCATGTCCAAAGGTAACCTTTGA GCCAATTCCTATACATTATTGTGCCCCAGCTGGTTGCAATTCTAAAATGTAATGATAAGA AATTCAATGGGACGGGTCCATGCAAAAACGTCAGCACAGTAGTGTACACATGGGATTAGG CCAGTAGTGTCAACTCAGCTGTTGTTGAATGGCAGTCTAGCAGAAGAAGATAATAATTAG ATCTGAAGATCTAACAAATAATGCAAAAATTATAATAGTACAGCTTAATGAGTCTGTCAA TTAATTGCACAAGGCCCTACAACAATACAAGAAAAGGTGAACATATGGGACCAGGGCGAG CACTCTACAGAAAAAATAGTTGGAGATATAAGACAAGCATATTGTAGCATTAGTGGAATG GGATGGAATAAAATTACAGCAGGTAGCTGACAAATTAAGAAACCTTCTTAATAAAACAAC AATAATTTTTAAACCACCCGCGAGGGGACCTAGAAATTACAACACACAGCTTTAATTGTA GAGGGGAATTTTTCTACTGCAACACATCAACTGTTTAATAATAGTGAATGGAAATCAAAT AGTAGTACAGGGGGAAATGAAAGTATAATCATACTCCTGCAGAATAAAACAAATTATAAA CATGTGGCAGGGAGTAGGAAAAGCAATGTATGCCCCTCCCATTGAGACACATCAGTTGTT CATCAAATATTACAGGACTATTGTTGACAAGAGATGGTGGTGTAACTAATTCGTGAGACC TTCAGACCTGGGGGAGGAGAC >hxb2 TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACA CACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCAC TGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCA ACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGG AGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAG AGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCG CTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT CCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGA GCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCT TGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTC AGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAG CGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGG CAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGA AGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAA AAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCA AGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGT AGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCA TTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACC AAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAA GCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAAC ATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAA GTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAA GGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCC ATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCA GTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCA GGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCA GTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTAT AGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTA GACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATG ACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTG GGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGC CATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATG ATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAA GAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGA AAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC TGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCC CCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAG CCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCC TCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATG ATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAA TTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATA AAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGT TGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAA AATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAA TAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTG GGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAAT GGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTC AATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATG TGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTA CCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCAC AGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTT TTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGAT CTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGA GGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGG GTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACA GCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTT ACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAG AAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAA AAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGA AGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAA CAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGG CAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAAC TGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGA TTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGA AAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTA AATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTG ACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGAT TAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAG ATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGG TCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT TAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATG AACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTG TAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGC ATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAA AAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAG CAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAA AAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTT GGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAG TAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAAC ATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGA TTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTA AAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCA GAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAA TACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATT ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACA TGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTAT AGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGG GATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCAT TTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCT GAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATA AGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAAC AAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAG CCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACC AAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGA ATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATG AAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGC TGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGG AGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCA GCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTG TTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAG AGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGT AACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAAT AGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGA CAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGA AATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGA TGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGA AGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTAC ATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTAT TGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATG AGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCT GTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGA GAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAA GAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATA ATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTC CAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTC TAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTAC AATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAG CAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAG TACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAA GAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATA TGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAG CTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAG GAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTA ATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAA ATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACA TGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTT CATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCG AGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAAT ATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGG TGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAG CAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGT CTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGT TGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGAT ACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCA CTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACA CGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAA TTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAAT GGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCA TAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGA ATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGG GACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCA TTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCT TCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGG GACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGG AACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGA CAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAA GAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGT AGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGAT AGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACA GCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTT CCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGC CACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGAT ATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACA CCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTT GAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTG AGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGC CTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACAT CGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGG ACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGG GTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACT GCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTG TGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA >gi|66864561|gb|DQ027778.1| HIV-1 isolate QA013_2282M_A10 from Kenya nonfunctional envelope glycoprotein (env) gene, partial sequence TCTCTGCGTTACCTTAGATTGTCATCATAATGTCACCACTGTCACCACTAACAATACCAA TGACACTGTATATCACCAATGCCACTATCACCAATGCCAATATCACCAAGGACGATGCCG ACATGAGAAACTGCTCTTAATGTGACCACAGTAATAAGGGATAAGCAACAGAAAGTATAC TCACTTTTTTATAGACTTGATCTAGCCAACTGAAAGTAATGATAGTTATAGTTATAGATT AATAAATTGTAACACCTCCGTCATTAAACAGGCGTCCAAAAGTAACCTTTGAGCCAATTC CCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTAAAGATAAGAAGTTCAAT GGAACAGGGCCATGCAGGAATGTCAGCACAGTACAATGCACACATGGGAAAGCCAGTAGT ATCAACTCAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTAAGAATTAGATCAAA ATATCACAAACAATGCCAAAAACATATTAGTACAATTGACCACACCTGTAAGAATTAATT GTACCACCTAACAACAATACAAGAAAAAGTGTACATATAGGACCAGGACAAGCATTCTAT GCAACAGGAGGAAATAGGAAATATAAGACAAGCATATTGTAATGTTAGTAAAACACAATG GAATACAGCTTTGCAAAAGGTCTAACAAATTAGAAGCATACTTTAACAAAACAATTAACA AAACAATAATCTTTACTCACTCATCAGGAGGATACAGAAATTACAACACATAGTTTTAAT TGTGGAGGAGAGTTTTTCTATTGTAATACATCAGGCCTTTAATAGCACTTAGGACAACGA TACCAACACACAGGAATCAAATGACACTATAATGATCCCATGCAGTAAAGCAAATTATAA ACATGTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAAAGGTGT GACTCAAATATTACAGGACTAATATTAACAAGAGATGGTAAGAATAATTCTAATAACAGT GACCTTCAGACCTAGAGGAGGAGAT >gi|66864559|gb|DQ027777.1| HIV-1 isolate QA013_1790M_C1 from Kenya envelope glycoprotein (env) gene, partial cds TCTCTGCGTTACCTTAGATTGTCATCATAATGTCACCACTGTCACCACTAACAATACCAA TGACACTGCATATCACCAATGCCAATATCACCAATGACAAGGCCGACATGAAAAACTGCT CTTACAATGTGACCACAAATAAGGGATAAGCAACAGAAAGTATACTCACTTTTTTATAGA CTTGATCTAGTACCAACTGAAAGTAGATAGTTATAGATTAATAAATTGTAACACCTCCGT CATTAAACAGGCTTGTCCAAAAGTAACCTTTGACAATTCCCATACATTATTGTGCCCCAG CTAGTTTTGCGATTCTAAAGTGTAAAGATAAGGAGTTCAATAACAGGGCCATGCAAGAAT GTCAGCACAGTACAATGCACACATGGGATCAAGCCAGTAGTATCAACTCCTGCTGTTAAA TGGCAGCCTAGCAGAAGGAGAGGTAAGAATTAGATCTGAAAATATCACAAACAATGCAAA ACATAATAGTACAATTGCCCACACCTATAACAATTACTTGTACCAGACCCAACAACAATA CAAGAAAGTGTACATATAGGACCAGGACAAGCATTCTATGCAACAGGTGCAATAATAGGG GATATAAGACGAGCATTGTAATGTTAATAAAACACAATGGAATACAGCTTTGCAAAAGGT AGCTAACAAATTAAAAACATATTAACAAAACAATAATCTTTACTCACTCATCAGGAGGGG ATATAGAAATTACAACACATAGTTTTAATTAGAGGAGAGTTTTTCTATTGTAATACATCA GGCCTGTTTAATAGCACTTGGGTAAACAATACCAACACAGGGGACAACTAACACAGAATC AAATGACAATATAACGATCCCATGCAGAATAAAGCAAATTATAAATGTGGCAGAGAACAG GACAAGCAATATATGCCCCTCCCATACAAGGAATAATAAGGTGTGAATCAAATTACAGGA CTAATATTAACAAAAGATAGTAAGAATAATGCTAATAGAACTGAAACCTTCAGACCTAGA GAGAGAT >gi|66864557|gb|DQ027776.1| HIV-1 isolate QA013_987M_B12 from Kenya envelope glycoprotein (env) gene, partial cds TCTCTGCGTTACTTTAGATTGTCATAATGTCACCAATGACACTGCCAGTATCATGAAAAA CTGCTCTTAATGTGACCACAGTAATAAGGGATAAGCAACAGAAAGTATACTCACTTTTTT ATAGACTTGATATAGTAAACTGAAAGTAATACTAGTTATAGATTAATAAATTGTAACACC TCCGTCATTAAACAGGCTTGTCCAAGTAACCTTTGAGCCAATTCCCATACATTATTGTGC CCCAGCTGGTTTTGCGATTCTAAAGTGTAAAGAAGGAGTTCAATGGAACAGGGCCATGCA AGAATGTCAGCACAGTACAATGCACACATGGGATCAAGCCAAGTATCAACTCAGCTGCTG TTAAATGGCAGCCTAGCAGAAGGAGAGGTAAGAATTAGATCTGAAAATAACAAACAATGC CAAAAACCTAATAGTACAATTGACCACACCTATAAAAATTAATTGTACTAGACCTAAACA ATACAAGAAAAAGCGTACATATAGGACCAGGACAAGCATTCTATGCAACAGGTGAAATAA TAGGGTATAAGACAAGCACATTGTAATGTTAATAAAACACAATGGGATAAAACTTTGCAA GAGGTAGCTAACATTAAAAACATACTTTAACAAAACAATAATCTTTACTCACTCATCAGG AGGGGATATAGAAATTACAACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATA CATCAAGCCTGTTTAATAGCACTTGGGGACAATACCAACACACAGGAGTCAAATAGCACA GAATCAAATGAAACTATAACGATCCCATGCAGAATAACAAATTATAAATATGTGGCAGAG AACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAATAAGGTGAATCAAATATTA CAGGACTAATATTAACAAGAGATGGTGGGAATGATTCTAGGGAAAATGAAACCCAGACCT GGAGGAGGAGAT >gi|66864555|gb|DQ027775.1| HIV-1 isolate QA013_765M_B1 from Kenya envelope glycoprotein (env) gene, partial cds TCTCTGCGTTACTTTAGATTGTCATAATGTCACCAATGACAATGCCAATATCATGAAAAA CTGCTCTTAATGTGACCACAGTAATAAGGGATAAGCAACAGAAAGTATACTCACTTTTTT ATAGACTTGATATAGTAAACTGAAAGTAATACTAGTTATAGATTAATAAATTGTAACACC TCCGTCATTAAACAGGCTTGTCCAAGTAACCTTTGAGCCAATTCCCATACATTATTGTGC CCCAGCTGGTTTTGCGACTCTAAAGTGTAAAGAAGGAGTTCAATGGAACAGGGCCATGCA AGAATGTCAGCACAGTACAATGCGCACATGGGATCAAGCCAAGTATCAACTCAGCTGCTG TTAAATGGCAGCCTAGCAGAAGGAGAGGTAAGAATTAGATCTGAAAATAACAAACAATGC CAAAAACCTAATAGTACAATTGACCACACCTATAAAAATTAATTGTACCAGACCTAAACA ATACAAGAAAAAGTGTACATATAGGACCAGGACAAGCATTCTATGCAACAGGTGAAATAA TAGGGTATAAGACAAGCACATTGTAATGTTAGTGAAACACAATGGCATAAAACTTTGCAA GAGGTAGCTAACATTAAAAACATACTTTAACAAAACAATAATCTTTGATCACTCATCAGG AGGGGATATAGAAATTACAACATAGTTTTAATTGTGGAGGAGAGTTTTTCTATTGTAATA CATCAGGCCTGTTTAATAGCACTTGGGAACGATGCCAGCACACAGGAGTCAAATAACACA GAATCAAATACCACTATAACGATCCCATGCAGAATAACAAGTTATAAATATGTGGCAGAG AACAGGACAAGCAATATATGCCCCTCCCATACAAGGAATAATAAGGTGAATCAAATATTA CAGGACTAATATTAACAAGAGATGGTGGGGATAATTCTAGGGAAAATGAAACCCAGACCT GGAGGAGGAGAT >gi|66864553|gb|DQ027774.1| HIV-1 isolate QA013_559M_A1 from Kenya envelope glycoprotein (env) gene, partial cds TCTCTGCGTTACTTTAGATTGTCATAATGTCACCACTGACAATGCCAATATCACCACCGA CATGAAAAAGCTCTTACAATGTGACCACAGTAATAAGGGATAAGCAACAGAAAGTATACT CACTTTTTTATAGACTTTATAGTACCAACTGAAAGTAATACTAGTTATAGATTAATAAAT TGTAACACCTCCGTCATTAAACAGGTGTCCAAAGGTAACCTTTGAGCCAATTCCCATACA TTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTAAAGATAAGGAGTTCAATGGAACAG GGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGGCAAGCCAGTAGTATCAACT CAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTAAGAATTAGATGAAAATATCAC AAACAATGCCAAAAACATAATAGTACAATTGACCACACCTATAAAAATTAATTGTATGAC CTAACAACAATACAAGAAAAAGTGTACATATAGGACCAGGACAAGCATTCTATGCAACAG GTGAAAATAGGGGATATAAGACAAGCACATTGTAATGTTAGTAAAACACAATGGCATAAA ACTTTGCAAGAGGGCTAACAAATTAAAAACATACTTTAACAAAACAATAATCTTTAATCA CTCATCAGGAGGGGATATAGATTACAACACATAGTTTTAATTGTGGAGGAGAGTTTTTCT ATTGTAATACATCAGGCCTGTTTAATAGCTTGGGGAAACCATGCCAGCATACAGGAGTCC AATAACACAGAATCAAATGACAATATAACGATCCCATAGAATAAAGCAAATTATAAATAT GTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGGTAATAAGGTGTGAAT CAAATATTACAGGACTAATATTAACAAGAGATGGTGGGGATAATCCTAGGGAATGAAACC TTCAGACAAAATGAAACCTTCAGACCTGGAGGAGGAGAT >gi|66864614|gb|DQ027773.1| HIV-1 isolate QA013_385M_B5 from Kenya envelope glycoprotein (env) gene, partial cds TCTCTGCGTTACTTTAGATTGTCATAATGTCACCAATGACAATGCCAATATCACCACCGA CATGAAAAAGCTCTTACAATGTGACCACAGTAATAAGGGATAAGCAACAGAAAGTATACT CACTTTTTTATAGACTTTATAGTACCAACTGAAAGTAATACTAGTTATAGATTAATAAAT TGTAACACCTCCGTCATTAAACAGGTGTCCAAAGGTAACCTTTGAGCCAATTCCCATACA TTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTAAAGATAAGGAGTTCAATGGAACAG GGCCATGCAAGAATGTCAGCACAGTACAATGCACACATGGGCAAGCCAGTAGTATCAACT CAGCTGCTGTTAAATGGCAGCCTAGCAGAAGGAGAGGTAAGAATTAGATGAAAATATCAC AAACAATGCCAAAAACATAATAGTACAATTGACCACACCTATAAAAATTAATTGTATGAC CTAACAACAATACAAGAAAAAGTGTACATATAGGACCAGGACAAGCATTCTATGCAACAG GTGAAAATAGGGGATATAAGACAAGCACATTGTAATGTTAGTAAAACACAATGGAATAAA ACTTTGCAAGAGGGCTAACAAATTAAAAACATACTTTAACAAAACAATAATCTTTAATCA CTCATCAGGAGGGGATATAGATTACAATACATAGTTTTAATTGTGGAGGAGAGTTTTTCT ATTGTAATACATCAGGCCTGTTTAATAGCTTGGGGAAACAATGCCAGCACACAGGAGTCA AATAACACAGAATCAAATGACACTATAACGATCCCATAGAATAAAGCAAATTATAAATAT GTGGCAGAGAACAGGACAAGCAATATATGCCCCTCCCATACAAGATAATAAGGTGTGAAT CAAATATTACAGGACTAATATTAACAAGAGATGGTGGGGATAATCCTAGGGAATGAAACC TTCAGACAAAATGAAACCTTCAGACCTGGAGGAGGAGAT seqmagick-0.8.4/examples/wrapped.fasta000066400000000000000000000006031376401056300177730ustar00rootroot00000000000000>SEQUENCE_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH seqmagick-0.8.4/examples/wrapped.phy000066400000000000000000000030471376401056300175020ustar00rootroot00000000000000 3 384 CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- --------SQ ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG ALGRTRHALR CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK---- --------FH FLEFQDKFNK KY-SHEEYLE RFEIFKSNLG KIEELNLIAI NHKADTKFGV NKFADLSSDE FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN---- RKGLPYRLGI NRFSDMSWEE FKSWMSKHRK TY-STEEYHH RLQTFASNWR KINAHN---- NGNHTFKMAL NQFSDMSFAE FKNYYLNNKE AIFTDDLPVA DYLDDEFINS IPTAFDWRTR G-AVTPVKNQ GQCGSCWSFS FQATRL-GAA QTCSATLAGN HLMRDA--AA LPETKDWRED G-IVSPVKNQ AHCGSCWTFS IKHKYLWSEP QNCSAT--KS NYLRGT--GP YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS TTGNVEGQHF ISQNKLVSLS EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG TTGALEAAYT QATGKNISLS EQQLVDCAGG FNNF------ --GCNGGLPS QAFEYIKYNG TTGALESAIA IATGKMLSLA EQQLVDCAQD FNNY------ --GCQGGLPS QAFEYILYNK GIQTESSYPY TAETGTQCNF NSANIGAKIS NFTMIP-KNE TVMAGYIVST GPLAIAADAV GIDTEESYPY KGVNGV-CHY KAENAAVQVL DSVNITLNAE DELKNAVGLV RPVSVAFQVI GIMGEDTYPY QGKDGY-CKF QPGKAIGFVK DVANITIYDE EAMVEAVALY NPVSFAFEVT E-WQFYIGGV F-DIPCN--P NSLDHGILIV GYSAKNTIFR KNMPYWIVKN SWGADWGEQG DGFRQYKSGV YTSDHCGTTP DDVNHAVLAV GYGVENGV-- ---PYWLIKN SWGADWGDNG QDFMMYRTGI YSSTSCHKTP DKVNHAVLAV GYGEKNGI-- ---PYWIVKN SWGPQWGMNG YIYLRRGKNT CGVSNFVSTS II-- YFKMEMGKNM CAIATCASYP VVAA YFLIERGKNM CGLAACASYP IPLV seqmagick-0.8.4/logo/000077500000000000000000000000001376401056300144345ustar00rootroot00000000000000seqmagick-0.8.4/logo/seqmagick_logo.png000066400000000000000000001610431376401056300201330ustar00rootroot00000000000000PNG  IHDRM9 pHYs   OiCCPPhotoshop ICC profilexڝSgTS=BKKoR RB&*! 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TEXTBatggtgcaaccatgctccccaggactgccgcctgggaagagtgtgccacagcttgcgggatgg_0areddoub?agrndoub?abludoub?dreddoub?dgrndoub?dbludoub?sreddoubsgrndoubsbludoubereddoubegrndoubebludoubshindoubshi2doubTrnsdoubrefldoubselflongshadlongtwosboolwirebooldeclboolwfszdoubRfAcdoub?mtIDTEXT%59fdc555-5f3e-11e0-b89c-fc19dda005d7maplVlLs Objcmapo TypelongNm tdtaCatggtgcaaccatgctccccaggactgccgcctgggaagagtgtgccacagcttgcgggatgg.psdsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo TypelongNm tdtaCatggtgcaaccatgctccccaggactgccgcctgggaagagtgtgccacagcttgcgggatgg.psdsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelong srghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelong srghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelong srghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelong srghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelong srghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm doub?AngldoubflaglongmstyboolIdntlongObjcmapo Typelongsrghdoub?uscldoub?vscldoub?uoffdoubvoffdoubMnm doubMxm 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doubkey3DCrossSectionOffsetdoubkey3DCrossSectionPlaneTilt1doubkey3DCrossSectionPlaneTilt2doubkey3DCrossSectionPlaneOpacitydoub?key3DCrossSectionAlignmentlongkey3DCrossSectionEnabledboolkey3DCrossSectionPlaneFlipboolkey3DCrossSectionPlaneVisiblebool$key3DCrossSectionIntersectionVisibleboolkey3DRenderSettingsObjckey3DRenderSettings key3DRenderFacesboolkey3DRenderFaceStylelongkey3DFaceColorObjckey3DFaceColorRd doub?Grn doub?Bl doub?key3DTextureTypelongkey3DRenderAntiAliaslongkey3DRenderReflectionsboolkey3DRenderRefractionsboolkey3DRenderShadowsboolkey3DRenderRemoveBackfacesboolkey3DRenderAdvancedIllumVideoboolkey3DRenderEdgesboolkey3DRenderEdgeStylelongkey3DLineColorObjckey3DLineColorRd doubGrn doubBl doubkey3DLineWidthdoub?key3DCreaseValuedoubkey3DRenderRemoveBackfaceLinesboolkey3DRenderRemoveHiddenLinesboolkey3DRenderVerticesboolkey3DRenderVerticesStylelongkey3DVertexColorObjckey3DVertexColorRd doubGrn doubBl 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˝ܻ ۻ ʻ ʻƜ ɻ̻ Ҝٻ Żʜ ɻŻڻʻȻ   »ѻ λû  ӻ  ջĻǻ ¿ ۻȻڻѻлջ»ª ˻˻֜ͻȻػª Żѻ Ż ˻ǻ ػĜػĻ Իʻλ ſ Żѻ ܻŪͻŻĜϿƻ ǻ »λȻ ǹջԻ ɻշͻ˻ջƻĴѻճ̻ Ǵ ͻͻ»ij   ϻȲ ȻȻҿ˻ĻǜȻ  ڻĻŻȻĻŻһ˻ʻʻ ǻǻĻ ǜ ˻վ ǜ޻ƻȻ Ƞֻڜ Ļ ѻ ڻ  һû޿ ջ Ȳ Ż˘ »ĻƻĪ˻ʻػ۾Ļʿššƙ *]az_[t_CUJbU][aXukU@P"* ֜ӯت׿û µһ˜   ˝ܻ ۻ ʻ ʻƜ ɻ̻ Ҝٻ Żʜ ɻŻڻʻȻ   »ѻ λû  ӻ  ջĻǻ ¿ ۻȻڻѻлջ»ª ˻˻֜ͻȻػª Żѻ Ż ˻ǻ ػĜػĻ Իʻλ ſ Żѻ ܻŪͻŻĜϿƻ ǻ »λȻ ǹջԻ ɻշͻ˻ջƻĴѻճ̻ Ǵ ͻͻ»ij   ϻȲ ȻȻҿ˻ĻǜȻ  ڻĻŻȻĻŻһ˻ʻʻ ǻǻĻ ǜ ˻վ ǜ޻ƻȻ Ƞֻڜ Ļ ѻ ڻ  һû޿ ջ Ȳ Ż˘ »ĻƻĪ˻ʻػ۾Ļʿššƙ *]az_[t_CUJbU][aXukU@P"* ֜ӯت׿û µһ˜   ˝ܻ ۻ ʻ ʻƜ ɻ̻ Ҝٻ Żʜ ɻŻڻʻȻ   »ѻ λû  ӻ  ջĻǻ ¿ ۻȻڻѻлջ»ª ˻˻֜ͻȻػª Żѻ Ż ˻ǻ ػĜػĻ Իʻλ ſ Żѻ ܻŪͻŻĜϿƻ ǻ »λȻ ǹջԻ ɻշͻ˻ջƻĴѻճ̻ Ǵ ͻͻ»ij   ϻȲ ȻȻҿ˻ĻǜȻ  ڻĻŻȻĻŻһ˻ʻʻ ǻǻĻ ǜ ˻վ ǜ޻ƻȻ Ƞֻڜ Ļ ѻ ڻ  һû޿ ջ Ȳ Ż˘ »ĻƻĪ˻ʻػ۾Ļʿššƙ 8BIMPatt8BIMTxt2Zp /DocumentResources << /FontSet << /Resources [ << /Resource << /StreamTag /CoolTypeFont /Identifier << /Name (Calibri-Bold) /Type 1 >> >> >> << /Resource << /StreamTag /CoolTypeFont /Identifier << /Name (MyriadPro-Regular) /Type 0 >> >> >> << /Resource << /StreamTag /CoolTypeFont /Identifier << /Name (AdobeInvisFont) /Type 0 >> >> >> << /Resource << /StreamTag /CoolTypeFont /Identifier << /Name (TimesNewRomanPSMT) /Type 1 >> >> >> ] >> /MojiKumiCodeToClassSet << /Resources [ << /Resource << /Name () >> >> ] /DisplayList [ << /Resource 0 >> ] >> /MojiKumiTableSet << /Resources [ << /Resource << /Name (Photoshop6MojiKumiSet4) /Members << /CodeToClass 0 /PredefinedTag 2 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet3) /Members << /CodeToClass 0 /PredefinedTag 4 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet2) /Members << /CodeToClass 0 /PredefinedTag 3 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet1) /Members << /CodeToClass 0 /PredefinedTag 1 >> >> >> << /Resource << /Name (YakumonoHankaku) /Members << /CodeToClass 0 /PredefinedTag 1 >> >> >> << /Resource << /Name (GyomatsuYakumonoHankaku) /Members << /CodeToClass 0 /PredefinedTag 3 >> >> >> << /Resource << /Name (GyomatsuYakumonoZenkaku) /Members << /CodeToClass 0 /PredefinedTag 4 >> >> >> << /Resource << /Name (YakumonoZenkaku) /Members << /CodeToClass 0 /PredefinedTag 2 >> >> >> ] /DisplayList [ << /Resource 0 >> << /Resource 1 >> << /Resource 2 >> << /Resource 3 >> << /Resource 4 >> << /Resource 5 >> << /Resource 6 >> << /Resource 7 >> ] >> /KinsokuSet << /Resources [ << /Resource << /Name (None) /Data << /NoStart () /NoEnd () /Keep () /Hanging () /PredefinedTag 0 >> >> >> << /Resource << /Name (PhotoshopKinsokuHard) /Data << /NoStart (!\),.:;?]}    0!! 0000 0 0 0000A0C0E0G0I0c000000000000000000000000 =]) /NoEnd (\([{  00 0 0000 ;[) /Keep (  % &) /Hanging (00 ) /PredefinedTag 1 >> >> >> << /Resource << /Name (PhotoshopKinsokuSoft) /Data << /NoStart (  0000 0 0 00000000 =]) /NoEnd (  00 0 000;[) /Keep (  % &) /Hanging (00 ) /PredefinedTag 2 >> >> >> << /Resource << /Name (Hard) /Data << /NoStart (!\),.:;?]}    0!! 0000 0 0 0000A0C0E0G0I0c000000000000000000000000 =]) /NoEnd (\([{  00 0 0000 ;[) /Keep (  % &) /Hanging (00 ) /PredefinedTag 1 >> >> >> << /Resource << /Name (Soft) /Data << /NoStart (  0000 0 0 00000000 =]) /NoEnd (  00 0 000;[) /Keep (  % &) /Hanging (00 ) /PredefinedTag 2 >> >> >> ] /DisplayList [ << /Resource 0 >> << /Resource 1 >> << /Resource 2 >> << /Resource 3 >> << /Resource 4 >> ] >> /StyleSheetSet << /Resources [ << /Resource << /Name (Normal RGB) /Features << /Font 1 /FontSize 12.0 /FauxBold false /FauxItalic false /AutoLeading true /Leading 0.0 /HorizontalScale 1.0 /VerticalScale 1.0 /Tracking 0 /BaselineShift 0.0 /CharacterRotation 0.0 /AutoKern 1 /FontCaps 0 /FontBaseline 0 /FontOTPosition 0 /StrikethroughPosition 0 /UnderlinePosition 0 /UnderlineOffset 0.0 /Ligatures true /DiscretionaryLigatures false /ContextualLigatures false /AlternateLigatures false /OldStyle false /Fractions false /Ordinals false /Swash false /Titling false /ConnectionForms false /StylisticAlternates false /Ornaments false /FigureStyle 0 /ProportionalMetrics false /Kana false /Italics false /Ruby false /BaselineDirection 2 /Tsume 0.0 /StyleRunAlignment 2 /Language 0 /JapaneseAlternateFeature 0 /EnableWariChu false /WariChuLineCount 2 /WariChuLineGap 0 /WariChuSubLineAmount << /WariChuSubLineScale .5 >> /WariChuWidowAmount 2 /WariChuOrphanAmount 2 /WariChuJustification 7 /TCYUpDownAdjustment 0 /TCYLeftRightAdjustment 0 /LeftAki -1.0 /RightAki -1.0 /JiDori 0 /NoBreak false /FillColor << /StreamTag /SimplePaint /Color << /Type 1 /Values [ 1.0 0.0 0.0 0.0 ] >> >> /StrokeColor << /StreamTag /SimplePaint /Color << /Type 1 /Values [ 1.0 0.0 0.0 0.0 ] >> >> /Blend << /StreamTag /SimpleBlender >> /FillFlag true /StrokeFlag false /FillFirst true /FillOverPrint false /StrokeOverPrint false /LineCap 0 /LineJoin 0 /LineWidth 1.0 /MiterLimit 4.0 /LineDashOffset 0.0 /LineDashArray [ ] /Type1EncodingNames [ ] /Kashidas 0 /DirOverride 0 /DigitSet 0 /DiacVPos 4 /DiacXOffset 0.0 /DiacYOffset 0.0 /OverlapSwash false /JustificationAlternates false /StretchedAlternates false /FillVisibleFlag true /StrokeVisibleFlag true /FillBackgroundColor << /StreamTag /SimplePaint /Color << /Type 1 /Values [ 1.0 1.0 1.0 0.0 ] >> >> /FillBackgroundFlag false /UnderlineStyle 0 /DashedUnderlineGapLength 3.0 /DashedUnderlineDashLength 3.0 /SlashedZero false /StylisticSets 0 /CustomFeature << /StreamTag /SimpleCustomFeature >> >> >> >> ] /DisplayList [ << /Resource 0 >> ] >> /ParagraphSheetSet << /Resources [ << /Resource << /Name (Normal RGB) /Features << /Justification 0 /FirstLineIndent 0.0 /StartIndent 0.0 /EndIndent 0.0 /SpaceBefore 0.0 /SpaceAfter 0.0 /DropCaps 1 /AutoLeading 1.2 /LeadingType 0 /AutoHyphenate true /HyphenatedWordSize 6 /PreHyphen 2 /PostHyphen 2 /ConsecutiveHyphens 0 /Zone 36.0 /HyphenateCapitalized true /HyphenationPreference .5 /WordSpacing [ .8 1.0 1.33 ] /LetterSpacing [ 0.0 0.0 0.0 ] /GlyphSpacing [ 1.0 1.0 1.0 ] /SingleWordJustification 6 /Hanging false /AutoTCY 0 /KeepTogether true /BurasagariType 0 /KinsokuOrder 0 /Kinsoku /nil /KurikaeshiMojiShori false /MojiKumiTable /nil /EveryLineComposer false /TabStops << >> /DefaultTabWidth 36.0 /DefaultStyle << >> /ParagraphDirection 0 /JustificationMethod 0 /ComposerEngine 0 /ListStyle /nil /ListTier 0 /ListSkip false /ListOffset 0 >> >> >> ] /DisplayList [ << /Resource 0 >> ] >> /TextFrameSet << /Resources [ << /Resource << /Bezier << /Points [ 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ] >> /Data << /Type 0 /LineOrientation 0 /TextOnPathTRange [ -1.0 -1.0 ] /RowGutter 0.0 /ColumnGutter 0.0 /FirstBaselineAlignment << /Flag 1 /Min 0.0 >> /PathData << /Spacing -1 >> >> >> >> ] >> /ListStyleSet << /Resources [ << /Resource << /Name (kPredefinedNumericListStyleTag) /PredefinedTag 1 >> >> << /Resource << /Name (kPredefinedUppercaseAlphaListStyleTag) /PredefinedTag 2 >> >> << /Resource << /Name (kPredefinedLowercaseAlphaListStyleTag) /PredefinedTag 3 >> >> << /Resource << /Name (kPredefinedUppercaseRomanNumListStyleTag) /PredefinedTag 4 >> >> << /Resource << /Name (kPredefinedLowercaseRomanNumListStyleTag) /PredefinedTag 5 >> >> << /Resource << /Name (kPredefinedBulletListStyleTag) /PredefinedTag 6 >> >> ] /DisplayList [ << /Resource 0 >> << /Resource 1 >> << /Resource 2 >> << /Resource 3 >> << /Resource 4 >> << /Resource 5 >> ] >> >> /DocumentObjects << /DocumentSettings << /HiddenGlyphFont << /AlternateGlyphFont 2 /WhitespaceCharacterMapping [ << /WhitespaceCharacter ( ) /AlternateCharacter (1) >> << /WhitespaceCharacter ( ) /AlternateCharacter (6) >> << /WhitespaceCharacter ( ) /AlternateCharacter (0) >> << /WhitespaceCharacter ( \)) /AlternateCharacter (5) >> << /WhitespaceCharacter () /AlternateCharacter (5) >> << /WhitespaceCharacter (0) /AlternateCharacter (1) >> << /WhitespaceCharacter () /AlternateCharacter (3) >> ] >> /NormalStyleSheet 0 /NormalParagraphSheet 0 /SuperscriptSize .583 /SuperscriptPosition .333 /SubscriptSize .583 /SubscriptPosition .333 /SmallCapSize .7 /UseSmartQuotes true /SmartQuoteSets [ << /Language 0 /OpenDoubleQuote ( ) /CloseDoubleQuote ( ) /OpenSingleQuote ( ) /CloseSingleQuote ( ) >> << /Language 1 /OpenDoubleQuote ( ) 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*kjkkkkkkkkkkkkkkkkkkkkkkkkkjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjiiihhhhhhhhhiiiiiihhhgggghhhijihgd`\WSPMLJJJKLMOQSTVWWXXXWVUSRQOOPQRTVX[]`ceghjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjkkkkkkkkkkkkkkkkkkjj *kjkkkkkkkkkkkkkkkkkjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjihfda^\ZXWWVVWWXYZ[\\]]^^^]]\[[ZZZ[\]^`acdfghijjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjkkji )kjkjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjihgfecbaa`````````aabbbbbbbaaaaabcceefghhijjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjR jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjihhhggggfffffffffffgggggggggghhhiijjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjP" jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj배jjjjjjjjjjjjjjjjjjjjjjjjjjjjjðjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjͰtjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtᰦjjjjjjjjjjjjjjjj~װjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtðtjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjᰰtjjjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjjjjjjjjjjjjjjjj~jjjjjjjjjjjjjj͝rhjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjÒjjjjjjjjjjjjjjjjjjjjjjj͜jjjjjjjjjjjjjjjjjjjjjjjjjj~jjjjjjtjjjjjjjjjjjtjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjjjjjjjjjjjjjtjjjjjjjjjjj͝rhjjjjjjjjjjjj~æjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj~jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjjjj~jjjjjjjjjjjjjjjjjjjjjjj~jjjjjjjjjjjjjjjjjjjj~jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjjjjjjjjjjjt~jjjjjjjjj͝rhjjjjjjjjjjj{jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjj~ʏjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjjjjjjjjjjjjjjjjjjʼnjjjjjjjjjjR" jjjjjjjjjjjjjjjjjjjjjjjj͝rhjjjjjjjjjjt갈ojjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtٴrjjjjjjjjjjjjjjjtjjjjjjjjjjjjjjjjjj~˝xjjjjjjjjjjݽjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjƗvjjjjjjjjjjR" 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jjjjjjjjjv@VjjjjjjjjjjjjjjjjjjjjjjjjjjjЪjjԤd@@_jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjњg\jjjjjjjjjjjjjjjjѪpjjjjjjjw@Vjjjjjjjjjjjjjjjצzfjjjjjjjjjjן\FgjjjjjjjjjjjjjˏKNjjjjjjjjjjjjjj㶌mjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjק}ijjjjjjjjjƚrjjjjjjjjjjjjj~䴇ejjjjjjjjjjjjjjjR" jjjjjjjjjާh@gjjjjjjjjjjjjjjjjjjjjjjjjjjjּjtڬk@@\jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjjjjjjjjjjjjjjjjjjjjjjjjӨtjjjjjjjjjjjjjjjjӪpjjjjjjjߧh@djjjjjjjjjjjjjjjjצzfjjjjjjjjjjϕYYjjjjjjjjjjjjjj†Kdjjjjjjjjjjjjjj㵉ijjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjק{gjjjjjjjjjӭnjjjjjjjjjjjjݪyYjjjjjjjjjjjjjjjR" jjjjjjjjt՛`Hjjjjjjjjjjjjjjjjjjjjjjjjjjjjަj@@VjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj~jjjjjjjjjjjjjjjjԪnjjjjjj~՛aHjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj̕`\jjjjjjjjjjjjjj쿆Tejjjjjjjjjjjjjj㴇gjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjקzfjjjjjjjjjŪ}jjjjjjjjjjjjԛhPjjjjjjjjjjjjjjjR" jjjjjjjjΔ_Vjjjjjjjjjjjjjjjjjjjjjjjjjjjj߭j@VjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjtjjjjjjjjjjjjjjjjj~jjjjjjjjjjjjjjjj֩ljjjjjjΕ_Vjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj˘ibjjjjjjjjjjjjjj쾋_gjjjjjjjjjjjjjj㳆fjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjצzfjjjjjjjjjʫjjjjjjjjjjjjňVOjjjjjjjjjjjjjjjR" jjjjjjjjȑ_\jjjjjjjjjjjjjjjjjjjjjjjjjjjjڧkQjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj͒jjjjjjjjjjjjjjj֧}ijjjjjjɒ`\jjjjjjjjjjjjjjjjjצzfjjjjjjjjjj̛pfjjjjjjjjjjjjjj쿏fijjjjjjjjjjjjjj㳅ejjjjjjjjjjjjjjjjjjjjjjצzfjjjjjjjjjjjjjjjjjjjqDVjjjjjjjjjjjjjjjR" jjjjjjjjŏ`bjjjjjjjjjjjjjjjjjjjjjjjjjjjjඇjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjӢvejjjjjjǒcbjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjjjjjjjjjצzfjjjjjjjjjjjjjjjjj̏S@bjjjjjjjjjjjjjjjR" jjjjjjjjÐcejjjjjjjjjjjjjjjjjjjjjjjjjjjjϮjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj~jjjjjjjjjjjȒf]jjjjjjƔhfjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjjjjjjtצzfjjjjjjjjjjͦjjjjݪh@KjjjjjjjjjjjjjjjjR" jjjjjjjjÒggjjjjjjjjjjjjjjjjjjjjjjjjjjjj‡jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjzjjjjjjjjjjěkHUjjjjjjǖlhjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjjjjjצzfjjjjjjjjjjz@@_jjjjjjjjjjjjjjjjR" jjjjjjjjŕlijjjjjjjjjjjjjjjjjjjjjjjjjjjj¦qjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjmlnxjjjjjjjjj˳wV@@Vjjjjjjɚqijjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjjjtïצzfjjjjjjjjjjj຀C@NjjjjjjjjjjjjjjjjjR" jjjjjjjjȚrjjjjjjjjjjjjjjjjjjjjjjjjjjjjj԰rjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjje[anjjjjjjjjȟy^PKKJJJJJJJJJJJJJJJJJJD@@@Cgjjjjjj͠xkjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjjjݽ~hXPLJJP_wצzfjjjjjjjjjjjjӬw@@FgjjjjjjjjjjjjjjjjjR" jjjjjjjj̡zkjjjjjjjjjjjjjjjjjjjjjjjjjjjjϤ|llޏjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj^RUasqjjjjjjjתn@@@@@@@@@@@@@@@@@@@@@@@@@@Kbjjjjjjjӧmjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjjΤwP@@@@@@@@@Qצzfjjjjjjjjjjjβ_@@FdjjjjjjjjjjjjjjjjjjR" jjjjjjjjөnjjjjjjjjjjjjjjjjjjjjjjjjjjjj͞thj{rjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj\PMZoːjjjjjjjΚZdjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjڱqjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjΜc@@CVVgjjjjjjjצzfjjjjjjjjjjѹ˿b@@@HdjjjjjjjjjjjjjjjjjjjR" jjjjjjjjڳsjjjjjjjjjjjjjjjjjjjjjjjjjjjj̝sgjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjhZSc~jjjjjjjΜdbjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj㽙xjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjjکh@C\jjjjjjjjjjjצzfjjjjjjjjjtͥ}hem|}o_L@@@@VjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjj㿛yjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rgjjoވjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjdkڹsjjjjjjէyejjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjʨjjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjj~ĆCFdjjjjjjjjjjjjצzfjjjjjjjjjvDQC@DLMMHA@@@@@FVjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjjͬjjjjjjjjjjjjjjjjjjjjjjjjjjjj͝qgjjjrjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjzٳwjjjjjj༘vjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj~׸mjjjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjn@_jjjjjjjjjjjjjצzfjjjjjjjj~љ[Kjj\VF@@@@@FVVdjjjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjj۾njjjjjjjjjjjjjjjjjjjjjjjjjjj͝rgjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj׬pjjjjjjjѵjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjj˱jjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjݦhHjjjjjjjjjjjjjjצzfjjjjjjjj͘`\jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjR" jjjjjjjj~Ѻjjjjjjjjjjjjjjjjjjjjjjjjjjj͝rgjjjjw݀jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjaM:*ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjԥ{ijjjjjjj̹ujjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjȨjjjjjjjjjjjjjjצzfjjjjjjjjjj͝rhjjjjjjjjjjjjjj쿑hijjjjjjjjjjjjjj㳅ejjjjjjjjjۧqYjjjjjjjjjjjjjjצzfjjjjjjjjӧ~jjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjR" 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EXTENSION_TO_TYPE = {'.aln': 'clustal', '.afa': 'fasta', '.fa': 'fasta', '.faa': 'fasta', '.fas': 'fasta', '.fasta': 'fasta', '.fastq': 'fastq', '.fq': 'fastq', '.ffn': 'fasta', '.fna': 'fasta', '.frn': 'fasta', '.gb': 'genbank', '.gbk': 'genbank', '.needle': 'emboss', '.nex': 'nexus', '.phy': 'phylip', '.phylip': 'phylip', '.phyx': 'phylip-relaxed', '.qual': 'qual', '.sff': 'sff-trim', '.sth': 'stockholm', '.sto': 'stockholm',} COMPRESS_EXT = { '.gz': gzip.open, # '.bz2': bz2.BZ2File, # '.bz': bz2.BZ2File, } class UnknownExtensionError(ValueError): pass def from_extension(extension): """ Look up the BioPython file type corresponding with input extension. Look up is case insensitive. """ if not extension.startswith('.'): raise ValueError("Extensions must begin with a period.") try: return EXTENSION_TO_TYPE[extension.lower()] except KeyError: raise UnknownExtensionError( "seqmagick does not know how to handle " + "files with extensions like this: " + extension) def from_filename(file_name): """ Look up the BioPython file type corresponding to an input file name. """ base, extension = os.path.splitext(file_name) if extension in COMPRESS_EXT: # Compressed file extension = os.path.splitext(base)[1] return from_extension(extension) def from_handle(fh, stream_default='fasta'): """ Look up the BioPython file type corresponding to a file-like object. For stdin, stdout, and stderr, ``stream_default`` is used. """ if fh in (sys.stdin, sys.stdout, sys.stderr): return stream_default return from_filename(fh.name) seqmagick-0.8.4/seqmagick/scripts/000077500000000000000000000000001376401056300171275ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/scripts/__init__.py000066400000000000000000000000001376401056300212260ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/scripts/cli.py000066400000000000000000000041311376401056300202470ustar00rootroot00000000000000#! /usr/bin/env python import argparse import logging import sys from seqmagick import __version__ as version from seqmagick import subcommands def main(argv=sys.argv[1:]): action, arguments = parse_arguments(argv) loglevel = { 0: logging.ERROR, 1: logging.WARNING, 2: logging.INFO, 3: logging.DEBUG, }.get(arguments.verbosity, logging.DEBUG) if arguments.verbosity > 1: logformat = '%(levelname)s %(module)s %(lineno)s %(message)s' else: logformat = '%(message)s' # set up logging logging.basicConfig(stream=sys.stderr, format=logformat, level=loglevel) return action(arguments) def parse_arguments(argv): """ Extract command-line arguments for different actions. """ parser = argparse.ArgumentParser(description='seqmagick - Manipulate ' + \ ' sequence files.', prog='seqmagick') parser.add_argument('-V', '--version', action='version', version='seqmagick v' + version, help="Print the version number and exit") parser.add_argument('-v', '--verbose', dest='verbosity', action='count', default=1, help="Be more verbose. Specify -vv or -vvv for even more") parser.add_argument('-q', '--quiet', action='store_const', const=0, dest='verbosity', help="Suppress output") # Subparsers subparsers = parser.add_subparsers(dest='subparser_name') parser_help = subparsers.add_parser('help', help='Detailed help for actions using help ') parser_help.add_argument('action') # Add actions actions = {} for name, mod in subcommands.itermodules(): subparser = subparsers.add_parser(name, help=mod.__doc__, description=mod.__doc__) mod.build_parser(subparser) actions[name] = mod.action arguments = parser.parse_args(argv) arguments.argv = argv action = arguments.subparser_name if action is None: parse_arguments(['-h']) if action == 'help': return parse_arguments([str(arguments.action), '-h']) return actions[action], arguments seqmagick-0.8.4/seqmagick/subcommands/000077500000000000000000000000001376401056300177535ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/subcommands/__init__.py000066400000000000000000000004501376401056300220630ustar00rootroot00000000000000commands = 'convert', 'info', 'mogrify', 'primer_trim', 'quality_filter', \ 'extract_ids', 'backtrans_align' def itermodules(root=__name__): for command in commands: yield (command.replace('_', '-'), __import__('%s.%s' % (root, command), fromlist=[command])) seqmagick-0.8.4/seqmagick/subcommands/backtrans_align.py000066400000000000000000000135211376401056300234510ustar00rootroot00000000000000""" Given a protein alignment and unaligned nucleotides, align the nucleotides using the protein alignment. Protein and nucleotide sequence files must contain the same number of sequences, in the same order, with the same IDs. """ # TODO: Add tests import itertools import logging import sys from Bio import SeqIO from Bio.Data import CodonTable from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from seqmagick import fileformat from . import common TRANSLATION_TABLES = { 'standard': CodonTable.unambiguous_dna_by_name["Standard"], 'standard-ambiguous': CodonTable.ambiguous_dna_by_name["Standard"], 'vertebrate-mito': CodonTable.unambiguous_dna_by_name["Vertebrate Mitochondrial"] } def build_parser(parser): parser.add_argument( 'protein_align', type=common.FileType('r'), help='Protein Alignment') parser.add_argument( 'nucl_align', type=common.FileType('r'), help='FASTA Alignment') parser.add_argument( '-o', '--out-file', type=common.FileType('w'), default=sys.stdout, metavar='destination_file', help='Output destination. Default: STDOUT') parser.add_argument( '-t', '--translation-table', choices=TRANSLATION_TABLES, default='standard-ambiguous', help='Translation table to use. [Default: %(default)s]') parser.add_argument( '-a', '--fail-action', choices=('fail', 'warn', 'none'), default='fail', help='Action to take on an ambiguous codon [default: %(default)s]') return parser def batch(iterable, chunk_size): """ Return items from iterable in chunk_size bits. If len(iterable) % chunk_size > 0, the last item returned will be shorter. """ i = iter(iterable) while True: r = list(itertools.islice(i, chunk_size)) if not r: break yield r class AlignmentMapper(object): def __init__(self, translation_table, unknown_action='fail'): self.translation_table = translation_table self.unknown_action = unknown_action def _validate_translation(self, aligned_prot, aligned_nucl): """ Given a seq for protein and nucleotide, ensure that the translation holds """ codons = [''.join(i) for i in batch(str(aligned_nucl), 3)] for codon, aa in zip(codons, str(aligned_prot)): # Check gaps if codon == '---' and aa == '-': continue try: trans = self.translation_table.forward_table[codon] if not trans == aa: raise ValueError("Codon {0} translates to {1}, not {2}".format( codon, trans, aa)) except (KeyError, CodonTable.TranslationError): if aa != 'X': if self.unknown_action == 'fail': raise ValueError("Unknown codon: {0} mapped to {1}".format( codon, aa)) elif self.unknown_action == 'warn': logging.warn('Cannot verify that unknown codon %s ' 'maps to %s', codon, aa) return True def map_alignment(self, prot_seq, nucl_seq): """ Use aligned prot_seq to align nucl_seq """ if prot_seq.id != nucl_seq.id: logging.warning( 'ID mismatch: %s != %s. Are the sequences in the same order?', prot_seq.id, nucl_seq.id) # Ungap nucleotides codons = batch(str(nucl_seq.seq.ungap('-')), 3) codons = [''.join(i) for i in codons] codon_iter = iter(codons) ungapped_prot = str(prot_seq.seq).replace('-', '') if len(ungapped_prot) != len(codons): table = self.translation_table.forward_table prot_str = ' '.join(' ' + p + ' ' for p in ungapped_prot) codon_str = ' '.join(codons) trans_str = ' '.join(' ' + table.get(codon, 'X') + ' ' for codon in codons) raise ValueError("""Length of codon sequence ({0}) does not match \ length of protein sequence ({1}) for {2} Protein: {3} Codons: {4} Trans. Codons: {5}""".format(len(codons), len(ungapped_prot), nucl_seq.id, prot_str, codon_str, trans_str)) try: nucl_align = ['---' if p == '-' else next(codon_iter) for p in str(prot_seq.seq)] except StopIteration: assert False # Should be checked above result = SeqRecord(Seq(''.join(nucl_align)), id=nucl_seq.id, description=nucl_seq.description) # Validate self._validate_translation(prot_seq.seq.upper(), result.seq.upper()) return result def map_all(self, prot_alignment, nucl_sequences): """ Convert protein sequences to nucleotide alignment """ zipped = itertools.zip_longest(prot_alignment, nucl_sequences) for p, n in zipped: if p is None: raise ValueError("Exhausted protein sequences") elif n is None: raise ValueError("Exhausted nucleotide sequences") yield self.map_alignment(p, n) def action(arguments): """ Run """ # Ignore SIGPIPE, for head support common.exit_on_sigpipe() logging.basicConfig() prot_sequences = SeqIO.parse(arguments.protein_align, fileformat.from_handle(arguments.protein_align)) nucl_sequences = SeqIO.parse(arguments.nucl_align, fileformat.from_handle(arguments.nucl_align)) instance = AlignmentMapper(TRANSLATION_TABLES[arguments.translation_table], arguments.fail_action) SeqIO.write(instance.map_all(prot_sequences, nucl_sequences), arguments.out_file, fileformat.from_filename(arguments.out_file.name)) seqmagick-0.8.4/seqmagick/subcommands/common.py000066400000000000000000000154531376401056300216250ustar00rootroot00000000000000""" Common functions for subcommands """ import argparse import contextlib import copy import functools import os import os.path import signal import sys import tempfile from seqmagick import fileformat def get_umask(): """ Gets the current umask """ current_umask = os.umask(0o777) os.umask(current_umask) return current_umask def apply_umask(permission=0o666, umask=None): """ Masks the provided permission with a umask. If umask is not given, the current umask is used. """ if umask is None: umask = get_umask() return permission & (~umask) @contextlib.contextmanager def atomic_write(path, mode='wt', permissions=None, file_factory=None, **kwargs): """ Open a file for atomic writing. Generates a temp file, renames to value of ``path``. Arguments: ``permissions``: Permissions to set (default: umask) ``file_factory``: If given, the handle yielded will be the result of calling file_factory(path) Additional arguments are passed to tempfile.NamedTemporaryFile """ if permissions is None: permissions = apply_umask() # Handle stdout: if path == '-': yield sys.stdout else: base_dir = os.path.dirname(path) kwargs['suffix'] = os.path.basename(path) tf = tempfile.NamedTemporaryFile( dir=base_dir, mode=mode, delete=False, **kwargs) # If a file_factory is given, close, and re-open a handle using the # file_factory if file_factory is not None: tf.close() tf = file_factory(tf.name) try: with tf: yield tf # Move os.rename(tf.name, path) os.chmod(path, permissions) except: os.remove(tf.name) raise def sequence_slices(string): """ Parses a list of slices from a string of format: start1:end1[,start2:end2[,start2:end3]] etc """ slices = string.split(',') return [cut_range(i) for i in slices] def cut_range(string): """ A custom argparse 'type' to deal with sequences ranges such as 5:500. Returns a 0-based slice corresponding to the selection defined by the slice """ value_range = string.split(':') if len(value_range) == 1: start = int(value_range[0]) stop = start elif len(value_range) == 2: start, stop = tuple(int(i) if i else None for i in value_range) else: msg = "{0} is not a valid, 1-indexed range.".format(string) raise argparse.ArgumentTypeError(msg) if start == 0 or (stop or sys.maxsize) < (start or 0): msg = "{0} is not a valid, 1-indexed range.".format(string) raise argparse.ArgumentTypeError(msg) # Convert from 1-indexed to 0-indexed if start is not None and start > 0: start -= 1 return slice(start, stop) def typed_range(type_func, minimum, maximum): """ Require variables to be of the specified type, between minimum and maximum """ @functools.wraps(type_func) def inner(string): result = type_func(string) if not result >= minimum and result <= maximum: raise argparse.ArgumentTypeError( "Please provide a value between {0} and {1}".format( minimum, maximum)) return result return inner def partial_append_action(fn, argument_keys=None): """ Creates a new class extending argparse.Action, which appends a partially-applied function to dest. The optional argument_keys argument should either be None (no additional arguments to fn) or an iterable of function keys to partially apply. """ if isinstance(argument_keys, str): argument_keys = [argument_keys] argument_keys = argument_keys or [] class PartialAppendAction(argparse.Action): def __init__(self, option_strings, dest, const=None, default=None, required=False, help=None, type=None, metavar=None, nargs=None, **kwargs): super(PartialAppendAction, self).__init__( option_strings=option_strings, dest=dest, nargs=len(argument_keys), const=const, default=default, required=required, metavar=metavar, type=type, help=help, **kwargs) def __call__(self, parser, namespace, values, option_string=None): items = copy.copy(getattr(namespace, self.dest, None)) or [] # If no value was set default to empty list if values is None: values = [] elif not isinstance(values, list): values = [values] if len(argument_keys) != len(values): raise ValueError("Unexpected number of values") # Generate keyword arguments for the input function kwargs = dict(list(zip(argument_keys, values))) f = functools.partial(fn, **kwargs) items.append(f) setattr(namespace, self.dest, items) return PartialAppendAction def positive_value(target_type): """ Wraps target_type in a function that requires the parsed argument be >= 0 """ def inner(string): value = target_type(string) if not value >= 0: raise argparse.ArgumentTypeError("Invalid positive number: " + string) return value return inner def _exit_on_signal(sig, status=None, message=None): def exit(sig, frame): if message: print(message, file=sys.stderr) raise SystemExit(status) signal.signal(sig, exit) def exit_on_sigint(status=1, message="Canceled."): """ Set program to exit on SIGINT, with provided status and message. """ _exit_on_signal(signal.SIGINT, status, message) def exit_on_sigpipe(status=None): """ Set program to exit on SIGPIPE """ _exit_on_signal(signal.SIGPIPE, status) class FileType(object): """ Near clone of argparse.FileType, supporting gzip and bzip """ def __init__(self, mode='rt'): self.mode = mode self.ext_map = fileformat.COMPRESS_EXT.copy() def _get_handle(self, file_path): ext = os.path.splitext(file_path)[1].lower() return self.ext_map.get(ext, open)(file_path, self.mode) def __call__(self, string): if string == '-': if 'r' in self.mode: return sys.stdin elif 'w' in self.mode: return sys.stdout else: raise ValueError("Invalid mode: {0}".format(string)) else: return self._get_handle(string) seqmagick-0.8.4/seqmagick/subcommands/convert.py000066400000000000000000000427341376401056300220170ustar00rootroot00000000000000""" Convert between sequence formats """ import argparse import functools import logging import random from Bio import SeqIO from Bio.SeqIO import FastaIO from seqmagick import transform from seqmagick.fileformat import from_handle from . import common ALPHABETS = { "dna": "DNA", "dna-ambiguous": "DNA", "rna": "RNA", "rna-ambiguous": "RNA", "protein": "protein", } def add_options(parser): """ Add optional arguments to the parser """ partial_action = common.partial_append_action file_mods = parser.add_argument_group("Sequence File Modification") file_mods.add_argument('--line-wrap', dest='line_wrap', metavar='N', type=int, help='Adjust line wrap for sequence strings. ' 'When N is 0, all line breaks are removed. Only fasta files ' 'are supported for the output format.') file_mods.add_argument('--sort', dest='sort', choices=['length-asc', 'length-desc', 'name-asc', 'name-desc'], help='Perform sorting by length or name, ascending or descending. ' 'ASCII sorting is performed for names') parser.epilog = """Filters using regular expressions are case-sensitive by default. Append "(?i)" to a pattern to make it case-insensitive.""" seq_mods = parser.add_argument_group("Sequence Modificaton") seq_mods.add_argument('--apply-function', type=module_function, metavar='/path/to/module.py:function_name[:parameter]', help="""Specify a custom function to apply to the input sequences, specified as /path/to/file.py:function_name. Function should accept an iterable of Bio.SeqRecord objects, and yield SeqRecords. If the parameter is specified, it will be passed as a string as the second argument to the function. Specify more than one to chain.""", default=[], action='append') seq_mods.add_argument('--cut', dest='transforms', metavar="start:end[,start2:end2]", type=common.sequence_slices, action=partial_action(transform.multi_cut_sequences, 'slices'), help="""Keep only the residues within the 1-indexed start and end positions specified, : separated. Includes last item. Start or end can be left unspecified to indicate start/end of sequence. A negative start may be provided to indicate an offset from the end of the sequence. Note that to prevent negative numbers being interpreted as flags, this should be written with an equals sign between `--cut` and the argument, e.g.: `--cut=-10:`""") seq_mods.add_argument('--relative-to', dest='cut_relative', metavar='ID', help="""Apply --cut relative to the indexes of non-gap residues in sequence identified by ID""") seq_mods.add_argument('--drop', dest='transforms', metavar='start:end[,start2:end2]', type=common.sequence_slices, action=partial_action(transform.drop_columns, 'slices'), help="""Remove the residues at the specified indices. Same format as `--cut`.""") seq_mods.add_argument('--dash-gap', action=partial_action(transform.dashes_cleanup), dest='transforms', help="""Replace any of the characters "?.:~" with a "-" for all sequences""") seq_mods.add_argument('--lower', action=partial_action(transform.lower_sequences), dest='transforms', help='Translate the sequences to lower case') seq_mods.add_argument('--mask', metavar="start1:end1[,start2:end2]", action=partial_action(transform.multi_mask_sequences, 'slices'), type=common.sequence_slices, dest='transforms', help="""Replace residues in 1-indexed slice with gap-characters. If --relative-to is also specified, coordinates are relative to the sequence ID provided.""") seq_mods.add_argument('--reverse', action=partial_action(transform.reverse_sequences), dest='transforms', help='Reverse the order of sites in sequences') seq_mods.add_argument('--reverse-complement', dest='transforms', action=partial_action(transform.reverse_complement_sequences), help='Convert sequences into reverse complements') seq_mods.add_argument('--squeeze', action=partial_action(transform.squeeze), dest='transforms', help='''Remove any gaps that are present in the same position across all sequences in an alignment (equivalent to --squeeze-threshold=1.0)''') seq_mods.add_argument('--squeeze-threshold', dest='transforms', action=partial_action(transform.squeeze, 'gap_threshold'), type=common.typed_range(float, 0.0, 1.0), metavar='PROP', help="""Trim columns from an alignment which have gaps in least the specified proportion of sequences.""") seq_mods.add_argument('--transcribe', dest='transforms', action=partial_action(transform.transcribe, 'transcribe'), choices=('dna2rna', 'rna2dna'), help="""Transcription and back transcription for generic DNA and RNA. Source sequences must be the correct alphabet or this action will likely produce incorrect results.""") seq_mods.add_argument('--translate', dest='transforms', action=partial_action(transform.translate, 'translate'), choices=['dna2protein', 'rna2protein', 'dna2proteinstop', 'rna2proteinstop'], help="""Translate from generic DNA/RNA to proteins. Options with "stop" suffix will NOT translate through stop codons . Source sequences must be the correct alphabet or this action will likely produce incorrect results.""") seq_mods.add_argument('--ungap', action=partial_action(transform.ungap_sequences), dest='transforms', help='Remove gaps in the sequence alignment') seq_mods.add_argument('--upper', action=partial_action(transform.upper_sequences), dest='transforms', help='Translate the sequences to upper case') seq_select = parser.add_argument_group("Record Selection") seq_select.add_argument('--deduplicate-sequences', action='store_const', const=None, default=False, dest='deduplicate_sequences', help='Remove any duplicate sequences ' 'by sequence content, keep the first instance seen') seq_select.add_argument('--deduplicated-sequences-file', action='store', metavar='FILE', dest='deduplicate_sequences', default=False, type=common.FileType('wt'), help='Write all of the deduplicated sequences to a file') seq_select.add_argument('--deduplicate-taxa', action=partial_action(transform.deduplicate_taxa), dest='transforms', help="""Remove any duplicate sequences by ID, keep the first instance seen""") seq_select.add_argument('--exclude-from-file', metavar='FILE', type=common.FileType('rt'), help="""Filter sequences, removing those sequence IDs in the specified file""", dest='transforms', action=partial_action(transform.exclude_from_file, 'handle')) seq_select.add_argument('--include-from-file', metavar='FILE', type=common.FileType('rt'), help="""Filter sequences, keeping only those sequence IDs in the specified file""", dest='transforms', action=partial_action(transform.include_from_file, 'handle')) seq_select.add_argument('--head', metavar='N', dest='transforms', action=partial_action(transform.head, 'head'), help="""Trim down to top N sequences. With the leading `-', print all but the last N sequences.""") seq_select.add_argument('--max-length', dest='transforms', metavar='N', action=partial_action(transform.max_length_discard, 'max_length'), type=int, help="""Discard any sequences beyond the specified maximum length. This operation occurs *before* all length-changing options such as cut and squeeze.""") seq_select.add_argument('--min-length', dest='transforms', metavar='N', action=partial_action(transform.min_length_discard, 'min_length'), type=int, help="""Discard any sequences less than the specified minimum length. This operation occurs *before* cut and squeeze.""") seq_select.add_argument('--min-ungapped-length', metavar='N', action=partial_action(transform.min_ungap_length_discard, 'min_length'), type=int, help="""Discard any sequences less than the specified minimum length, excluding gaps. This operation occurs *before* cut and squeeze.""", dest='transforms') seq_select.add_argument('--pattern-include', metavar='REGEX', action=partial_action(transform.name_include, 'filter_regex'), dest='transforms', help="""Filter the sequences by regular expression in ID or description""") seq_select.add_argument('--pattern-exclude', metavar='REGEX', action=partial_action(transform.name_exclude, 'filter_regex'), dest='transforms', help="""Filter the sequences by regular expression in ID or description""") seq_select.add_argument('--prune-empty', action=partial_action(transform.prune_empty), dest='transforms', help="Prune sequences containing only gaps ('-')") seq_select.add_argument('--sample', metavar='N', dest='transforms', type=int, action=partial_action(transform.sample, 'k'), help = """ Select a random sampling of sequences """) seq_select.add_argument('--sample-seed', metavar='N', type=int, help = """Set random seed for sampling of sequences""") seq_select.add_argument('--seq-pattern-include', metavar='REGEX', action=partial_action(transform.seq_include, 'filter_regex'), dest='transforms', help="""Filter the sequences by regular expression in sequence""") seq_select.add_argument('--seq-pattern-exclude', metavar='REGEX', action=partial_action(transform.seq_exclude, 'filter_regex'), dest='transforms', help="""Filter the sequences by regular expression in sequence""") seq_select.add_argument('--tail', metavar='N', dest='transforms', action=partial_action(transform.tail, 'tail'), help="""Trim down to bottom N sequences. Use +N to output sequences starting with the Nth.""") id_mods = parser.add_argument_group("Sequence ID Modification") id_mods.add_argument('--first-name', action=partial_action(transform.first_name_capture), dest='transforms', help='''Take only the first whitespace-delimited word as the name of the sequence''') id_mods.add_argument('--name-suffix', metavar='SUFFIX', action=partial_action(transform.name_append_suffix, 'suffix'), dest='transforms', help='Append a suffix to all IDs.') id_mods.add_argument('--name-prefix', metavar='PREFIX', action=partial_action(transform.name_insert_prefix, 'prefix'), dest='transforms', help="""Insert a prefix for all IDs.""") id_mods.add_argument('--pattern-replace', nargs=2, metavar=('search_pattern', 'replace_pattern'), action=partial_action(transform.name_replace, ('search_regex', 'replace_pattern')), dest='transforms', help="""Replace regex pattern "search_pattern" with "replace_pattern" in sequence ID and description""") id_mods.add_argument('--strip-range', dest='transforms', action=partial_action(transform.strip_range), help="""Strip ranges from sequences IDs, matching """) format_group = parser.add_argument_group('Format Options') format_group.add_argument('--input-format', metavar='FORMAT', help="Input file format (default: determine from extension)") format_group.add_argument('--output-format', metavar='FORMAT', help="Output file format (default: determine from extension)") parser.add_argument('--alphabet', choices=ALPHABETS, help="""Input alphabet. Required for writing NEXUS.""") return parser def build_parser(parser): """ Add shared arguments to the convert or mogrify parser. """ add_options(parser) parser.add_argument('source_file', type=common.FileType('rt'), help="Input sequence file") parser.add_argument('dest_file', help="Output file") return parser def append_annotation_iterator(records_iterator, alphabet): for record in records_iterator: record.annotations["molecule_type"] = ALPHABETS[alphabet] yield record def transform_file(source_file, destination_file, arguments): # Get just the file name, useful for naming the temporary file. source_file_type = (arguments.input_format or from_handle(source_file)) destination_file_type = (arguments.output_format or from_handle(destination_file)) # Get an iterator. sorters = {'length': transform.sort_length, 'name': transform.sort_name,} directions = {'asc': 1, 'desc': 0} if arguments.sort: # Sorted iterator key, direction = arguments.sort.split('-') records = sorters[key](source_file=source_file, source_file_type=source_file_type, direction=directions[direction]) else: # Unsorted iterator. records = SeqIO.parse(source_file, source_file_type) ######################################### # Apply generator functions to iterator.# ######################################### # Apply all the transform functions in transforms if arguments.transforms: # TODO: might be nice to somehow pass this directly into sample action if arguments.sample_seed is not None: random.seed(arguments.sample_seed) # Special case handling for --cut and --relative-to if arguments.cut_relative: for o, n in ((transform.multi_cut_sequences, transform.cut_sequences_relative), (transform.multi_mask_sequences, transform.mask_sequences_relative)): # Add a function to trim any columns which are gaps in the # sequence ID try: f = next(f for f in arguments.transforms if f.func == o) except StopIteration: continue i = arguments.transforms.index(f) arguments.transforms.pop(i) arguments.transforms.insert(i, functools.partial(n, record_id=arguments.cut_relative, **f.keywords)) for function in arguments.transforms: records = function(records) if (arguments.deduplicate_sequences or arguments.deduplicate_sequences is None): records = transform.deduplicate_sequences( records, arguments.deduplicate_sequences) # Apply all the partial functions if arguments.apply_function: for apply_function in arguments.apply_function: records = apply_function(records) # Only the fasta format is supported, as SeqIO.write does not have a 'wrap' # parameter. if (arguments.line_wrap is not None and destination_file_type == 'fasta'): logging.info("Attempting to write fasta with %d line breaks.", arguments.line_wrap) with destination_file: writer = FastaIO.FastaWriter( destination_file, wrap=arguments.line_wrap) writer.write_file(records) else: # Mogrify requires writing all changes to a temporary file by default, # but convert uses a destination file instead if one was specified. Get # sequences from an iterator that has generator functions wrapping it. # After creation, it is then copied back over the original file if all # tasks finish up without an exception being thrown. This avoids # loading the entire sequence file up into memory. logging.info("Applying transformations, writing to %s", destination_file) # Append datatype annotation, mandatory for Nexus files conversion. if arguments.alphabet != None: records = append_annotation_iterator(records, arguments.alphabet) SeqIO.write(records, destination_file, destination_file_type) def module_function(string): """ Load a function from a python module using a file name, function name specification of format: /path/to/x.py:function_name[:parameter] """ parts = string.split(':', 2) if len(parts) < 2: raise ValueError( "Illegal specification. Should be module:function[:parameter]") module_path, function_name = parts[:2] # Import the module module_vars = {} exec(compile(open(module_path).read(), module_path, 'exec'), module_vars) try: function = module_vars[function_name] except KeyError: raise argparse.ArgumentTypeError("{0} has no attribute '{1}'".format( module_path, function_name)) if len(parts) == 3: old_function = function function = lambda r: old_function(r, parts[2]) return function def action(arguments): with arguments.source_file as src, \ common.atomic_write( arguments.dest_file, file_factory=common.FileType('wt')) as dest: transform_file(src, dest, arguments) seqmagick-0.8.4/seqmagick/subcommands/extract_ids.py000066400000000000000000000024201376401056300226340ustar00rootroot00000000000000""" Extract the sequence IDs from a file """ import sys from Bio import SeqIO from seqmagick import fileformat from . import common def build_parser(parser): parser.add_argument( 'sequence_file', type=common.FileType('rt'), help="Sequence file") parser.add_argument( '-o', '--output-file', type=common.FileType('wt'), default=sys.stdout, help="Destination file") parser.add_argument( '--input-format', help="Input format for sequence file") parser.add_argument( '-d', '--include-description', action='store_true', default=False, help='Include the sequence description in output [default: %(default)s]') def action(arguments): common.exit_on_sigpipe() # Determine file format for input and output source_format = (arguments.input_format or fileformat.from_handle(arguments.sequence_file)) with arguments.sequence_file: sequences = SeqIO.parse(arguments.sequence_file, source_format) if arguments.include_description: ids = (sequence.description for sequence in sequences) else: ids = (sequence.id for sequence in sequences) with arguments.output_file: for i in ids: print(i, file=arguments.output_file) seqmagick-0.8.4/seqmagick/subcommands/info.py000066400000000000000000000140351376401056300212630ustar00rootroot00000000000000""" Info action """ import collections import csv import multiprocessing import sys from functools import partial from Bio import SeqIO from seqmagick import fileformat from . import common def build_parser(parser): parser.add_argument('source_files', metavar='sequence_files', nargs='+') parser.add_argument('--input-format', help="""Input format. Overrides extension for all input files""") parser.add_argument('--out-file', dest='destination_file', type=common.FileType('wt'), default=sys.stdout, metavar='destination_file', help='Output destination. Default: STDOUT') parser.add_argument('--format', dest='output_format', choices=('tab', 'csv', 'align'), help="""Specify output format as tab-delimited, CSV or aligned in a borderless table. Default is tab-delimited if the output is directed to a file, aligned if output to the console.""") parser.add_argument('--threads', default=1, type=int, help="""Number of threads (CPUs). [%(default)s] """) class SeqInfoWriter(object): """ Base writer for sequence files """ def __init__(self, sequence_files, rows, output): self.sequence_files = sequence_files self.rows = rows self.output = output def write_row(self, row): raise NotImplementedError("Override in subclass") def write_header(self, header): self.write_row(header) def write(self): header = ('name', 'alignment', 'min_len', 'max_len', 'avg_len', 'num_seqs') self.write_header(header) for row in self.rows: self.write_row(_SeqFileInfo(*row)) class CsvSeqInfoWriter(SeqInfoWriter): delimiter = ',' def __init__(self, sequence_files, rows, output): super(CsvSeqInfoWriter, self).__init__(sequence_files, rows, output) self.writer = csv.writer(self.output, delimiter=self.delimiter, lineterminator='\n') def write_row(self, row): # To cope with header if hasattr(row, '_replace'): row = row._replace(avg_len='{0:.2f}'.format(row.avg_len)) self.writer.writerow(row) class TsvSeqInfoWriter(CsvSeqInfoWriter): delimiter = '\t' class AlignedSeqInfoWriter(SeqInfoWriter): def __init__(self, sequence_files, rows, output): super(AlignedSeqInfoWriter, self).__init__(sequence_files, rows, output) self.max_name_length = max(len(f) for f in self.sequence_files) def write_header(self, header): fmt = ('{0:' + str(self.max_name_length + 1) + 's}{1:10s}' '{2:>10s}{3:>10s}{4:>10s}{5:>10s}') print(fmt.format(*header), file=self.output) def write_row(self, row): fmt = ('{name:' + str(self.max_name_length + 1) + 's}{alignment:10s}' '{min_len:10d}{max_len:10d}{avg_len:10.2f}{num_seqs:10d}') print(fmt.format(**row._asdict()), file=self.output) _WRITERS = {'csv': CsvSeqInfoWriter, 'tab': TsvSeqInfoWriter, 'align': AlignedSeqInfoWriter} _HEADERS = ('name', 'alignment', 'min_len', 'max_len', 'avg_len', 'num_seqs') _SeqFileInfo = collections.namedtuple('SeqFileInfo', _HEADERS) def summarize_sequence_file(source_file, file_type=None): """ Summarizes a sequence file, returning a tuple containing the name, whether the file is an alignment, minimum sequence length, maximum sequence length, average length, number of sequences. """ is_alignment = True avg_length = None min_length = sys.maxsize max_length = 0 sequence_count = 0 # Get an iterator and analyze the data. with common.FileType('rt')(source_file) as fp: if not file_type: file_type = fileformat.from_handle(fp) for record in SeqIO.parse(fp, file_type): sequence_count += 1 sequence_length = len(record) if max_length != 0: # If even one sequence is not the same length as the others, # we don't consider this an alignment. if sequence_length != max_length: is_alignment = False # Lengths if sequence_length > max_length: max_length = sequence_length if sequence_length < min_length: min_length = sequence_length # Average length if sequence_count == 1: avg_length = float(sequence_length) else: avg_length = avg_length + ((sequence_length - avg_length) / sequence_count) # Handle an empty file: if avg_length is None: min_length = max_length = avg_length = 0 if sequence_count <= 1: is_alignment = False return (source_file, str(is_alignment).upper(), min_length, max_length, avg_length, sequence_count) def action(arguments): """ Given one more more sequence files, determine if the file is an alignment, the maximum sequence length and the total number of sequences. Provides different output formats including tab (tab-delimited), csv and align (aligned as if part of a borderless table). """ # Ignore SIGPIPE, for head support common.exit_on_sigpipe() common.exit_on_sigint() handle = arguments.destination_file output_format = arguments.output_format if not output_format: try: output_format = 'align' if handle.isatty() else 'tab' except AttributeError: output_format = 'tab' writer_cls = _WRITERS[output_format] ssf = partial(summarize_sequence_file, file_type = arguments.input_format) # if only one thread, do not use the multithreading so parent process # can be terminated using ctrl+c if arguments.threads > 1: pool = multiprocessing.Pool(processes=arguments.threads) summary = pool.imap(ssf, arguments.source_files) else: summary = (ssf(f) for f in arguments.source_files) with handle: writer = writer_cls(arguments.source_files, summary, handle) writer.write() seqmagick-0.8.4/seqmagick/subcommands/mogrify.py000066400000000000000000000015221376401056300220010ustar00rootroot00000000000000""" Modify sequence file(s) in place. """ import logging from . import convert, common def build_parser(parser): """ """ convert.add_options(parser) parser.add_argument( 'input_files', metavar="sequence_file", nargs='+', type=common.FileType('rt'), help="Sequence file(s) to mogrify") return parser def action(arguments): """ Run mogrify. Most of the action is in convert, this just creates a temp file for the output. """ for input_file in arguments.input_files: logging.info(input_file) # Generate a temporary file with common.atomic_write( input_file.name, file_factory=common.FileType('wt')) as tf: convert.transform_file(input_file, tf, arguments) if hasattr(input_file, 'close'): input_file.close() seqmagick-0.8.4/seqmagick/subcommands/primer_trim.py000066400000000000000000000256731376401056300226730ustar00rootroot00000000000000""" Find a primer sequence in a gapped alignment, trim to amplicon """ import argparse import itertools import logging import operator import sys from Bio import SeqIO, pairwise2 from Bio.Seq import Seq from seqmagick import transform, fileformat from . import common def build_parser(parser): parser.add_argument( 'source_file', type=argparse.FileType('r'), help="Source alignment file") parser.add_argument( 'output_file', type=argparse.FileType('w'), help="Destination trimmed file") parser.add_argument( 'forward_primer', type=iupac_ambiguous_sequence, help="The forward primer used") parser.add_argument( 'reverse_primer', type=iupac_ambiguous_sequence, help="""The reverse primer used. By default the reverse primer is assumed to be a subsequence of the top strand (that is, the reverse complement of an actual downstream PCR primer). Use --reverse-is-revcomp if this is not the case.""") parser.add_argument( '--reverse-is-revcomp', dest="reverse_complement", default=False, action='store_true', help="""Reverse primer is written as the reverse complement of the top strand (default: %(default)s)""") parser.add_argument( '--source-format', default=None, help='Alignment format (default: detect from extension') parser.add_argument( '--output-format', default=None, help='Alignment format (default: detect from extension') parser.add_argument( '--include-primers', action="store_true", default=False, help="""Include the primers in the output (default: %(default)s)""") parser.add_argument( '--max-hamming-distance', type=common.positive_value(int), default=1, help="""Maximum Hamming distance between primer and alignment site (default: %(default)s). IUPAC ambiguous bases in the primer matching unambiguous bases in the alignment are not penalized""") parser.add_argument( '--prune-action', default='trim', choices=list(_ACTIONS.keys()), help="""Action to take. Options are trim (trim to the region defined by the two primers, decreasing the width of the alignment), or isolate (convert all characters outside the primer-defined area to gaps). default: %(default)s""") # Sequence-related functions def ungap_index_map(sequence, gap_chars='-'): """ Returns a dict mapping from an index in the ungapped sequence to an index in the gapped sequence. >>> ungap_index_map('AC-TG-') {0: 0, 1: 1, 2: 3, 3: 4} """ counter = itertools.count(0).__next__ ungap_indexes = [ counter() if c not in gap_chars else None for c in iter(sequence) ] return dict( (ungapped, gapped) for ungapped, gapped in zip(ungap_indexes, range(len(sequence))) if ungapped is not None) def gap_index_map(sequence, gap_chars='-'): """ Opposite of ungap_index_map: returns mapping from gapped index to ungapped index. >>> gap_index_map('AC-TG-') {0: 0, 1: 1, 3: 2, 4: 3} """ return dict( (v, k) for k, v in list(ungap_index_map(sequence, gap_chars).items())) def _iupac_ambiguous_equal(ambig_base, unambig_base): """ Tests two bases for equality, accounting for IUPAC ambiguous DNA ambiguous base may be IUPAC ambiguous, unambiguous must be one of ACGT """ iupac_translation = { 'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'U': 'U', 'R': 'AG', 'Y': 'CT', 'S': 'GC', 'W': 'AT', 'K': 'GT', 'M': 'AC', 'B': 'CGT', 'D': 'AGT', 'H': 'ACT', 'V': 'ACG', 'N': 'ACGT', '-': '-' } for i in (ambig_base, unambig_base): if not len(i) == 1: raise ValueError("only one base may be passed.") return unambig_base.upper() in iupac_translation[ambig_base.upper()] def hamming_distance(s1, s2, equality_function=operator.eq): """ Returns the hamming distance between two strings. """ if not len(s1) == len(s2): raise ValueError("String lengths are not equal") # Number of non-matching characters: return sum(not equality_function(c1, c2) for c1, c2 in zip(s1, s2)) class PrimerNotFound(Exception): pass class PrimerOrderError(Exception): def __init__(self, forward_indexes, reverse_indexes): super(PrimerOrderError, self).__init__( "Reverse primer before forward primer: {0} > {1}".format( forward_indexes, reverse_indexes)) class PrimerAligner(object): """ Get positions of pairwise alignments of a primer to a sequence. """ def __init__(self, primer, match=5, difference=-4, gap_open=-10, gap_extend=-0.5, penalize_end_gaps=False): self.primer = primer self.match = match self.difference = difference self.gap_open = gap_open self.gap_extend = gap_extend self.penalize_end_gaps = penalize_end_gaps def align(self, sequence): """ Aligns the primer to the given query sequence, returning a tuple of: hamming_distance, start, end Where hamming distance is the distance between the primer and aligned sequence, and start and end give the start and end index of the primer relative to the input sequence. """ seq_aln, primer_aln, score, start, end = pairwise2.align.globalms( str(sequence).upper(), str(self.primer).upper(), self.match, self.difference, self.gap_open, self.gap_extend, one_alignment_only=True, penalize_end_gaps=self.penalize_end_gaps)[0] # Get an ungapped mapping on the sequence index_map = gap_index_map(seq_aln) ungap_map = ungap_index_map(primer_aln) # Trim to primer start = ungap_map[0] end = ungap_map[len(self.primer) - 1] trimmed = seq_aln[start:end + 1] ham_dist = hamming_distance(primer_aln[start:end + 1], trimmed, _iupac_ambiguous_equal) # assert primer_aln[start:end].replace('-', '') == str(self.primer) # TODO: handle start or end being gap better. For now, just give up # and return maxint for the hamming distance if trimmed.endswith('-'): tail = len(trimmed) - len(trimmed.rstrip('-')) end = index_map[end - tail] + 1 ham_dist = sys.maxsize else: end = index_map[end] if trimmed.startswith('-'): start = 0 ham_dist = sys.maxsize else: start = index_map[start] return ham_dist, start, end @property def max_score(self): """ Maximum possible alignment score """ return len(self.primer) * self.match # Types for argparse def iupac_ambiguous_sequence(string): return Seq(string, IUPAC.ambiguous_dna) def locate_primers(sequences, forward_primer, reverse_primer, reverse_complement, max_hamming_distance): """ Find forward and reverse primers in a set of sequences, return two tuples: (forward_start, forward_end), (reverse_start, reverse_end) """ forward_loc = None reverse_loc = None seq_length = None # Reverse complement the reverse primer, if appropriate if reverse_complement: reverse_primer = reverse_primer.reverse_complement() forward_aligner = PrimerAligner(forward_primer) reverse_aligner = PrimerAligner(reverse_primer) for i, sequence in enumerate(sequences): if seq_length is None: seq_length = len(sequence) elif len(sequence) != seq_length: raise ValueError(("Sequence Length Heterogeneity: {0} != {1}. " "Is this an alignment?").format( len(sequence), seq_length)) index_map = ungap_index_map(sequence.seq) if forward_loc is None: ham_dist, start, end = forward_aligner.align(sequence.seq.ungap()) if ham_dist <= max_hamming_distance: forward_loc = index_map[start], index_map[end] logging.info("Forward in sequence %d: indexes %d to %d", i + 1, *forward_loc) if reverse_loc is None: ham_dist, start, end = reverse_aligner.align(sequence.seq.ungap()) if ham_dist <= max_hamming_distance: reverse_loc = index_map[start], index_map[end] logging.info("Reverse in sequence %d: indexes %d to %d", i + 1, *reverse_loc) if forward_loc and reverse_loc: # Both found # Check order if forward_loc[0] > reverse_loc[0]: raise PrimerOrderError(forward_loc[0], reverse_loc[0]) return forward_loc, reverse_loc else: logging.debug( "Sequence %d: %d/2 primers found", i + 1, sum(j is not None for j in (forward_loc, reverse_loc))) # Did not find either the forward or reverse primer: if not forward_loc: raise PrimerNotFound(forward_primer) else: raise PrimerNotFound(reverse_primer) def trim(sequences, start, end): """ Slice the input sequences from start to end """ logging.info("Trimming from %d to %d", start, end) return (sequence[start:end] for sequence in sequences) # Prune actions _ACTIONS = {'trim': trim, 'isolate': transform.isolate_region} def action(arguments): """ Trim the alignment as specified """ # Determine file format for input and output source_format = (arguments.source_format or fileformat.from_handle(arguments.source_file)) output_format = (arguments.output_format or fileformat.from_handle(arguments.output_file)) # Load the alignment with arguments.source_file: sequences = SeqIO.parse( arguments.source_file, source_format) # Locate primers (forward_start, forward_end), (reverse_start, reverse_end) = locate_primers( sequences, arguments.forward_primer, arguments.reverse_primer, arguments.reverse_complement, arguments.max_hamming_distance) # Generate slice indexes if arguments.include_primers: start = forward_start end = reverse_end + 1 else: start = forward_end + 1 end = reverse_start # Rewind the input file arguments.source_file.seek(0) sequences = SeqIO.parse( arguments.source_file, source_format) # Apply the transformation prune_action = _ACTIONS[arguments.prune_action] transformed_sequences = prune_action(sequences, start, end) with arguments.output_file: SeqIO.write(transformed_sequences, arguments.output_file, output_format) seqmagick-0.8.4/seqmagick/subcommands/quality_filter.py000066400000000000000000000577741376401056300234060ustar00rootroot00000000000000""" Filter reads based on quality scores """ import collections import csv import itertools import logging import os import sys import time from Bio import SeqIO import pygtrie as trie from Bio.SeqIO import QualityIO from seqmagick import fileformat, __version__ from .common import typed_range, FileType def trie_match(string, trie): def has_prefix(teststring, trie): for key in trie.keys(): if key.startswith(teststring): return True return False longest = None for i in range(len(string)): substr = string[:i + 1] if not has_prefix(substr, trie): break if trie.has_key(substr): longest = substr return longest # Default minimummean quality score DEFAULT_MEAN_SCORE = 25.0 # Tools for working with ambiguous bases # Map from Ambiguous Base to regex _AMBIGUOUS_MAP = { 'R': 'GA', 'Y': 'TC', 'K': 'GT', 'M': 'AC', 'S': 'GC', 'W': 'AT', 'B': 'GTC', 'D': 'GAT', 'H': 'ACT', 'V': 'GCA', 'N': 'AGCT', } def all_unambiguous(sequence_str): """ All unambiguous versions of sequence_str """ result = [[]] for c in sequence_str: result = [i + [a] for i in result for a in _AMBIGUOUS_MAP.get(c, c)] return [''.join(i) for i in result] def build_parser(parser): """ Generate a subparser """ parser.add_argument( 'sequence_file', type=FileType('r'), help="""Input fastq file. A fasta-format file may also be provided if --input-qual is also specified.""") parser.add_argument( '--input-qual', type=FileType('r'), help="""The quality scores associated with the input file. Only used if input file is fasta.""") parser.add_argument( 'output_file', type=FileType('w'), help="""Output file. Format determined from extension.""") output_group = parser.add_argument_group("Output") output_group.add_argument( '--report-out', type=FileType('w'), default=sys.stdout, help="""Output file for report [default: stdout]""") output_group.add_argument( '--details-out', type=FileType('w'), help="""Output file to report fate of each sequence""") output_group.add_argument( '--no-details-comment', action='store_false', default=True, dest='details_comment', help="""Do not write comment lines with version and call to start --details-out""") parser.add_argument( '--min-mean-quality', metavar='QUALITY', type=float, default=DEFAULT_MEAN_SCORE, help="""Minimum mean quality score for each read [default: %(default)s]""") parser.add_argument( '--min-length', metavar='LENGTH', type=int, default=200, help="""Minimum length to keep sequence [default: %(default)s]""") parser.add_argument( '--max-length', metavar='LENGTH', type=int, default=1000, help="""Maximum length to keep before truncating [default: %(default)s]. This operation occurs before --max-ambiguous""") window_group = parser.add_argument_group('Quality window options') window_group.add_argument( '--quality-window-mean-qual', type=float, help="""Minimum quality score within the window defined by --quality-window. [default: same as --min-mean-quality]""") window_group.add_argument( '--quality-window-prop', help="""Proportion of reads within quality window to that must pass filter. Floats are [default: %(default).1f]""", default=1.0, type=typed_range(float, 0.0, 1.0)) window_group.add_argument( '--quality-window', type=int, metavar='WINDOW_SIZE', default=0, help="""Window size for truncating sequences. When set to a non-zero value, sequences are truncated where the mean mean quality within the window drops below --min-mean-quality. [default: %(default)s]""") parser.add_argument( '--ambiguous-action', choices=('truncate', 'drop'), help="""Action to take on ambiguous base in sequence (N's). [default: no action]""") parser.add_argument( '--max-ambiguous', default=None, help="""Maximum number of ambiguous bases in a sequence. Sequences exceeding this count will be removed.""", type=int) parser.add_argument( '--pct-ambiguous', help="""Maximun percent of ambiguous bases in a sequence. Sequences exceeding this percent will be removed.""", type=float) barcode_group = parser.add_argument_group('Barcode/Primer') primer_group = barcode_group.add_mutually_exclusive_group() primer_group.add_argument( '--primer', help="""IUPAC ambiguous primer to require""") primer_group.add_argument( '--no-primer', help="""Do not use a primer.""", action='store_const', const='', dest='primer') barcode_group.add_argument( '--barcode-file', help="""CSV file containing sample_id,barcode[,primer] in the rows. A single primer for all sequences may be specified with `--primer`, or `--no-primer` may be used to indicate barcodes should be used without a primer check.""", type=FileType('r')) barcode_group.add_argument( '--barcode-header', action='store_true', default=False, help="""Barcodes have a header row [default: %(default)s]""") barcode_group.add_argument( '--map-out', help="""Path to write sequence_id,sample_id pairs""", type=FileType('w'), metavar='SAMPLE_MAP') barcode_group.add_argument( '--quoting', help="""A string naming an attribute of the csv module defining the quoting behavior for `SAMPLE_MAP`. [default: %(default)s]""", default='QUOTE_MINIMAL', choices=[s for s in dir(csv) if s.startswith('QUOTE_')]) def mean(sequence): """ Calculates the arithmetic mean of a list / tuple """ return sum(sequence) / float(len(sequence)) def moving_average(iterable, n): """ From Python collections module documentation moving_average([40, 30, 50, 46, 39, 44]) --> 40.0 42.0 45.0 43.0 """ it = iter(iterable) d = collections.deque(itertools.islice(it, n - 1)) d.appendleft(0) s = sum(d) for elem in it: s += elem - d.popleft() d.append(elem) yield s / float(n) class FailedFilter(Exception): """ A read failed filtering """ def __init__(self, value=None): self.value = value class RecordEventListener(object): """ Contains and dispatches to handlers on events around sequence records Event handlers take a single positional argument, the record, and optional additional keyword arguments. """ def __init__(self): self.listeners = collections.defaultdict(set) def __call__(self, event, record, **kwargs): """ Trigger an event :param event: Event name :param record: Record affected :param **kwargs: Optional additional arguments to pass to handlers """ if event in self.listeners: for listener in self.listeners[event]: listener(record, **kwargs) def register_handler(self, event, handler): """ Register ``handler`` for ``event`` """ self.listeners[event].add(handler) def iterable_hook(self, name, iterable): """ Fire an event named ``name`` with each item in iterable """ for record in iterable: self(name, record) yield record class RecordReportHandler(object): """ Generates a report to a CSV file detailing every record processed. Listens for events: [read, write, failed_filter, found_barcode] """ HEADERS = ('sequence_name', 'in_length', 'in_mean_qual', 'sample', 'out_length', 'out_mean_qual', 'fail_filter', 'fail_value') def __init__(self, fp, args, write_comments=True): if write_comments: fp.write('# Generated by `seqmagick quality-filter` version {0}\n'. format(__version__)) fp.write('# Arguments: {0}\n'.format(' '.join(args))) fp.write('# Working directory: {0}\n'.format(os.getcwd())) self.writer = csv.DictWriter( fp, self.HEADERS, lineterminator='\n', quoting=csv.QUOTE_NONNUMERIC) self.writer.writeheader() self.current_record = None self.read = 0 self.failed = 0 self.start = time.time() self.last_report = 0.0 def register_with(self, listener): listener.register_handler('failed_filter', self._record_failed) listener.register_handler('read', self._read_record) listener.register_handler('write', self._wrote_record) listener.register_handler('found_barcode', self._found_barcode) def _write(self): assert self.current_record self.writer.writerow(self.current_record) self.current_record = None def _record_failed(self, record, filter_name, value=None): self.current_record.update({ 'fail_filter': filter_name, 'fail_value': value }) self._write() self.failed += 1 self._report() def _read_record(self, record): self.current_record = { 'sequence_name': record.id, 'in_length': len(record) } if 'phred_quality' in record.letter_annotations: self.current_record['in_mean_qual'] = mean( record.letter_annotations['phred_quality']) self.read += 1 def _found_barcode(self, record, sample, barcode=None): """Hook called when barcode is found""" assert record.id == self.current_record['sequence_name'] self.current_record['sample'] = sample def _wrote_record(self, record): self.current_record['out_length'] = len(record) if 'phred_quality' in record.letter_annotations: self.current_record['out_mean_qual'] = mean( record.letter_annotations['phred_quality']) self._write() self._report() def _report(self): if not sys.stdout.isatty(): return t = time.time() if t - self.last_report < 0.4 or not self.read: return self.last_report = t sys.stderr.write( '{0:10.1f}s Processed {1:10d} records; {2:10d} passed ({3:6.2f}%)\r'. format(t - self.start, self.read, self.read - self.failed, float(self.read - self.failed) / self.read * 100.0)) class BaseFilter(object): """ Base class for filters """ report_fields = ('name', 'passed_unchanged', 'passed_changed', 'failed', 'total_filtered', 'proportion_passed') def __init__(self, listener=None): self.passed_unchanged = 0 self.passed_changed = 0 self.failed = 0 self.listener = listener def filter_record(self, record): """ Filter a record. If the filter succeeds, returns a SeqRecord. If it fails, raises an instance of FailedFilter with an optional value. """ raise NotImplementedError("Override in subclass") def filter_records(self, records): """ Apply the filter to records """ for record in records: try: filtered = self.filter_record(record) assert (filtered) # Quick tracking whether the sequence was modified if filtered.seq == record.seq: self.passed_unchanged += 1 else: self.passed_changed += 1 yield filtered except FailedFilter as e: self.failed += 1 v = e.value if self.listener: self.listener( 'failed_filter', record, filter_name=self.name, value=v) @property def passed(self): return self.passed_changed + self.passed_unchanged @property def total_filtered(self): return self.passed + self.failed @property def proportion_passed(self): if not self.total_filtered: return 0 return float(self.passed) / self.total_filtered def report_dict(self): return dict((f, getattr(self, f)) for f in self.report_fields) class QualityScoreFilter(BaseFilter): """ Quality score filter - requires that the average base quality over the length of the read is greater than some threshold. """ def __init__(self, min_mean_score=DEFAULT_MEAN_SCORE): super(QualityScoreFilter, self).__init__() self.min_mean_score = min_mean_score self.name = "Quality Score [min_mean: {0}]".format(min_mean_score) def filter_record(self, record): """ Filter a single record """ quality_scores = record.letter_annotations['phred_quality'] mean_score = mean(quality_scores) if mean_score >= self.min_mean_score: return record else: raise FailedFilter(mean_score) class WindowQualityScoreFilter(BaseFilter): """ Filter records, truncating records when the mean score drops below a certain value. """ def __init__(self, window_size, min_mean_score=DEFAULT_MEAN_SCORE): super(WindowQualityScoreFilter, self).__init__() self.min_mean_score = min_mean_score assert window_size and window_size > 0 self.window_size = window_size self.name = ("Windowed Quality Score " + "[min_mean-quality: {0}; window_size: {1}]").format( min_mean_score, window_size) def filter_record(self, record): """ Filter a single record """ quality_scores = record.letter_annotations['phred_quality'] # Simple case - window covers whole sequence if len(record) <= self.window_size: mean_score = mean(quality_scores) if mean_score >= self.min_mean_score: return record else: raise FailedFilter(mean_score) # Find the right clipping point. Start clipping at the beginning of the # sequence, then extend the window to include regions with acceptable # mean quality scores. clip_right = 0 for i, a in enumerate( moving_average(quality_scores, self.window_size)): if a >= self.min_mean_score: clip_right = i + self.window_size else: break if clip_right: return record[:clip_right] else: # First window failed - record fails raise FailedFilter() class AmbiguousBaseFilter(BaseFilter): """ Filter records, taking some action if 'N' is encountered in the sequence. action - either 'truncate' (drop N and any sequence following) or 'drop' (remove sequences with 'N's) """ name = 'Ambiguous Base' def __init__(self, action): super(AmbiguousBaseFilter, self).__init__() if action not in ('truncate', 'drop'): raise ValueError("Unknown action: {0}".format(action)) self.action = action self.name = AmbiguousBaseFilter.name + " [{0}]".format(action) def filter_record(self, record): """ Filter a record, truncating or dropping at an 'N' """ nloc = record.seq.find('N') if nloc == -1: return record elif self.action == 'truncate': return record[:nloc] elif self.action == 'drop': raise FailedFilter() else: assert False class MaxAmbiguousFilter(BaseFilter): """ Filters records exceeding some minimum number of ambiguous bases """ name = "Maximum Ambiguous Bases" def __init__(self, max_ambiguous): super(MaxAmbiguousFilter, self).__init__() assert max_ambiguous is not None self.max_ambiguous = max_ambiguous self.name = self.name + ' [{0}]'.format(max_ambiguous) def filter_record(self, record): n_count = record.seq.upper().count('N') if n_count > self.max_ambiguous: raise FailedFilter(n_count) else: assert n_count <= self.max_ambiguous return record class PctAmbiguousFilter(BaseFilter): """ Filters records exceeding some minimum percent of ambiguous bases """ name = "Percent Ambiguous Bases" def __init__(self, pct_ambiguous): super(PctAmbiguousFilter, self).__init__() assert pct_ambiguous is not None self.pct_ambiguous = pct_ambiguous self.name = self.name + ' [{0}]'.format(pct_ambiguous) def filter_record(self, record): n_count = record.seq.upper().count('N') if n_count == 0: return record pct_ambig = n_count / float(len(record.seq)) if pct_ambig > self.pct_ambiguous: raise FailedFilter(pct_ambig) else: assert pct_ambig <= self.pct_ambiguous return record class MinLengthFilter(BaseFilter): """ Remove records which don't meet minimum length """ def __init__(self, min_length): super(MinLengthFilter, self).__init__() assert min_length > 0 self.min_length = min_length self.name = "Minimum Length [{0}]".format(min_length) def filter_record(self, record): """ Filter record, dropping any that don't meet minimum length """ if len(record) >= self.min_length: return record else: raise FailedFilter(len(record)) class MaxLengthFilter(BaseFilter): """ Truncate long sequences """ name = "Maximum Length" def __init__(self, max_length): super(MaxLengthFilter, self).__init__() self.max_length = max_length self.name = self.name + " [{0}]".format(max_length) def filter_record(self, record): """ Filter record, truncating any over some maximum length """ if len(record) >= self.max_length: return record[:self.max_length] else: return record class PrimerBarcodeFilter(BaseFilter): """ Filter that checks that the sequence starts with a known barcode/primer combination. Sequences that pass the filter have the barcode and primer removed. If an output_file is provided, (sequence_id, sample_id) tuples are written to it. """ name = "Primer/Barcode" def __init__(self, trie, output_file=None, trim=True, quoting=csv.QUOTE_MINIMAL): super(PrimerBarcodeFilter, self).__init__() self.trim = True self.trie = trie def filter_record(self, record): m = trie_match(str(record.seq), self.trie) if m: if self.listener: self.listener( 'found_barcode', record, barcode=m, sample=self.trie[m]) if self.trim: record = record[len(m):] return record else: raise FailedFilter() def parse_barcode_file(fp, primer=None, header=False): """ Load label, barcode, primer records from a CSV file. Returns a map from barcode -> label Any additional columns are ignored """ tr = trie.StringTrie() reader = csv.reader(fp) if header: # Skip header next(reader) # Skip blank rows records = (record for record in reader if record) for record in records: specimen, barcode = record[:2] if primer is not None: pr = primer else: pr = record[2] for sequence in all_unambiguous(barcode + pr): if sequence in tr: raise ValueError("Duplicate sample: {0}, {1} both have {2}", specimen, tr[sequence], sequence) logging.info('%s->%s', sequence, specimen) tr[sequence] = specimen return tr def action(arguments): """ Given parsed arguments, filter input files. """ if arguments.quality_window_mean_qual and not arguments.quality_window: raise ValueError("--quality-window-mean-qual specified without " "--quality-window") filters = [] input_type = fileformat.from_handle(arguments.sequence_file) output_type = fileformat.from_handle(arguments.output_file) with arguments.sequence_file as fp: if arguments.input_qual: sequences = QualityIO.PairedFastaQualIterator( fp, arguments.input_qual) else: sequences = SeqIO.parse(fp, input_type) listener = RecordEventListener() if arguments.details_out: rh = RecordReportHandler(arguments.details_out, arguments.argv, arguments.details_comment) rh.register_with(listener) # Track read sequences sequences = listener.iterable_hook('read', sequences) # Add filters if arguments.min_mean_quality and input_type == 'fastq': qfilter = QualityScoreFilter(arguments.min_mean_quality) filters.append(qfilter) if arguments.max_length: max_length_filter = MaxLengthFilter(arguments.max_length) filters.append(max_length_filter) if arguments.min_length: min_length_filter = MinLengthFilter(arguments.min_length) filters.append(min_length_filter) if arguments.max_ambiguous is not None: max_ambig_filter = MaxAmbiguousFilter(arguments.max_ambiguous) filters.append(max_ambig_filter) if arguments.pct_ambiguous is not None: pct_ambig_filter = PctAmbiguousFilter(arguments.pct_ambiguous) filters.append(pct_ambig_filter) if arguments.ambiguous_action: ambiguous_filter = AmbiguousBaseFilter(arguments.ambiguous_action) filters.append(ambiguous_filter) if arguments.quality_window: min_qual = (arguments.quality_window_mean_qual or arguments.min_mean_quality) window_filter = WindowQualityScoreFilter(arguments.quality_window, min_qual) filters.insert(0, window_filter) if arguments.barcode_file: with arguments.barcode_file: tr = parse_barcode_file(arguments.barcode_file, arguments.primer, arguments.barcode_header) f = PrimerBarcodeFilter(tr) filters.append(f) if arguments.map_out: barcode_writer = csv.writer( arguments.map_out, quoting=getattr(csv, arguments.quoting), lineterminator='\n') def barcode_handler(record, sample, barcode=None): barcode_writer.writerow((record.id, sample)) listener.register_handler('found_barcode', barcode_handler) for f in filters: f.listener = listener sequences = f.filter_records(sequences) # Track sequences which passed all filters sequences = listener.iterable_hook('write', sequences) with arguments.output_file: SeqIO.write(sequences, arguments.output_file, output_type) rpt_rows = (f.report_dict() for f in filters) # Write report with arguments.report_out as fp: writer = csv.DictWriter( fp, BaseFilter.report_fields, lineterminator='\n', delimiter='\t') writer.writeheader() writer.writerows(rpt_rows) seqmagick-0.8.4/seqmagick/test/000077500000000000000000000000001376401056300164175ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/test/__init__.py000066400000000000000000000000001376401056300205160ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/test/integration/000077500000000000000000000000001376401056300207425ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/test/integration/__init__.py000066400000000000000000000005061376401056300230540ustar00rootroot00000000000000""" Integration tests, mostly to ensure that basic commands continue working after commits. Tests invoke seqmagick.scripts.cli.main, and compare the produced output to the expected. """ import os.path data_dir = os.path.join(os.path.dirname(__file__), "data") def data_path(*args): return os.path.join(data_dir, *args) seqmagick-0.8.4/seqmagick/test/integration/data/000077500000000000000000000000001376401056300216535ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/test/integration/data/__init__.py000066400000000000000000000000001376401056300237520ustar00rootroot00000000000000seqmagick-0.8.4/seqmagick/test/integration/data/input1.fasta000066400000000000000000000001201376401056300241040ustar00rootroot00000000000000>test1 test sequence 1 ACGT >test2 test sequence 2 AAAA >test3 sequence 3 ACGA seqmagick-0.8.4/seqmagick/test/integration/data/input2.fasta000066400000000000000000000001221376401056300241070ustar00rootroot00000000000000>test1 test sequence 1 AC-GT >test2 test sequence 2 A-AAA >test3 sequence 3 A---A seqmagick-0.8.4/seqmagick/test/integration/data/input2.fasta.bz2000066400000000000000000000001331376401056300246050ustar00rootroot00000000000000BZh91AY&SYaAh ߀@8( . HTڟ=Lh6ht[yF8dBeAI,رЋ!Etw$S Pseqmagick-0.8.4/seqmagick/test/integration/data/input2.fasta.gz000066400000000000000000000001241376401056300245300ustar00rootroot00000000000000VwNinput2.fasta+I-.1T ũyɩ \κ!\v a#4I#.G]GGG1B(ӁJRseqmagick-0.8.4/seqmagick/test/integration/data/input3.fasta000066400000000000000000000000661376401056300241170ustar00rootroot00000000000000>HXB2 AA--CGT >Sequence 1 -AACTCT >Sequence 3 TAG-ATG seqmagick-0.8.4/seqmagick/test/integration/data/input4_ambig.fasta000066400000000000000000000000521376401056300252520ustar00rootroot00000000000000>sequence1 GCYCCCAAG >sequence2 CCC-CC--- seqmagick-0.8.4/seqmagick/test/integration/data/input5.fasta000066400000000000000000000001241376401056300241140ustar00rootroot00000000000000>test1 ACGT >test2 AAAA >test3 ACGA >test4 ACGT >test5 AAAA >test6 ACGA >test7 ACGA seqmagick-0.8.4/seqmagick/test/integration/data/input6.fasta000066400000000000000000000001261376401056300241170ustar00rootroot00000000000000>test1 test sequence 1 RNA AC-GU >test2 test sequence 2 A-AAA >test3 sequence 3 A---A seqmagick-0.8.4/seqmagick/test/integration/data/output2.fasta000066400000000000000000000001221376401056300243100ustar00rootroot00000000000000>test1 test sequence 1 AC-GT >test2 test sequence 2 A-AAA >test3 sequence 3 A---A seqmagick-0.8.4/seqmagick/test/integration/data/output2.nex000066400000000000000000000002051376401056300240060ustar00rootroot00000000000000#NEXUS begin data; dimensions ntax=3 nchar=5; format datatype=dna missing=? gap=-; matrix test1 AC-GT test2 A-AAA test3 A---A ; end; seqmagick-0.8.4/seqmagick/test/integration/data/output2.phy000066400000000000000000000000701376401056300240140ustar00rootroot00000000000000 3 5 test1 AC-GT test2 A-AAA test3 A---A seqmagick-0.8.4/seqmagick/test/integration/data/output2_ungap_cut.fasta000066400000000000000000000000601376401056300263560ustar00rootroot00000000000000>test2 test sequence 2 AAA >test3 sequence 3 AA seqmagick-0.8.4/seqmagick/test/integration/data/output3.fasta000066400000000000000000000000551376401056300243160ustar00rootroot00000000000000>HXB2 A--C >Sequence 1 AACT >Sequence 3 AG-A seqmagick-0.8.4/seqmagick/test/integration/data/output3.nex000066400000000000000000000002051376401056300240070ustar00rootroot00000000000000#NEXUS begin data; dimensions ntax=3 nchar=5; format datatype=rna missing=? gap=-; matrix test1 AC-GU test2 A-AAA test3 A---A ; end; seqmagick-0.8.4/seqmagick/test/integration/data/output4.fasta000066400000000000000000000000361376401056300243160ustar00rootroot00000000000000>sequence1 APK >sequence2 PX- seqmagick-0.8.4/seqmagick/test/integration/data/output4.nex000066400000000000000000000002111376401056300240050ustar00rootroot00000000000000#NEXUS begin data; dimensions ntax=3 nchar=5; format datatype=protein missing=? gap=-; matrix test1 AC-GT test2 A-AAA test3 A---A ; end; seqmagick-0.8.4/seqmagick/test/integration/data/output5.fasta000066400000000000000000000000301376401056300243110ustar00rootroot00000000000000>test5 AAAA >test3 ACGA seqmagick-0.8.4/seqmagick/test/integration/test_convert.py000066400000000000000000000155661376401056300240500ustar00rootroot00000000000000from io import StringIO import os import os.path import logging import random import shlex import shutil import sys import unittest import tempfile from seqmagick.subcommands.common import FileType from seqmagick.scripts import cli d = os.path.dirname(__file__) data_dir = os.path.join(d, "data") def p(*args): return os.path.join(data_dir, *args) class CommandLineTestMixIn(object): in_suffix = '' out_suffix = '' def setUp(self): self.input_file = tempfile.NamedTemporaryFile(suffix=self.in_suffix) shutil.copy(self.input_path, self.input_file.name) with tempfile.NamedTemporaryFile(suffix=self.out_suffix) as tf: self.output_file = tf.name def test_run(self): command = self.command.format( input=self.input_file.name, output=self.output_file) cli.main(shlex.split(command)) with FileType('rt')(self.output_file) as fp: actual = fp.read() with FileType('rt')(self.expected_path) as fp: expected = fp.read() self.assertEqual(expected, actual) def tearDown(self): self.input_file.close() if os.path.isfile(self.output_file): os.remove(self.output_file) class BasicConvertTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.phy' input_path = p('input2.fasta') expected_path = p('output2.phy') command = 'convert {input} {output}' @unittest.skipIf(sys.version_info.major == 3, 'bzip2 not supported') class BzipInputConvertTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta.bz2' out_suffix = '.phy' input_path = p('input2.fasta.bz2') expected_path = p('output2.phy') command = 'convert {input} {output}' @unittest.skipIf(sys.version_info.major == 3, 'bzip2 not supported') class BzipOutputConvertTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.phy.bz2' input_path = p('input2.fasta') expected_path = p('output2.phy') command = 'convert {input} {output}' class GzipInputConvertTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta.gz' out_suffix = '.phy' input_path = p('input2.fasta.gz') expected_path = p('output2.phy') command = 'convert {input} {output}' class GzipOutputConvertTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.phy.gz' input_path = p('input2.fasta') expected_path = p('output2.phy') command = 'convert {input} {output}' class ConvertToNexusTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' input_path = p('input2.fasta') expected_path = p('output2.nex') command = 'convert {input} {output} --output-format nexus --alphabet dna-ambiguous' class ConvertToNexusRNATestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' input_path = p('input6.fasta') expected_path = p('output3.nex') command = 'convert {input} {output} --output-format nexus --alphabet rna' class ConvertToNexusProteinTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' input_path = p('input2.fasta') expected_path = p('output4.nex') command = 'convert {input} {output} --output-format nexus --alphabet protein' class ConvertUngapCutTestCase(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.fasta' input_path = p('input2.fasta') expected_path = p('output2_ungap_cut.fasta') command = 'convert --ungap --cut 1:3 --tail 2 {input} {output}' class ConvertToStdOutTestCase(unittest.TestCase): def setUp(self): self.out = StringIO() self.err = StringIO() self.actual_stdout = sys.stdout self.actual_stderr = sys.stderr sys.stdout = self.out sys.stderr = self.err def tearDown(self): sys.stdout = self.actual_stdout sys.stderr = self.actual_stderr def test_convert(self): in_path = p('input2.fasta') cli.main(['convert', in_path, '-', '--output-format', 'fasta']) actual = self.out.getvalue() with open(in_path) as fp: expected = fp.read() self.assertEqual(expected, actual) def test_convert_noformat(self): in_path = p('input2.fasta') cli.main(['convert', in_path, '-']) actual = self.out.getvalue() with open(in_path) as fp: expected = fp.read() self.assertEqual(expected, actual) class TestCutRelative(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.fasta' input_path = p('input3.fasta') expected_path = p('output3.fasta') command = 'convert --cut 2:3 --relative-to HXB2 {input} {output}' def test_unknown_seq(self): args = ['convert', '--cut', '2:3', '--relative-to', 'OTHER', self.input_path, '-', '--output-format', 'fasta'] self.assertRaises(ValueError, cli.main, args) class TestTranslateAmbiguous(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.fasta' input_path = p('input4_ambig.fasta') expected_path = p('output4.fasta') command = 'convert --translate dna2protein {input} {output}' def setUp(self): super(TestTranslateAmbiguous, self).setUp() self.orig_level = logging.getLogger(None).level logging.getLogger(None).setLevel(logging.FATAL) def tearDown(self): super(TestTranslateAmbiguous, self).tearDown() logging.getLogger(None).setLevel(self.orig_level) class TestSample(CommandLineTestMixIn, unittest.TestCase): in_suffix = '.fasta' out_suffix = '.fasta' input_path = p('input5.fasta') expected_path = p('output5.fasta') command = 'convert --sample 2 --sample-seed 0 {input} {output}' def setUp(self): super(TestSample, self).setUp() self.orig_level = logging.getLogger(None).level logging.getLogger(None).setLevel(logging.FATAL) random.seed(1) def tearDown(self): super(TestSample, self).tearDown() logging.getLogger(None).setLevel(self.orig_level) class TestStdin(TestTranslateAmbiguous, unittest.TestCase): command = 'convert --translate dna2protein - {output}' def setUp(self): super(TestStdin, self).setUp() self.orig_stdin = sys.stdin sys.stdin = open(p('input4_ambig.fasta'), 'r') def tearDown(self): super(TestStdin, self).tearDown() sys.stdin.close() sys.stdin = self.orig_stdin class TestConvertFromStdin(TestTranslateAmbiguous, unittest.TestCase): command = 'convert --translate dna2protein - {output}' def setUp(self): super(TestConvertFromStdin, self).setUp() self.orig_stdin = sys.stdin sys.stdin = open(p('input4_ambig.fasta'), 'r') def tearDown(self): super(TestConvertFromStdin, self).tearDown() sys.stdin.close() sys.stdin = self.orig_stdin seqmagick-0.8.4/seqmagick/test/integration/test_extract_ids.py000066400000000000000000000022751376401056300246720ustar00rootroot00000000000000import sys import unittest import tempfile from seqmagick.scripts import cli from seqmagick.test.integration import data_path class ExtractIdsMixin(object): expected = """test1 test2 test3 """ expected_desc = """test1 test sequence 1 test2 test sequence 2 test3 sequence 3 """ def setUp(self): self.tempfile = tempfile.NamedTemporaryFile('r+t') def tearDown(self): self.tempfile.close() def test_ids(self): args = ['extract-ids', self.seq_file, '-o', self.tempfile.name] cli.main(args) self.assertEqual(self.expected, self.tempfile.read()) def test_descriptions(self): args = ['extract-ids', self.seq_file, '-o', self.tempfile.name, '-d'] cli.main(args) self.assertEqual(self.expected_desc, self.tempfile.read()) class SimpleExtractIdsTestCase(ExtractIdsMixin, unittest.TestCase): seq_file = data_path('input2.fasta') @unittest.skipIf(sys.version_info.major == 3, 'bzip2 not supported') class Bz2ExtractIdsTestCase(ExtractIdsMixin, unittest.TestCase): seq_file = data_path('input2.fasta.bz2') class GzipExtractIdsTestCase(ExtractIdsMixin, unittest.TestCase): seq_file = data_path('input2.fasta.gz') seqmagick-0.8.4/seqmagick/test/integration/test_info.py000066400000000000000000000023561376401056300233140ustar00rootroot00000000000000import sys import unittest import tempfile from seqmagick.scripts import cli from seqmagick.test.integration import data_path class InfoMixin(object): expected = """name\talignment\tmin_len\tmax_len\tavg_len\tnum_seqs {0}\tTRUE\t5\t5\t5.00\t3 """ threads = 1 def setUp(self): self.infile = tempfile.NamedTemporaryFile() self.tempfile = tempfile.NamedTemporaryFile('w+t') def tearDown(self): self.infile.close() self.tempfile.close() def test_info(self): args = ['info', self.seq_file, '--out-file', self.tempfile.name, '--threads', str(self.threads)] cli.main(args) self.assertEqual(self.expected.format(self.seq_file), self.tempfile.read()) class SimpleInfoTestCase(InfoMixin, unittest.TestCase): seq_file = data_path('input2.fasta') class MultithreadedInfoTestCase(InfoMixin, unittest.TestCase): seq_file = data_path('input2.fasta') threads = 2 class SimpleGzipInfoTestCase(InfoMixin, unittest.TestCase): seq_file = data_path('input2.fasta.gz') @unittest.skipIf(sys.version_info.major == 3, 'bzip2 not supported') class SimpleBzip2InfoTestCase(InfoMixin, unittest.TestCase): seq_file = data_path('input2.fasta.bz2') seqmagick-0.8.4/seqmagick/test/integration/test_mogrify.py000066400000000000000000000030701376401056300240270ustar00rootroot00000000000000 import os import os.path import shlex import shutil import tempfile from seqmagick.scripts import cli from seqmagick.subcommands.common import FileType from seqmagick.test.integration import data_path from . import test_convert class CommandLineTestMixIn(object): def setUp(self): with tempfile.NamedTemporaryFile( 'wt', suffix=os.path.basename(self.input_path), delete=False) as tf: self.input_file = tf.name shutil.copyfile(self.input_path, self.input_file) def test_run(self): command = self.command.format(input=self.input_file) try: cli.main(shlex.split(command)) except SystemExit as e: self.fail(e) with FileType('rt')(self.input_file) as fp: actual = fp.read() with FileType('rt')(self.expected_path) as fp: expected = fp.read() self.assertEqual(expected, actual) def tearDown(self): os.remove(self.input_file) class MogrifyUngapCutTestCase( CommandLineTestMixIn, test_convert.ConvertUngapCutTestCase): command = 'mogrify --ungap --cut 1:3 --tail 2 {input}' class MogrifyBzipInputTestCase( CommandLineTestMixIn, test_convert.BzipInputConvertTestCase): command = 'mogrify {input}' expected_path = data_path('output2.fasta') out_suffix = 'fasta.bz2' class MogrifyGzipInputTestCase( CommandLineTestMixIn, test_convert.GzipInputConvertTestCase): command = 'mogrify {input}' expected_path = data_path('output2.fasta') out_suffix = 'fasta.gz' seqmagick-0.8.4/seqmagick/test/test_primer_trim.py000066400000000000000000000070231376401056300223630ustar00rootroot00000000000000""" Tests for primer trim """ import unittest from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from seqmagick.subcommands import primer_trim class PrimerAlignerTestCase(unittest.TestCase): def setUp(self): self.primer = 'AACTGCATTTGAATGG' self.instance = primer_trim.PrimerAligner( self.primer, match=5.0, gap_open=-10.0) def test_max_score(self): self.assertEqual(len(self.primer) * 5.0, self.instance.max_score) def test_align_exact(self): sequence = ('ACTCTGTGTCACTTTAAACTGCATTTGAATGGAAGAGTAATAGTAGCAATAACGGCA' 'CTGATCAG') hamming_distance, start, end = self.instance.align(sequence) self.assertEqual(0, hamming_distance) self.assertEqual(16, start) self.assertEqual(31, end) def test_align_gap(self): sequence = ('ACTCTGTGTCACTTTAAACTGCATTGAATGGAAGAGTAATAGTAGCAATAACGGCA' 'CTGATCAG') hamming_distance, start, end = self.instance.align(sequence) expected_distance = 1 self.assertEqual(expected_distance, hamming_distance) self.assertEqual(16, start) self.assertEqual(30, end) class HammingDistanceTestCase(unittest.TestCase): def test_unequal_length(self): s1 = 'test' s2 = 'te' self.assertRaises(ValueError, primer_trim.hamming_distance, s1, s2) def test_no_difference(self): s1 = s2 = 'test' self.assertEqual(0, primer_trim.hamming_distance(s1, s2)) def test_all_different(self): s1 = 'test' s2 = 'ACGT' self.assertEqual(4, primer_trim.hamming_distance(s1, s2)) def test_basic(self): s1 = 'ACGT' s2 = 'AGGT' self.assertEqual(1, primer_trim.hamming_distance(s1, s2)) def test_ambiguous(self): s1 = 'ACYT' s2 = 'ACCT' self.assertEqual(0, primer_trim.hamming_distance( s1, s2, primer_trim._iupac_ambiguous_equal)) s2 = 'ACTT' self.assertEqual(0, primer_trim.hamming_distance( s1, s2, primer_trim._iupac_ambiguous_equal)) def _alignment_record(sequence): return SeqRecord(Seq(sequence)) class LocatePrimersTestCase(unittest.TestCase): """ Test for locate primers """ def setUp(self): self.sequences = [_alignment_record('--A--ACTGGACGTATTC-CCCC')] def test_basic(self): forward = 'TGG' reverse = 'TTC' forward_idx, reverse_idx = primer_trim.locate_primers( self.sequences, forward, reverse, False, 1) self.assertEqual((7, 9), forward_idx) self.assertEqual((15, 17), reverse_idx) def test_no_forward(self): forward = 'GGGGGG' reverse = 'TTC' self.assertRaises(primer_trim.PrimerNotFound, primer_trim.locate_primers, self.sequences, forward, reverse, False, 1) def test_no_reverse(self): forward = 'TGG' reverse = 'GGGG' self.assertRaises(primer_trim.PrimerNotFound, primer_trim.locate_primers, self.sequences, forward, reverse, False, 1) def test_bad_order(self): """ Should fail if reverse primer occurs before forward primer """ reverse = 'TGG' forward = 'TTC' self.assertRaises(primer_trim.PrimerOrderError, primer_trim.locate_primers, self.sequences, forward, reverse, False, 1) seqmagick-0.8.4/seqmagick/test/test_subcommands_backtrans_align.py000066400000000000000000000052031376401056300255450ustar00rootroot00000000000000import unittest from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.Data import CodonTable from seqmagick.subcommands import backtrans_align class BatchTestCase(unittest.TestCase): def test_no_input(self): i = [] b = backtrans_align.batch(i, 1) self.assertRaises(StopIteration, next, b) def test_singletons(self): i = list(range(3)) b = backtrans_align.batch(i, 1) self.assertEqual([[0], [1], [2]], list(b)) def test_doubles(self): i = list(range(6)) b = backtrans_align.batch(i, 2) self.assertEqual([[0, 1], [2, 3], [4, 5]], list(b)) def test_partial(self): i = list(range(5)) b = backtrans_align.batch(i, 2) self.assertEqual([[0, 1], [2, 3], [4]], list(b)) class AlignmentMapperTestCase(unittest.TestCase): def setUp(self): self.instance = backtrans_align.AlignmentMapper(CodonTable.unambiguous_dna_by_name['Standard']) def test_validate_valid(self): nucl = 'TTTAAG' prot = 'FK' self.assertTrue(self.instance._validate_translation(prot, nucl)) def test_validate_invalid(self): nucl = 'AAGTTT' prot = 'KK' self.assertRaisesRegex(ValueError, r'Codon TTT translates to F, not K', self.instance._validate_translation, prot, nucl) def test_map_alignment(self): nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF SeqRecord(Seq('AAGGTCTTC'), id='2'), # KVF SeqRecord(Seq('GGGGTTTTT'), id='3')] # GVF prot = [SeqRecord(Seq('-K-F'), id='1'), SeqRecord(Seq('-KVF'), id='2'), SeqRecord(Seq('G-VF'), id='3')] result = self.instance.map_all(prot, nucl) result = [(s.id, str(s.seq)) for s in result] self.assertEqual([('1', '---AAG---TTT'), ('2', '---AAGGTCTTC'), ('3', 'GGG---GTTTTT')], result) def test_map_alignment_insufficient_codons(self): nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF SeqRecord(Seq('AAGGTC'), id='2')] # KV prot = [SeqRecord(Seq('K-F'), id='1'), SeqRecord(Seq('KVF'), id='2')] mapped = self.instance.map_all(prot, nucl) self.assertRaises(ValueError, list, mapped) def test_map_alignment_excess_codons(self): nucl = [SeqRecord(Seq('AAGTTT'), id='1'), # KF SeqRecord(Seq('AAGGTCTTC'), id='2')] # KVF prot = [SeqRecord(Seq('K-F'), id='1'), SeqRecord(Seq('KV-'), id='2')] mapped = self.instance.map_all(prot, nucl) self.assertRaises(ValueError, list, mapped) seqmagick-0.8.4/seqmagick/test/test_subcommands_common.py000066400000000000000000000137461376401056300237260ustar00rootroot00000000000000import argparse import os import os.path import sys import unittest import tempfile from seqmagick.subcommands import common d = os.path.dirname(__file__) data_dir = os.path.join(d, "integration", "data") def p(*args): return os.path.join(data_dir, *args) class PartialAppendTestCase(unittest.TestCase): def setUp(self): self.namespace = argparse.Namespace() def test_single_arg(self): def head(records, n): return records[:n] a_cls = common.partial_append_action(head, 'n') a = a_cls([], 'functions') a(None, self.namespace, 2) f = self.namespace.functions[0] self.assertEqual([0, 1], f(list(range(10)))) def test_no_arg(self): def head(records): return records[:2] a_cls = common.partial_append_action(head) a = a_cls([], 'functions') a(None, self.namespace, None) f = self.namespace.functions[0] self.assertEqual([0, 1], f(list(range(10)))) def test_multi_arg(self): def fake_slice(records, i, j): return records[i:j] a_cls = common.partial_append_action(fake_slice, ['i', 'j']) a = a_cls([], 'functions') a(None, self.namespace, [0, 2]) f = self.namespace.functions[0] self.assertEqual([0, 1], f(list(range(10)))) class PositiveValueTestCase(unittest.TestCase): def test_negative(self): self.assertRaises(argparse.ArgumentTypeError, common.positive_value(int), '-1') def test_positive(self): self.assertEqual(1, common.positive_value(int)('1')) def test_zero(self): self.assertEqual(0, common.positive_value(int)('0')) class CutRangeTestCase(unittest.TestCase): def test_out_of_order(self): self.assertRaises(argparse.ArgumentTypeError, common.cut_range, '10:5') def test_start(self): actual = common.cut_range('5:10') self.assertEqual(4, actual.start) self.assertEqual(10, actual.stop) def test_negative(self): actual = common.cut_range('-500:') self.assertEqual(-500, actual.start) self.assertIsNone(actual.stop) actual = common.cut_range('-500:-203') self.assertEqual(-500, actual.start) self.assertEqual(-203, actual.stop) def test_no_start(self): actual = common.cut_range(':10') self.assertEqual(None, actual.start) self.assertEqual(10, actual.stop) def test_no_end(self): actual = common.cut_range('5:') self.assertEqual(4, actual.start) class SequenceSlicesTestCase(unittest.TestCase): def test_single(self): actual = common.sequence_slices(':10') self.assertEqual([slice(None, 10)], actual) def test_multiple(self): actual = common.sequence_slices('1:10,3:20') self.assertEqual([slice(0, 10), slice(2, 20)], actual) class AtomicWriteTestCase(unittest.TestCase): initial_content = "Initial Content" new_content = "New Content" def setUp(self): with tempfile.NamedTemporaryFile('wt', delete=False) as tf: tf.write(self.initial_content) self.input_file = tf.name def test_exception_leaves_unchanged(self): try: with common.atomic_write(self.input_file) as tf: raise IOError() except IOError: with open(self.input_file) as fp: self.assertEqual(self.initial_content, fp.read()) # Ensure deleted self.assertFalse(os.path.exists(tf.name)) def test_write(self): with common.atomic_write(self.input_file) as fp: self.assertNotEqual(self.input_file, fp.name) fp.write(self.new_content) self.assertFalse(os.path.exists(fp.name)) with open(self.input_file) as fp: self.assertEqual(self.new_content, fp.read()) def tearDown(self): os.remove(self.input_file) class ApplyUmaskTestCase(unittest.TestCase): def setUp(self): # Set umask self.orig_umask = common.get_umask() def tearDown(self): os.umask(self.orig_umask) def test_provided_umask(self): self.assertEqual('0o770', oct(common.apply_umask(0o777, 0o07))) self.assertEqual('0o660', oct(common.apply_umask(0o666, 0o07))) self.assertEqual('0o644', oct(common.apply_umask(0o666, 0o22))) def test_user_umask(self): os.umask(0o07) self.assertEqual('0o770', oct(common.apply_umask(0o777))) self.assertEqual('0o660', oct(common.apply_umask(0o666))) class FileTypeTestCase(unittest.TestCase): def setUp(self): # used in methods test_read_*() self.testfile = 'input2.fasta' with open(p(self.testfile)) as f: self.expected = f.read() def test_stdin(self): self.assertIs(sys.stdin, common.FileType('r')('-')) def test_stdout(self): self.assertIs(sys.stdout, common.FileType('w')('-')) def test_read(self): with tempfile.NamedTemporaryFile('w+t') as tf: tf.write('TEST') tf.flush() with common.FileType('r')(tf.name) as fp: self.assertEqual(tf.name, fp.name) self.assertEqual('TEST', fp.read()) def test_write(self): with tempfile.NamedTemporaryFile('w+t') as tf: with common.FileType('w')(tf.name) as fp: fp.write('TEST') fp.flush() self.assertEqual(tf.name, fp.name) self.assertEqual('TEST', tf.read()) def test_read_text(self): with common.FileType('rt')(p(self.testfile)) as fp: self.assertEqual(fp.read(), self.expected) def test_read_gz(self): with common.FileType('rt')(p(self.testfile + '.gz')) as fp: self.assertEqual(fp.read(), self.expected) @unittest.skipIf(sys.version_info.major == 3, 'bzip2 not supported') def test_read_bz2(self): with common.FileType('rt')(p(self.testfile + '.bz2')) as fp: self.assertEqual(fp.read(), self.expected) seqmagick-0.8.4/seqmagick/test/test_subcommands_convert.py000066400000000000000000000116021376401056300241030ustar00rootroot00000000000000""" Tests for seqmagick.subcommands.convert - mostly integration with seqmagick.transform """ import argparse import os import tempfile import unittest from seqmagick.subcommands import convert from seqmagick import transform # Test populating the transform class PopulateTransformsMixIn(object): """ Tests that transforms list is populated """ def setUp(self): self.parser = convert.build_parser(argparse.ArgumentParser()) with tempfile.NamedTemporaryFile(delete=False) as tf: self.infile = tf.name with tempfile.NamedTemporaryFile(delete=False) as tf: self.outfile = tf.name def tearDown(self): os.remove(self.infile) os.remove(self.outfile) def test_parse(self): arguments = [self.infile, self.outfile] arguments.extend(self.arguments) try: parsed_arguments = self.parser.parse_args(arguments) except SystemExit: self.fail("Couldn't parse arguments") functions = [f.func for f in parsed_arguments.transforms] self.assertEqual(self.functions, functions) self.close_all_files(parsed_arguments) def close_all_files(self, parsed_arguments): for attr in dir(parsed_arguments): arg = getattr(parsed_arguments, attr) if hasattr(arg, 'close'): arg.close() class OrderRespectedTestCase(PopulateTransformsMixIn, unittest.TestCase): """ Ensure that order of arguments translates to order of functions to apply. """ arguments = ['--upper', '--translate', 'dna2protein', '--lower', '--squeeze'] functions = [transform.upper_sequences, transform.translate, transform.lower_sequences, transform.squeeze] class SequenceModTransformsTestCase(PopulateTransformsMixIn, unittest.TestCase): arguments = ['--dash-gap', '--lower', '--reverse', '--reverse-complement', '--transcribe', 'dna2rna', '--translate', 'dna2protein', '--ungap', '--upper',] functions = [transform.dashes_cleanup, transform.lower_sequences, transform.reverse_sequences, transform.reverse_complement_sequences, transform.transcribe, transform.translate, transform.ungap_sequences, transform.upper_sequences] class SeqSelectTransformsTestCase(PopulateTransformsMixIn, unittest.TestCase): def setUp(self): with tempfile.NamedTemporaryFile(delete=False) as tf: self.exclude_from = tf.name self.arguments = ['--deduplicate-taxa', '--exclude-from-file', self.exclude_from, '--include-from-file', self.exclude_from, '--head', '10', '--max-length', '50', '--min-length', '50', '--min-ungapped-length', '50', '--pattern-include', 'pattern', '--pattern-exclude', 'pattern', '--prune-empty', '--seq-pattern-include', 'pattern', '--seq-pattern-exclude', 'pattern', ] self.functions = [transform.deduplicate_taxa, transform.exclude_from_file, transform.include_from_file, transform.head, transform.max_length_discard, transform.min_length_discard, transform.min_ungap_length_discard, transform.name_include, transform.name_exclude, transform.prune_empty, transform.seq_include, transform.seq_exclude, ] super(SeqSelectTransformsTestCase, self).setUp() def tearDown(self): super(SeqSelectTransformsTestCase, self).tearDown() os.remove(self.exclude_from) class IdModificationTransformsTestCase(PopulateTransformsMixIn, unittest.TestCase): arguments = ['--first-name', '--name-suffix', 'suffix', '--name-prefix', 'prefix', '--pattern-replace', '.', 'N', '--strip-range'] functions = [ transform.first_name_capture, transform.name_append_suffix, transform.name_insert_prefix, transform.name_replace, transform.strip_range] class ArgumentTypeTestCase(PopulateTransformsMixIn, unittest.TestCase): arguments = ['--cut', '1:5'] functions = [transform.multi_cut_sequences] def test_argument_type(self): arguments = [self.infile, self.outfile] arguments.extend(self.arguments) try: parsed_arguments = self.parser.parse_args(arguments) except SystemExit: self.fail("Couldn't parse arguments") keywords = [f.keywords for f in parsed_arguments.transforms] self.assertEqual([{'slices': [slice(0, 5)]}], keywords) self.close_all_files(parsed_arguments) seqmagick-0.8.4/seqmagick/test/test_subcommands_quality_filter.py000066400000000000000000000233461376401056300254700ustar00rootroot00000000000000from io import StringIO import sys import unittest from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from seqmagick.subcommands import quality_filter IS_PYPY = hasattr(sys, 'pypy_version_info') class QualityFilterTestCase(unittest.TestCase): def setUp(self): self.instance = quality_filter.QualityScoreFilter(25.0) self.sequence = SeqRecord(Seq('ACGT')) def test_nowindow_fail(self): self.sequence.letter_annotations['phred_quality'] = [25, 25, 24, 25] instance = quality_filter.QualityScoreFilter() self.assertRaises(quality_filter.FailedFilter, instance.filter_record, self.sequence) def test_nowindow_pass(self): self.sequence.letter_annotations['phred_quality'] = [25, 25, 25, 25] instance = quality_filter.QualityScoreFilter() result = instance.filter_record(self.sequence) self.assertEqual(self.sequence.seq, result.seq) class WindowQualityFilterTestCase(unittest.TestCase): def setUp(self): self.instance = quality_filter.WindowQualityScoreFilter(2, 25) self.sequence = SeqRecord(Seq('ACGT')) def test_window_pass(self): self.sequence.letter_annotations['phred_quality'] = [25, 25, 25, 25] result = self.instance.filter_record(self.sequence) self.assertEqual(str(self.sequence), str(result)) def test_window_truncate_noseq(self): self.sequence.letter_annotations['phred_quality'] = [25, 24, 25, 25] self.assertRaises(quality_filter.FailedFilter, self.instance.filter_record, self.sequence) def test_window_truncate_mid(self): self.sequence.letter_annotations['phred_quality'] = [25, 25, 23, 25] result = self.instance.filter_record(self.sequence) self.assertEqual(2, len(result)) self.assertEqual('AC', str(result.seq)) class AmbiguousBaseFilterTestCase(unittest.TestCase): """ Tests for ambiguous_base_filter """ def setUp(self): self.records = [ SeqRecord(Seq('ACGT')), SeqRecord(Seq('NNNN')), SeqRecord(Seq('NACT')), SeqRecord(Seq('ACGTN')), SeqRecord(Seq('GGNTTACT')), ] def test_drop(self): """ Test that the first record (with no Ns) does not get filtered """ instance = quality_filter.AmbiguousBaseFilter('drop') actual = list(instance.filter_records(self.records)) self.assertEqual(1, len(actual)) self.assertEqual(1, instance.passed) self.assertEqual(4, instance.failed) self.assertEqual(self.records[0].seq, actual[0].seq) def test_truncate(self): instance = quality_filter.AmbiguousBaseFilter('truncate') actual = list(instance.filter_records(self.records)) self.assertEqual(5, len(actual)) self.assertEqual(0, instance.failed) self.assertEqual(5, instance.passed) self.assertEqual(['ACGT', '', '', 'ACGT', 'GG'], [str(s.seq) for s in actual]) def test_invalid_action(self): self.assertRaises(ValueError, quality_filter.AmbiguousBaseFilter, 'other') class MaxAmbiguousFilterTestCase(unittest.TestCase): def setUp(self): self.records = [ SeqRecord(Seq('ACGT')), SeqRecord(Seq('NNNN')), SeqRecord(Seq('NACT')), SeqRecord(Seq('ACNTN')), SeqRecord(Seq('GGNTTNACT')), ] def test_none(self): instance = quality_filter.MaxAmbiguousFilter(0) filtered = list(instance.filter_records(self.records)) self.assertEqual(len(filtered), 1) self.assertEqual(str(self.records[0].seq), str(filtered[0].seq)) def test_10(self): instance = quality_filter.MaxAmbiguousFilter(10) filtered = list(instance.filter_records(self.records)) self.assertEqual(filtered, self.records) def test_1(self): instance = quality_filter.MaxAmbiguousFilter(1) filtered = list(instance.filter_records(self.records)) self.assertEqual([self.records[i] for i in (0, 2)], filtered) class PctAmbiguousFilterTestCase(unittest.TestCase): def setUp(self): self.records = [ SeqRecord(Seq('ACGT')), SeqRecord(Seq('NNNN')), SeqRecord(Seq('NACT')), SeqRecord(Seq('ACNTN')), SeqRecord(Seq('GGNTTNACT')), ] def test_none(self): instance = quality_filter.PctAmbiguousFilter(0) filtered = list(instance.filter_records(self.records)) self.assertEqual(len(filtered), 1) self.assertEqual(str(self.records[0].seq), str(filtered[0].seq)) def test_10(self): instance = quality_filter.PctAmbiguousFilter(100) filtered = list(instance.filter_records(self.records)) self.assertEqual(filtered, self.records) def test_1(self): instance = quality_filter.PctAmbiguousFilter(0.23) filtered = list(instance.filter_records(self.records)) print(filtered) self.assertEqual([self.records[i] for i in (0, 4)], filtered) class MinLengthFilterTestCase(unittest.TestCase): def setUp(self): self.sequences = [ SeqRecord(Seq('ACGT')), SeqRecord(Seq('ACTTT')), ] def test_none_pass(self): instance = quality_filter.MinLengthFilter(6) actual = list(instance.filter_records(self.sequences)) self.assertEqual([], actual) def test_all_pass(self): instance = quality_filter.MinLengthFilter(4) actual = list(instance.filter_records(self.sequences)) self.assertEqual(self.sequences, actual) def test_some_pass(self): instance = quality_filter.MinLengthFilter(5) actual = list(instance.filter_records(self.sequences)) self.assertEqual(self.sequences[1:], actual) class MaxLengthFilterTestCase(unittest.TestCase): def setUp(self): self.sequences = [ SeqRecord(Seq('ACGT')), SeqRecord(Seq('ACTTT')), ] def test_none_truncated(self): instance = quality_filter.MaxLengthFilter(6) actual = list(instance.filter_records(self.sequences)) self.assertEqual(self.sequences, actual) def test_some_truncated(self): instance = quality_filter.MaxLengthFilter(4) actual = list(instance.filter_records(self.sequences)) self.assertEqual(['ACGT', 'ACTT'], [str(s.seq) for s in actual]) def test_all_truncated(self): instance = quality_filter.MaxLengthFilter(3) actual = list(instance.filter_records(self.sequences)) self.assertEqual(['ACG', 'ACT'], [str(s.seq) for s in actual]) self.assertEqual([i.id for i in self.sequences], [i.id for i in actual]) class PrimerBarcodeFilterTestCase(unittest.TestCase): def setUp(self): self.sequences = [ SeqRecord(Seq('ACCGTTACGAT'), 'seq1'), SeqRecord(Seq('ACTGTTACGCT'), 'seq2'), SeqRecord(Seq('AACTGTTA'), 'seq3'), # Homopolymer in bc SeqRecord(Seq('ACCGTA'), 'seq4'), # Error in primer ] barcode_str = """Sample1,ACC\nSample2,ACT\n""" self.primer = 'GTTA' self.trie = quality_filter.parse_barcode_file( StringIO(barcode_str), primer=self.primer) self.outfile = StringIO() self.instance = quality_filter.PrimerBarcodeFilter( self.trie, self.outfile) def test_filter_trim(self): actual = list(self.instance.filter_records(self.sequences)) self.assertEqual(2, len(actual)) self.assertEqual(['CGAT', 'CGCT'], [str(s.seq) for s in actual]) class RecordEventListenerTestCase(unittest.TestCase): def test_send(self): events = [] record = object() def e_handler(record, n=1): events.append(n) rle = quality_filter.RecordEventListener() rle.register_handler('e', e_handler) rle('e', record) self.assertEqual(events, [1]) rle('e', record, n=5) self.assertEqual(events, [1, 5]) # Test another event rle('other', record, n=5) self.assertEqual(events, [1, 5]) class BarcodePrimerTrieTestCase(unittest.TestCase): def setUp(self): self.barcode_str = """p1d1bc205,TACTAGCG,CATTGCCTATG p1d1bc206,TACTCGTC,CATTGCCTATG p1d1bc207,TACTGTGC,CATTGCCTATG p1d1bc208,TACTGCAG,CATTGCCTATG p1d1bc209,TACACAGC,CATTGCCTATG p1d1bc210,TACAGTCG,CAYGGCTA p1d1bc211,TACGTACG,CAYGGCTA p1d1bc212,TACGTCTC,CAYGGCTA p1d1bc213,TACGAGAC,CAYGGCTA""" self.fp = StringIO(self.barcode_str) def test_primer_provided(self): res = quality_filter.parse_barcode_file(self.fp, primer='CATTGCCTATG') self.assertEqual(9, len(list(res.keys()))) self.assertEqual('p1d1bc210', res['TACAGTCGCATTGCCTATG']) self.assertEqual(None, quality_filter.trie_match('TACAGTCGCATTGCCTAT', res)) self.assertEqual('TACAGTCGCATTGCCTATG', quality_filter.trie_match('TACAGTCGCATTGCCTATGCTACCTA', res)) def test_primer_in_file(self): res = quality_filter.parse_barcode_file(self.fp, primer=None) self.assertEqual(13, len(list(res.keys()))) # Test ambiguities self.assertEqual('p1d1bc212', res['TACGTCTCCATGGCTA']) self.assertEqual('p1d1bc212', res['TACGTCTCCACGGCTA']) self.assertIsNone(res.get('TACGTCTCCAAGGCTA')) self.assertIsNone(res.get('TACGTCTCCAGGGCTA')) class AllUnambiguousTestCase(unittest.TestCase): def test_one_nt(self): self.assertEqual(set('ACGT'), set(quality_filter.all_unambiguous('N'))) def test_four_nt(self): self.assertEqual( set(['ACCG', 'ACCA']), set(quality_filter.all_unambiguous('ACCR'))) self.assertEqual(4**4, len(quality_filter.all_unambiguous('NNNN'))) seqmagick-0.8.4/seqmagick/test/test_transform.py000066400000000000000000000616711376401056300220560ustar00rootroot00000000000000""" Tests for seqmagick.transform """ from io import StringIO import functools import logging import unittest from Bio import SeqIO from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq from seqmagick import transform logging.basicConfig(level=logging.FATAL) def _alignment_record(sequence): return SeqRecord(Seq(sequence)) def seqrecord(sequence_id, sequence_text, description=None): """ Quick shortcut to make a SeqRecord """ record = SeqRecord(Seq(sequence_text), id=sequence_id) if description: record.description = description return record class PatternReplaceTestCase(unittest.TestCase): def create_sequences(self): return [seqrecord('test_sequence_1', 'ACTGT'), seqrecord('test_REPLACE_2', 'ACTGT'), seqrecord('other_sequence', 'ATGAG'), ] def setUp(self): super(PatternReplaceTestCase, self).setUp() self.sequences = self.create_sequences() def tearDown(self): super(PatternReplaceTestCase, self).tearDown() # from http://stackoverflow.com/questions/13923072/shortening-fasta-header-perl def test_pattern_replace_anchored_transform_id(self): sequences = [seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC', description='gi|351517969|ref|NW_003613580.1| Cricetulus griseus unplaced genomic scaffold'), seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC', description='gi|351517969|ref|NW_003613580.1|'), seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC')] # capture the identifier after three groups of pipe-separated characters transformed = list(transform.name_replace(sequences, r'^(?:[^|]+\|){3}([^|]+)\|', r'\1')) self.assertEqual(str(sequences[0].seq), str(transformed[0].seq)) self.assertEqual('NW_003613580.1', transformed[0].id) self.assertEqual('NW_003613580.1 Cricetulus griseus unplaced genomic scaffold', transformed[0].description) self.assertEqual(str(sequences[1].seq), str(transformed[1].seq)) self.assertEqual('NW_003613580.1', transformed[1].id) self.assertEqual('NW_003613580.1', transformed[1].description) self.assertEqual(str(sequences[2].seq), str(transformed[2].seq)) self.assertEqual('NW_003613580.1', transformed[2].id) self.assertEqual('', transformed[2].description) # from http://stackoverflow.com/questions/15155728/modifying-fasta-headers-with-unix-command-line-tools def test_pattern_replace_anchored_id_from_description(self): sequences = [seqrecord('hg19_ct_UserTrack_3545_691', 'GATGG', description='hg19_ct_UserTrack_3545_691 range=chr1:8121498-8121502 5\'pad=0 3\'pad=0 strand=+ repeatMasking=none')] transformed = next(transform.name_replace(sequences, r'^\S+ range=(\S+)', r'\1')) self.assertEqual(str(sequences[0].seq), str(transformed.seq)) self.assertEqual('chr1:8121498-8121502', transformed.id) self.assertEqual('chr1:8121498-8121502 5\'pad=0 3\'pad=0 strand=+ repeatMasking=none', transformed.description) # from http://stackoverflow.com/questions/23280240/how-to-rename-fasta-file-headers-using-sed def test_pattern_replace_anchored_add_to_description(self): sequences = [seqrecord('Bra000001', 'CTTAT', description='Bra000001')] transformed = next(transform.name_replace(sequences, r'^(Bra\d+)$', r'\1 Brassica rapa')) self.assertEqual(str(sequences[0].seq), str(transformed.seq)) self.assertEqual('Bra000001', transformed.id) self.assertEqual('Bra000001 Brassica rapa', transformed.description) def test_pattern_replace_anchored_remove_from_description(self): sequences = [seqrecord('Bra000001', 'CTTAT', description='Bra000001 Brassica rapa')] transformed = next(transform.name_replace(sequences, r' .*$', '')) self.assertEqual(str(sequences[0].seq), str(transformed.seq)) self.assertEqual('Bra000001', transformed.id) self.assertEqual('Bra000001', transformed.description) def test_pattern_replace_anchored_nomatch(self): sequences = [seqrecord('hello', 'A', description='hello friend')] transformed = next(transform.name_replace(sequences, r'^hello$', 'bye')) self.assertEqual(str(sequences[0].seq), str(transformed.seq)) self.assertEqual('hello', transformed.id) self.assertEqual('hello friend', transformed.description) def test_pattern_replace_anchored_match(self): sequences = [seqrecord('hello', 'A', description='hello friend'), seqrecord('hello', 'A')] transformed = list(transform.name_replace(sequences, r'^hello\b', 'bye')) self.assertEqual(str(sequences[0].seq), str(transformed[0].seq)) self.assertEqual('bye', transformed[0].id) self.assertEqual('bye friend', transformed[0].description) self.assertEqual(str(sequences[1].seq), str(transformed[1].seq)) self.assertEqual('bye', transformed[1].id) self.assertEqual('', transformed[1].description) def test_pattern_replace_none(self): result = transform.name_replace(self.sequences, 'ZZZ', 'MATCH') result = list(result) self.assertEqual(self.sequences, result) def test_pattern_replace_static(self): result = transform.name_replace(self.sequences, '_REPLACE_', '_DONE_') result = list(result) expected = self.create_sequences() expected[1].id = 'test_DONE_2' self.assertEqual(self.sequences, result) def test_pattern_replace_case_insensitive(self): """ Substitutions are case insensitive """ result = transform.name_replace(self.sequences, '_replace_', '_DONE_') result = list(result) expected = self.create_sequences() expected[1].id = 'test_DONE_2' self.assertEqual(self.sequences, result) def test_pattern_replace_group(self): """ Make sure capturing groups work """ result = transform.name_replace(self.sequences, '_(repl)ace_', '_DONE-\\1_') result = list(result) expected = self.create_sequences() expected[1].id = 'test_DONE-repl_2' self.assertEqual(self.sequences, result) class SqueezeTestCase(unittest.TestCase): def setUp(self): super(SqueezeTestCase, self).setUp() self.sequences = [ seqrecord('sequence_1', 'AC-G--'), seqrecord('sequence_2', '-C-GT-'), seqrecord('sequence_3', '-T-AG-'), ] def test_gap_proportion(self): actual = transform.gap_proportion(self.sequences) self.assertEqual([2./3, 0.0, 1.0, 0.0, 1./3, 1.0], actual) def test_basic_squeeze(self): result = list(transform.squeeze(self.sequences, 1.0)) self.assertEqual([4, 4, 4], [len(i) for i in result]) self.assertEqual([i.id for i in self.sequences], [i.id for i in result]) expected = [ seqrecord('sequence_1', 'ACG-'), seqrecord('sequence_2', '-CGT'), seqrecord('sequence_3', '-TAG'), ] self.assertEqual([str(i.seq) for i in expected], [str(i.seq) for i in result]) def test_squeeze_none(self): """ Threshold of 0.001 - nothing should be squeezed. """ result = list(transform.squeeze(self.sequences, 1.01)) self.assertEqual([str(i.seq) for i in self.sequences], [str(i.seq) for i in result]) class SeqPatternTestCase(unittest.TestCase): def setUp(self): super(SeqPatternTestCase, self).setUp() self.sequences = [ seqrecord('s1', 'AC-G--'), seqrecord('s2', '-C-GT-'), seqrecord('s3', '-T-AG-'), ] self.tests = [('^$', set()), ('.*', {'s1', 's2', 's3'}), ('^AC', {'s1'}), ('^ac', set()), ('(?i)^ac', {'s1'})] def test_include(self): result = transform.seq_include(self.sequences, '^$') for regex, expected in self.tests: result = {seq.id for seq in transform.seq_include(self.sequences, regex)} self.assertEqual(expected, result) def test_exclude(self): result = transform.seq_include(self.sequences, '^$') for regex, expected_include in self.tests: result = {seq.id for seq in transform.seq_exclude(self.sequences, regex)} expected = {seq.id for seq in self.sequences if seq.id not in expected_include} self.assertEqual(expected, result) class HeadTestCase(unittest.TestCase): """ Test for transform.head """ def setUp(self): self.sequences = [seqrecord('sequence{0}'.format(i), 'A'*(i+1)) for i in range(100)] def test_zero(self): result = list(transform.head(self.sequences, '0')) self.assertEqual([], result) def test_more_seqs_than_available(self): """ Specifying more sequences than are in input records should return them all """ result = list(transform.head(self.sequences, '10000')) self.assertEqual([s.id for s in self.sequences], [r.id for r in result]) self.assertEqual([str(s.seq) for s in self.sequences], [str(r.seq) for r in result]) def test_values(self): """ Try specifying some values. """ for h in range(len(self.sequences) + 1): result = list(transform.head(self.sequences, str(h))) self.assertEqual(h, len(result)) self.assertEqual([s.id for s in self.sequences[:h]], [r.id for r in result]) self.assertEqual([str(s.seq) for s in self.sequences[:h]], [str(r.seq) for r in result]) def test_minus_zero(self): """ Test that -0 returns all sequences """ result = list(transform.head(self.sequences, '-0')) self.assertEqual([s.id for s in self.sequences], [r.id for r in result]) self.assertEqual([str(s.seq) for s in self.sequences], [str(r.seq) for r in result]) def test_minus_values(self): """ Try specifying some minus values. """ for h in range(1, len(self.sequences) + 1): result = list(transform.head(self.sequences, str(-h))) self.assertEqual(h, len(self.sequences) - len(result)) self.assertEqual([s.id for s in self.sequences[:-h]], [r.id for r in result]) self.assertEqual([str(s.seq) for s in self.sequences[:-h]], [str(r.seq) for r in result]) class TailTestCase(unittest.TestCase): def setUp(self): self.records = [ seqrecord('sequence_1', 'AC-G--'), seqrecord('sequence_2', '-C-GT-'), seqrecord('sequence_3', '-T-AG-'), ] def _do_test(self, size): actual = list(transform.tail(self.records, str(size))) expected = self.records[-size:] self.assertEqual([e.id for e in expected], [a.id for a in actual]) self.assertEqual([str(e.seq) for e in expected], [str(a.seq) for a in actual]) def test_tail_1(self): self._do_test(1) def test_tail_2(self): self._do_test(2) def test_tail_3(self): self._do_test(3) def test_plus_zero(self): """ Test that +0 returns all sequences """ result = list(transform.tail(self.records, '+0')) self.assertEqual([s.id for s in self.records], [r.id for r in result]) self.assertEqual([str(s.seq) for s in self.records], [str(r.seq) for r in result]) def test_plus_values(self): """ Try specifying some plus values. """ for h in range(1, len(self.records) + 1): result = list(transform.tail(self.records, '+{}'.format(h))) self.assertEqual(len(self.records) + 1 - h, len(result)) self.assertEqual([s.id for s in self.records[h-1:]], [r.id for r in result]) self.assertEqual([str(s.seq) for s in self.records[h-1:]], [str(r.seq) for r in result]) class IsolateRegionTestCase(unittest.TestCase): def setUp(self): self.sequences = [_alignment_record('--A--ACTGGACGTATTC-CCCC'), _alignment_record('--AGCACTGGA---ATTC-CCCC')] def test_no_isolation(self): result = list(transform.isolate_region(self.sequences, 0, len(self.sequences[0]))) self.assertEqual(self.sequences, result) def test_single_loc(self): start = 2 end = 3 result = list(transform.isolate_region(self.sequences, start, end)) for seq in result: self.assertEqual('--A--------------------', str(seq.seq)) def test_middle(self): expected = ['--A--ACTGGA------------', '--AGCACTGGA------------'] start = 1 end = 11 actual = list(transform.isolate_region(self.sequences, start, end)) actual = [str(s.seq) for s in actual] self.assertEqual(expected, actual) def test_invalid(self): self.assertRaises(ValueError, transform.isolate_region( self.sequences, 5, 5).__next__) self.assertRaises(ValueError, transform.isolate_region( self.sequences, 10, 5).__next__) class MinUngapLengthTestCase(unittest.TestCase): def setUp(self): self.sequences = [_alignment_record('--AAC--'), _alignment_record('AAAA...'), _alignment_record('-------'), _alignment_record('ACGRAGT')] def test_none_pass(self): result = list(transform.min_ungap_length_discard(self.sequences, 8)) self.assertEqual([], result) def test_all_pass(self): result = list(transform.min_ungap_length_discard(self.sequences, 0)) self.assertEqual(self.sequences, result) def test_partial(self): result = transform.min_ungap_length_discard(self.sequences, 4) self.assertEqual( [self.sequences[1].seq, self.sequences[3].seq], [seq.seq for seq in result]) class IncludeExcludeMixIn(object): def setUp(self): ids = """sequenceid1 sequenceid2 sequenceid4 """ self.handle = StringIO(ids) self.sequences = [seqrecord("sequenceid1", "AAA"), seqrecord("sequenceid2", "BBB"), seqrecord("sequenceid3", "CCC"), seqrecord("sequenceid4", "DDD", description='sequence id 4'), seqrecord("test", "EEE", description='test sequence'), ] class IncludeFromFileTestCase(IncludeExcludeMixIn, unittest.TestCase): def test_filter(self): expected = [self.sequences[0], self.sequences[1], self.sequences[3]] actual = list(transform.include_from_file(self.sequences, self.handle)) self.assertEqual(3, len(actual)) self.assertEqual(expected, actual) class ExcludeFromFileTestCase(IncludeExcludeMixIn, unittest.TestCase): def test_filter(self): expected = [self.sequences[2], self.sequences[4]] actual = list(transform.exclude_from_file(self.sequences, self.handle)) self.assertEqual(2, len(actual)) self.assertEqual(expected, actual) class NameIncludeTestCase(IncludeExcludeMixIn, unittest.TestCase): def test_filter_id(self): expected = self.sequences[:2] actual = list(transform.name_include(self.sequences, r'sequenceid[12]')) self.assertEqual(2, len(actual)) self.assertEqual(expected, actual) def test_filter_description(self): expected = self.sequences[3:] actual = list(transform.name_include(self.sequences, r'sequence id 4|test seq')) self.assertEqual(2, len(actual)) self.assertEqual(expected, actual) class NameExcludeTestCase(IncludeExcludeMixIn, unittest.TestCase): def test_filter_id(self): expected = self.sequences[2:] actual = list(transform.name_exclude(self.sequences, r'sequenceid[12]')) self.assertEqual(3, len(actual)) self.assertEqual(expected, actual) def test_filter_description(self): expected = self.sequences[:3] actual = list(transform.name_exclude(self.sequences, r'sequence id 4|test seq')) self.assertEqual(expected, actual) class CutTestCase(unittest.TestCase): def setUp(self): self.sequences = [SeqRecord(Seq("ABC"), id="sequenceid1"), SeqRecord(Seq("BCD"), id="sequenceid2"), SeqRecord(Seq("DEF"), id="sequence id 4"), SeqRecord(Seq("EFG"), id="test sequence"), ] def test_no_sequences(self): actual = list(transform._cut_sequences(self.sequences, slice(0, 0))) for sequence in actual: self.assertEqual(0, len(sequence)) def test_full_sequence(self): actual = list(transform._cut_sequences(self.sequences, slice(0, 3))) self.assertEqual(['ABC', 'BCD', 'DEF', 'EFG'], [str(s.seq) for s in actual]) def test_cut_sequences(self): actual = list(transform._cut_sequences(self.sequences, slice(0, 2))) self.assertEqual(['AB', 'BC', 'DE', 'EF'], [str(s.seq) for s in actual]) actual = list(transform._cut_sequences(self.sequences, slice(1, None))) self.assertEqual(['BC', 'CD', 'EF', 'FG'], [str(s.seq) for s in actual]) class CodonWarningTableTestCase(unittest.TestCase): def warn(self, *args, **kwargs): self.warnings.append((args, kwargs)) def setUp(self): self.warnings = [] self.warning_dict = transform.CodonWarningTable({'UUU': 'F'}) self.old_warn = transform.logging.warning transform.logging.warning = self.warn def tearDown(self): transform.logging.warning = self.old_warn def test_nowarn(self): actual = self.warning_dict['UUU'] self.assertEqual('F', actual) self.assertEqual([], self.warnings) def test_warn(self): codon = 'UU-' actual = self.warning_dict[codon] self.assertEqual('X', actual) self.assertEqual([(("Unknown Codon: %s", codon), {})], self.warnings) class TranslateTestCase(unittest.TestCase): def test_dna_protein_nogap(self): sequences = [seqrecord('A', 'TTTTTATAA')] expected = ['FL*'] actual = transform.translate(sequences, 'dna2protein') self.assertEqual(expected, [str(i.seq) for i in actual]) def test_dna_protein_nogap_stop(self): sequences = [seqrecord('A', 'TTTTTATAA')] expected = ['FL'] actual = transform.translate(sequences, 'dna2proteinstop') self.assertEqual(expected, [str(i.seq) for i in actual]) def test_dna_protein_gap(self): sequences = [seqrecord('A', 'TTTTT-TAA')] expected = ['FX*'] actual = transform.translate(sequences, 'dna2protein') self.assertEqual(expected, [str(i.seq) for i in actual]) def test_dna_protein_gap_stop(self): sequences = [seqrecord('A', '---TTATAA')] expected = ['-L'] actual = transform.translate(sequences, 'dna2proteinstop') self.assertEqual(expected, [str(i.seq) for i in actual]) class UngapSequencesTestCase(unittest.TestCase): def test_dot_gap(self): sequences = [SeqRecord(Seq("AAA"), id="s1"), SeqRecord(Seq("A.G"), id="s2"), SeqRecord(Seq(".A."), id="s3"),] ungapped = list(transform.ungap_sequences(sequences)) self.assertEqual(["AAA", "AG", "A"], [str(s.seq) for s in ungapped]) def test_dash_gap(self): sequences = [SeqRecord(Seq("AAA"), id="s1"), SeqRecord(Seq("A-G"), id="s2"), SeqRecord(Seq("-A-"), id="s3"),] ungapped = list(transform.ungap_sequences(sequences)) self.assertEqual(["AAA", "AG", "A"], [str(s.seq) for s in ungapped]) # Name Modification functions class IdModifyMixin(object): """ Mixin to ease testing name prefix and suffix """ def setUp(self): self.input_fp = StringIO(self.initial_fasta) self.output_fp = StringIO() def test_modify(self): records = SeqIO.parse(self.input_fp, 'fasta') records = self.__class__.modify_fn(records) SeqIO.write(records, self.output_fp, 'fasta') self.assertEqual(self.target_fasta, self.output_fp.getvalue().strip()) class NamePrefixTestCase(IdModifyMixin, unittest.TestCase): initial_fasta = """>seq1 ACGT >gi|260674|gb|S52561.1| {long terminal repeat} [human immunodeficiency virus type] ACGT""" target_fasta = """>pre.seq1 ACGT >pre.gi|260674|gb|S52561.1| {long terminal repeat} [human immunodeficiency virus type] ACGT""" modify_fn = functools.partial(transform.name_insert_prefix, prefix="pre.") class NameSuffixTestCase(IdModifyMixin, unittest.TestCase): initial_fasta = """>seq1 ACGT >gi|260674|gb|S52561.1| {long terminal repeat} [human immunodeficiency virus type] ACGT""" target_fasta = """>seq1.post ACGT >gi|260674|gb|S52561.1|.post {long terminal repeat} [human immunodeficiency virus type] ACGT""" modify_fn = functools.partial(transform.name_append_suffix, suffix=".post") class MultiCutTestCase(unittest.TestCase): def setUp(self): self.inputs = [seqrecord("Sequence 1", "ACGT--TCAGA")] def test_multicut(self): actual = list(transform.multi_cut_sequences(self.inputs, [slice(None, 2), slice(8, None)])) self.assertEqual(['ACAGA'], [str(s.seq) for s in actual]) class MultiMaskSequences(unittest.TestCase): def setUp(self): self.sequences = [SeqRecord(Seq("AAA"), id="sequenceid1"), SeqRecord(Seq("BBB"), id="sequenceid2"), SeqRecord(Seq("DDDD"), id="sequence id 4"), SeqRecord(Seq("EEE"), id="test sequence"), ] def test_mask_whole(self): masks = [slice(0, 200)] actual = list(transform.multi_mask_sequences(self.sequences, masks)) self.assertEqual(len(self.sequences), len(actual)) for e, a in zip(self.sequences, actual): self.assertEqual(e.id, a.id) self.assertEqual('-'*len(e), str(a.seq)) def test_mask(self): masks = [slice(1, 2)] actual = list(transform.multi_mask_sequences(self.sequences, masks)) self.assertEqual(len(self.sequences), len(actual)) self.assertEqual(['A-A', 'B-B', 'D-DD', 'E-E'], [str(a.seq) for a in actual]) class RecordBufferTestCase(unittest.TestCase): def setUp(self): self.sequences = [SeqRecord(Seq("AAA"), id="s1"), SeqRecord(Seq("A-G"), id="s2"), SeqRecord(Seq("-A-"), id="s3"),] self.seq_iter = iter(self.sequences) def _compare(self, records): self.assertEqual(len(self.sequences), len(records)) for e, a in zip(self.sequences, records): self.assertEqual(e.id, a.id) self.assertEqual(e.description, a.description) self.assertEqual(str(e.seq), str(a.seq)) def test_single_pass(self): with transform._record_buffer(self.seq_iter) as iter_f: records = list(iter_f()) self._compare(records) def test_multi_pass(self): with transform._record_buffer(self.seq_iter) as iter_f: records = list(iter_f()) self._compare(records) records = list(iter_f()) self._compare(records) class DropColumnsTestCase(unittest.TestCase): def setUp(self): self.sequences = [SeqRecord(Seq("AAA"), id="s1"), SeqRecord(Seq("A-G"), id="s2"), SeqRecord(Seq("-A-"), id="s3"),] def test_basic(self): r = list(transform.drop_columns(self.sequences, [slice(1, None)])) self.assertEqual([i.id for i in self.sequences], [i.id for i in r]) self.assertEqual(['A', 'A', '-'], [str(i.seq) for i in r]) def test_multi(self): r = list(transform.drop_columns(self.sequences, [slice(0, 1), slice(2, None)])) self.assertEqual([i.id for i in self.sequences], [i.id for i in r]) self.assertEqual(['A', '-', 'A'], [str(i.seq) for i in r]) class DashesCleanupTestCase(unittest.TestCase): def setUp(self): self.sequences = [SeqRecord(Seq("A~-.?~GT"), id="s1"), SeqRecord(Seq("A-GGGG?-"), id="s2"), SeqRecord(Seq("-A-:ACA-"), id="s3"), SeqRecord(Seq("ACTGGTCA"), id="s4"),] def test_basic(self): actual = list(transform.dashes_cleanup(self.sequences)) actual = [(i.id, str(i.seq)) for i in actual] self.assertEqual( [('s1', 'A-----GT'), ('s2', 'A-GGGG--'), ('s3', '-A--ACA-'), ('s4', 'ACTGGTCA')], actual) seqmagick-0.8.4/seqmagick/transform.py000066400000000000000000000633771376401056300200450ustar00rootroot00000000000000""" Functions to transform / filter sequences """ import collections import contextlib import pickle as pickle import gzip import itertools import logging import re import string import tempfile import random from Bio import SeqIO from Bio.Data import CodonTable from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.SeqUtils.CheckSum import seguid from functools import reduce # Characters to be treated as gaps GAP_CHARS = "-." GAP_TABLE = {ord(c): None for c in GAP_CHARS} # Size of temporary file buffer: default to 256MB DEFAULT_BUFFER_SIZE = 268435456 # 256 * 2**20 @contextlib.contextmanager def _record_buffer(records, buffer_size=DEFAULT_BUFFER_SIZE): """ Buffer for transform functions which require multiple passes through data. Value returned by context manager is a function which returns an iterator through records. """ with tempfile.SpooledTemporaryFile(buffer_size, mode='wb+') as tf: pickler = pickle.Pickler(tf) for record in records: pickler.dump(record) def record_iter(): tf.seek(0) # _file is used below because it implements the necessary methods for pickle.Unpickler(), namely 'readinto' which is newly required in 3.8. See https://docs.python.org/3/library/tempfile.html#tempfile.SpooledTemporaryFile for details on the _file attribute of tempfile.SpooledTemporaryFile. unpickler = pickle.Unpickler(tf._file) while True: try: yield unpickler.load() except EOFError: break yield record_iter def dashes_cleanup(records, prune_chars='.:?~'): """ Take an alignment and convert any undesirable characters such as ? or ~ to -. """ logging.info( "Applying _dashes_cleanup: converting any of '{}' to '-'.".format(prune_chars)) translation_table = {ord(c): '-' for c in prune_chars} for record in records: record.seq = Seq(str(record.seq).translate(translation_table)) yield record def deduplicate_sequences(records, out_file): """ Remove any duplicate records with identical sequences, keep the first instance seen and discard additional occurences. """ logging.info('Applying _deduplicate_sequences generator: ' 'removing any duplicate records with identical sequences.') checksum_sequences = collections.defaultdict(list) for record in records: checksum = seguid(record.seq) sequences = checksum_sequences[checksum] if not sequences: yield record sequences.append(record.id) if out_file is not None: with out_file: for sequences in checksum_sequences.values(): out_file.write('%s\n' % (' '.join(sequences),)) def deduplicate_taxa(records): """ Remove any duplicate records with identical IDs, keep the first instance seen and discard additional occurences. """ logging.info('Applying _deduplicate_taxa generator: ' + \ 'removing any duplicate records with identical IDs.') taxa = set() for record in records: # Default to full ID, split if | is found. taxid = record.id if '|' in record.id: try: taxid = int(record.id.split("|")[0]) except: # If we couldn't parse an integer from the ID, just fall back # on the ID logging.warn("Unable to parse integer taxid from %s", taxid) if taxid in taxa: continue taxa.add(taxid) yield record def first_name_capture(records): """ Take only the first whitespace-delimited word as the name of the sequence. Essentially removes any extra text from the sequence's description. """ logging.info('Applying _first_name_capture generator: ' 'making sure ID only contains the first whitespace-delimited ' 'word.') whitespace = re.compile(r'\s+') for record in records: if whitespace.search(record.description): yield SeqRecord(record.seq, id=record.id, description="") else: yield record def include_from_file(records, handle): """ Filter the records, keeping only sequences whose ID is contained in the handle. """ ids = set(i.strip() for i in handle) for record in records: if record.id.strip() in ids: yield record def exclude_from_file(records, handle): """ Filter the records, keeping only sequences whose ID is not contained in the handle. """ ids = set(i.strip() for i in handle) for record in records: if record.id.strip() not in ids: yield record def isolate_region(sequences, start, end, gap_char='-'): """ Replace regions before and after start:end with gap chars """ # Check arguments if end <= start: raise ValueError("start of slice must precede end ({0} !> {1})".format( end, start)) for sequence in sequences: seq = sequence.seq start_gap = gap_char * start end_gap = gap_char * (len(seq) - end) seq = Seq(start_gap + str(seq[start:end]) + end_gap) sequence.seq = seq yield sequence def _cut_sequences(records, cut_slice): """ Cut sequences given a slice. """ for record in records: yield record[cut_slice] def drop_columns(records, slices): """ Drop all columns present in ``slices`` from records """ for record in records: # Generate a set of indices to remove drop = set(i for slice in slices for i in range(*slice.indices(len(record)))) keep = [i not in drop for i in range(len(record))] record.seq = Seq(''.join(itertools.compress(record.seq, keep))) yield record def multi_cut_sequences(records, slices): # If only a single slice is specified, use _cut_sequences, # since this preserves per-letter annotations if len(slices) == 1: for sequence in _cut_sequences(records, slices[0]): yield sequence else: # For multiple slices, concatenate the slice results for record in records: pieces = (record[s] for s in slices) # SeqRecords support addition as concatenation yield reduce(lambda x, y: x + y, pieces) def _update_slices(record, slices): n = itertools.count().__next__ # Generate a map from indexes in the specified sequence to those in the # alignment ungap_map = dict((n(), i) for i, base in enumerate(str(record.seq)) if base not in GAP_CHARS) def update_slice(s): """ Maps a slice relative to ungapped record_id to a slice valid for the whole alignment. """ start, end = s.start, s.stop if start is not None: try: start = ungap_map[start] except KeyError: raise KeyError("""No index {0} in {1}.""".format( start, record.id)) if end is not None: # We need the base in the slice identified by end, not the base # at end, otherwise insertions between end-1 and end will be # included. try: end = ungap_map[end - 1] + 1 except KeyError: logging.warn("""No index %d in %s. Keeping columns to end of alignment.""", end, record.id) end = None return slice(start, end) return [update_slice(s) for s in slices] def cut_sequences_relative(records, slices, record_id): """ Cuts records to slices, indexed by non-gap positions in record_id """ with _record_buffer(records) as r: try: record = next(i for i in r() if i.id == record_id) except StopIteration: raise ValueError("Record with id {0} not found.".format(record_id)) new_slices = _update_slices(record, slices) for record in multi_cut_sequences(r(), new_slices): yield record def multi_mask_sequences(records, slices): """ Replace characters sliced by slices with gap characters. """ for record in records: record_indices = list(range(len(record))) keep_indices = reduce(lambda i, s: i - frozenset(record_indices[s]), slices, frozenset(record_indices)) seq = ''.join(b if i in keep_indices else '-' for i, b in enumerate(str(record.seq))) record.seq = Seq(seq) yield record def mask_sequences_relative(records, slices, record_id): with _record_buffer(records) as r: try: record = next(i for i in r() if i.id == record_id) except StopIteration: raise ValueError("Record with id {0} not found.".format(record_id)) new_slices = _update_slices(record, slices) for record in multi_mask_sequences(r(), new_slices): yield record def lower_sequences(records): """ Convert sequences to all lowercase. """ logging.info('Applying _lower_sequences generator: ' 'converting sequences to all lowercase.') for record in records: yield record.lower() def upper_sequences(records): """ Convert sequences to all uppercase. """ logging.info('Applying _upper_sequences generator: ' 'converting sequences to all uppercase.') for record in records: yield record.upper() def prune_empty(records): """ Remove any sequences which are entirely gaps ('-') """ for record in records: if not all(c == '-' for c in str(record.seq)): yield record def _reverse_annotations(old_record, new_record): """ Copy annotations form old_record to new_record, reversing any lists / tuples / strings. """ # Copy the annotations over for k, v in list(old_record.annotations.items()): # Trim if appropriate if isinstance(v, (tuple, list)) and len(v) == len(old_record): assert len(v) == len(old_record) v = v[::-1] new_record.annotations[k] = v # Letter annotations must be lists / tuples / strings of the same # length as the sequence for k, v in list(old_record.letter_annotations.items()): assert len(v) == len(old_record) new_record.letter_annotations[k] = v[::-1] def reverse_sequences(records): """ Reverse the order of sites in sequences. """ logging.info('Applying _reverse_sequences generator: ' 'reversing the order of sites in sequences.') for record in records: rev_record = SeqRecord(record.seq[::-1], id=record.id, name=record.name, description=record.description) # Copy the annotations over _reverse_annotations(record, rev_record) yield rev_record def reverse_complement_sequences(records): """ Transform sequences into reverse complements. """ logging.info('Applying _reverse_complement_sequences generator: ' 'transforming sequences into reverse complements.') for record in records: rev_record = SeqRecord(record.seq.reverse_complement(), id=record.id, name=record.name, description=record.description) # Copy the annotations over _reverse_annotations(record, rev_record) yield rev_record def ungap_sequences(records, gap_chars=GAP_TABLE): """ Remove gaps from sequences, given an alignment. """ logging.info('Applying _ungap_sequences generator: removing all gap characters') for record in records: yield ungap_all(record, gap_chars) def ungap_all(record, gap_chars=GAP_TABLE): record = SeqRecord( Seq(str(record.seq).translate(gap_chars)), id=record.id, description=record.description ) return record def _update_id(record, new_id): """ Update a record id to new_id, also modifying the ID in record.description """ old_id = record.id record.id = new_id # At least for FASTA, record ID starts the description record.description = re.sub('^' + re.escape(old_id), new_id, record.description) return record def name_append_suffix(records, suffix): """ Given a set of sequences, append a suffix for each sequence's name. """ logging.info('Applying _name_append_suffix generator: ' 'Appending suffix ' + suffix + ' to all ' 'sequence IDs.') for record in records: new_id = record.id + suffix _update_id(record, new_id) yield record def name_insert_prefix(records, prefix): """ Given a set of sequences, insert a prefix for each sequence's name. """ logging.info('Applying _name_insert_prefix generator: ' 'Inserting prefix ' + prefix + ' for all ' 'sequence IDs.') for record in records: new_id = prefix + record.id _update_id(record, new_id) yield record def name_include(records, filter_regex): """ Given a set of sequences, filter out any sequences with names that do not match the specified regular expression. Ignore case. """ logging.info('Applying _name_include generator: ' 'including only IDs matching ' + filter_regex + ' in results.') regex = re.compile(filter_regex) for record in records: if regex.search(record.id) or regex.search(record.description): yield record def name_exclude(records, filter_regex): """ Given a set of sequences, filter out any sequences with names that match the specified regular expression. Ignore case. """ logging.info('Applying _name_exclude generator: ' 'excluding IDs matching ' + filter_regex + ' in results.') regex = re.compile(filter_regex) for record in records: if not regex.search(record.id) and not regex.search(record.description): yield record def name_replace(records, search_regex, replace_pattern): """ Given a set of sequences, replace all occurrences of search_regex with replace_pattern. Ignore case. If the ID and the first word of the description match, assume the description is FASTA-like and apply the transform to the entire description, then set the ID from the first word. If the ID and the first word of the description do not match, apply the transform to each individually. """ regex = re.compile(search_regex) for record in records: maybe_id = record.description.split(None, 1)[0] if maybe_id == record.id: record.description = regex.sub(replace_pattern, record.description) record.id = record.description.split(None, 1)[0] else: record.id = regex.sub(replace_pattern, record.id) record.description = regex.sub(replace_pattern, record.description) yield record def seq_include(records, filter_regex): """ Filter any sequences who's seq does not match the filter. Ignore case. """ regex = re.compile(filter_regex) for record in records: if regex.search(str(record.seq)): yield record def seq_exclude(records, filter_regex): """ Filter any sequences whose seq matches the filter. Ignore case. """ regex = re.compile(filter_regex) for record in records: if not regex.search(str(record.seq)): yield record def sample(records, k, random_seed=None): """Choose a length-``k`` subset of ``records``, retaining the input order. If k > len(records), all are returned. If an integer ``random_seed`` is provided, sets ``random.seed()`` """ if random_seed is not None: random.seed(random_seed) result = [] for i, record in enumerate(records): if len(result) < k: result.append(record) else: r = random.randint(0, i) if r < k: result[r] = record return result def head(records, head): """ Limit results to the top N records. With the leading `-', print all but the last N records. """ logging.info('Applying _head generator: ' 'limiting results to top ' + head + ' records.') if head == '-0': for record in records: yield record elif '-' in head: with _record_buffer(records) as r: record_count = sum(1 for record in r()) end_index = max(record_count + int(head), 0) for record in itertools.islice(r(), end_index): yield record else: for record in itertools.islice(records, int(head)): yield record def tail(records, tail): """ Limit results to the bottom N records. Use +N to output records starting with the Nth. """ logging.info('Applying _tail generator: ' 'limiting results to top ' + tail + ' records.') if tail == '+0': for record in records: yield record elif '+' in tail: tail = int(tail) - 1 for record in itertools.islice(records, tail, None): yield record else: with _record_buffer(records) as r: record_count = sum(1 for record in r()) start_index = max(record_count - int(tail), 0) for record in itertools.islice(r(), start_index, None): yield record # Squeeze-related def gap_proportion(sequences, gap_chars='-'): """ Generates a list with the proportion of gaps by index in a set of sequences. """ aln_len = None gaps = [] for i, sequence in enumerate(sequences): if aln_len is None: aln_len = len(sequence) gaps = [0] * aln_len else: if not len(sequence) == aln_len: raise ValueError(("Unexpected sequence length {0}. Is this " "an alignment?").format(len(sequence))) # Update any gap positions in gap list for j, char in enumerate(sequence.seq): if char in gap_chars: gaps[j] += 1 sequence_count = float(i + 1) gap_props = [i / sequence_count for i in gaps] return gap_props def squeeze(records, gap_threshold=1.0): """ Remove any gaps that are present in the same position across all sequences in an alignment. Takes a second sequence iterator for determining gap positions. """ with _record_buffer(records) as r: gap_proportions = gap_proportion(r()) keep_columns = [g < gap_threshold for g in gap_proportions] for record in r(): sequence = str(record.seq) # Trim squeezed = itertools.compress(sequence, keep_columns) yield SeqRecord(Seq(''.join(squeezed)), id=record.id, description=record.description) def strip_range(records): """ Cut off trailing /- ranges from IDs. Ranges must be 1-indexed and the stop integer must not be less than the start integer. """ logging.info('Applying _strip_range generator: ' 'removing /- ranges from IDs') # Split up and be greedy. cut_regex = re.compile(r"(?P.*)\/(?P\d+)\-(?P\d+)") for record in records: name = record.id match = cut_regex.match(str(record.id)) if match: sequence_id = match.group('id') start = int(match.group('start')) stop = int(match.group('stop')) if start > 0 and start <= stop: name = sequence_id yield SeqRecord(record.seq, id=name, description='') def transcribe(records, transcribe): """ Perform transcription or back-transcription. transcribe must be one of the following: dna2rna rna2dna """ logging.info('Applying _transcribe generator: ' 'operation to perform is ' + transcribe + '.') for record in records: sequence = str(record.seq) description = record.description name = record.id if transcribe == 'dna2rna': dna = Seq(sequence, IUPAC.ambiguous_dna) rna = dna.transcribe() yield SeqRecord(rna, id=name, description=description) elif transcribe == 'rna2dna': rna = Seq(sequence, IUPAC.ambiguous_rna) dna = rna.back_transcribe() yield SeqRecord(dna, id=name, description=description) # Translate-related functions class CodonWarningTable(object): """ Translation table for codons tht prints a warning when an unknown codon is requested, then returns the value passed as missing_char """ def __init__(self, wrapped, missing_char='X'): self.wrapped = wrapped self.missing_char = missing_char self.seen = set() def get(self, codon, missing=None): try: return self.__getitem__(codon) except KeyError: return missing def __getitem__(self, codon): if codon == '---': return '-' elif '-' in codon: if codon not in self.seen: logging.warning("Unknown Codon: %s", codon) self.seen.add(codon) return self.missing_char else: return self.wrapped.__getitem__(codon) def __contains__(self, value): return value in self.wrapped def translate(records, translate): """ Perform translation from generic DNA/RNA to proteins. Bio.Seq does not perform back-translation because the codons would more-or-less be arbitrary. Option to translate only up until reaching a stop codon. translate must be one of the following: dna2protein dna2proteinstop rna2protein rna2proteinstop """ logging.info('Applying translation generator: ' 'operation to perform is ' + translate + '.') to_stop = translate.endswith('stop') source_type = translate[:3] # Get a translation table table = {'dna': CodonTable.ambiguous_dna_by_name["Standard"], 'rna': CodonTable.ambiguous_rna_by_name["Standard"]}[source_type] # Handle ambiguities by replacing ambiguous codons with 'X' # TODO: this copy operation causes infinite recursion with python3.6 - # not sure why it was here to begin with. # table = copy.deepcopy(table) table.forward_table = CodonWarningTable(table.forward_table) for record in records: sequence = str(record.seq) seq = Seq(sequence) protein = seq.translate(table, to_stop=to_stop) yield SeqRecord(protein, id=record.id, description=record.description) def max_length_discard(records, max_length): """ Discard any records that are longer than max_length. """ logging.info('Applying _max_length_discard generator: ' 'discarding records longer than ' '.') for record in records: if len(record) > max_length: # Discard logging.debug('Discarding long sequence: %s, length=%d', record.id, len(record)) else: yield record def min_length_discard(records, min_length): """ Discard any records that are shorter than min_length. """ logging.info('Applying _min_length_discard generator: ' 'discarding records shorter than %d.', min_length) for record in records: if len(record) < min_length: logging.debug('Discarding short sequence: %s, length=%d', record.id, len(record)) else: yield record def min_ungap_length_discard(records, min_length): """ Discard any records that are shorter than min_length after removing gaps. """ for record in records: if len(ungap_all(record)) >= min_length: yield record def sort_length(source_file, source_file_type, direction=1): """ Sort sequences by length. 1 is ascending (default) and 0 is descending. """ direction_text = 'ascending' if direction == 1 else 'descending' logging.info('Indexing sequences by length: %s', direction_text) # Adapted from the Biopython tutorial example. # Get the lengths and ids, and sort on length len_and_ids = sorted((len(rec), rec.id) for rec in SeqIO.parse(source_file, source_file_type)) if direction == 0: ids = reversed([seq_id for (length, seq_id) in len_and_ids]) else: ids = [seq_id for (length, seq_id) in len_and_ids] del len_and_ids # free this memory # SeqIO.index does not handle gzip instances if isinstance(source_file, gzip.GzipFile): tmpfile = tempfile.NamedTemporaryFile() source_file.seek(0) tmpfile.write(source_file.read()) tmpfile.seek(0) source_file = tmpfile record_index = SeqIO.index(source_file.name, source_file_type) for seq_id in ids: yield record_index[seq_id] def sort_name(source_file, source_file_type, direction=1): """ Sort sequences by name. 1 is ascending (default) and 0 is descending. """ direction_text = 'ascending' if direction == 1 else 'descending' logging.info("Indexing sequences by name: %s", direction_text) # Adapted from the Biopython tutorial example. # Sort on id ids = sorted((rec.id) for rec in SeqIO.parse(source_file, source_file_type)) if direction == 0: ids = reversed(ids) # SeqIO.index does not handle gzip instances if isinstance(source_file, gzip.GzipFile): tmpfile = tempfile.NamedTemporaryFile() source_file.seek(0) tmpfile.write(source_file.read()) tmpfile.seek(0) source_file = tmpfile record_index = SeqIO.index(source_file.name, source_file_type) for id in ids: yield record_index[id] seqmagick-0.8.4/setup.py000077500000000000000000000032031376401056300152070ustar00rootroot00000000000000#!/usr/bin/env python import os import sys import subprocess from setuptools import setup, find_packages subprocess.call( ('mkdir -p seqmagick/data && ' 'git describe --tags --dirty > seqmagick/data/ver.tmp ' '&& mv seqmagick/data/ver.tmp seqmagick/data/ver ' '|| rm -f seqmagick/data/ver.tmp'), shell=True, stderr=open(os.devnull, "w")) # must import __version__ after call to 'git describe' above from seqmagick import __version__ setup(name='seqmagick', version=__version__, description='Tools for converting and modifying sequence files ' 'from the command-line', url='http://github.com/fhcrc/seqmagick', download_url='http://pypi.python.org/pypi/seqmagick', author='Matsen Group', # author_email='http://matsen.fhcrc.org/', packages=find_packages(), entry_points={ 'console_scripts': [ 'seqmagick = seqmagick.scripts.cli:main' ]}, package_data={ 'seqmagick': ['data/*'], 'seqmagick.test.integration': ['data/*'] }, setup_requires=['nose>=1.0'], python_requires='>=3.5', test_suite='nose.collector', install_requires=['biopython>=1.78', 'pygtrie>=2.1'], classifiers=[ 'License :: OSI Approved :: GNU General Public License (GPL)', 'Development Status :: 4 - Beta', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', 'Topic :: Scientific/Engineering :: Bio-Informatics', ], license="GPL V3") seqmagick-0.8.4/tox.ini000066400000000000000000000002641376401056300150110ustar00rootroot00000000000000[tox] envlist = py27,pypy [testenv] deps = numpy nose rednose biopython commands = nosetests --rednose [] [testenv:pypy] deps = nose rednose biopython