pax_global_header00006660000000000000000000000064122623457370014525gustar00rootroot0000000000000052 comment=105a189a102d66d246bd618f07af2b861916272c fastx_toolkit-0.0.14/000077500000000000000000000000001226234573700145015ustar00rootroot00000000000000fastx_toolkit-0.0.14/.gitignore000066400000000000000000000017371226234573700165010ustar00rootroot00000000000000syntax: glob ## vim temporary files .*.swp ## GNU auto-tools generated files config.h config.h.in config.log config.status config/ltmain.sh config/compile INSTALL ## Distribution tarballs fastx*.tar.bz2 ## Intermediate files *.o *.a *.Po Makefile Makefile.in libtool *.m4 autom4te.cache/* configure stamp-h1 ## The compiled binaries src/fastx_collapser/fastx_collapser src/fastx_reverse_complement/fastx_reverse_complement src/fastx_trimmer/fastx_trimmer src/fastq_quality_filter/fastq_quality_filter src/fastq_to_fasta/fastq_to_fasta src/fasta_nucleotide_changer/fasta_nucleotide_changer src/fastx_quality_stats/fastx_quality_stats src/fasta_formatter/fasta_formatter src/fastx_uncollapser/fastx_uncollapser src/fastx_renamer/fastx_renamer src/fastq_quality_trimmer/fastq_quality_trimmer src/fastx_artifacts_filter/fastx_artifacts_filter src/fastx_clipper/fastx_clipper src/fastq_quality_converter/fastq_quality_converter src/seqalign_test/seqalign_test src/fastq_masker/fastq_masker fastx_toolkit-0.0.14/.hgignore000066400000000000000000000017071226234573700163110ustar00rootroot00000000000000syntax: glob ## vim temporary files .*.swp ## GNU auto-tools generated files config.h config.h.in config.log config.status config/ltmain.sh ## Distribution tarballs fastx*.tar.bz2 ## Intermediate files *.o *.a *.Po Makefile Makefile.in libtool *.m4 autom4te.cache/* configure stamp-h1 ## The compiled binaries src/fastx_collapser/fastx_collapser src/fastx_reverse_complement/fastx_reverse_complement src/fastx_trimmer/fastx_trimmer src/fastq_quality_filter/fastq_quality_filter src/fastq_to_fasta/fastq_to_fasta src/fasta_nucleotide_changer/fasta_nucleotide_changer src/fastx_quality_stats/fastx_quality_stats src/fasta_formatter/fasta_formatter src/fastx_uncollapser/fastx_uncollapser src/fastx_renamer/fastx_renamer src/fastq_quality_trimmer/fastq_quality_trimmer src/fastx_artifacts_filter/fastx_artifacts_filter src/fastx_clipper/fastx_clipper src/fastq_quality_converter/fastq_quality_converter src/seqalign_test/seqalign_test src/fastq_masker/fastq_masker fastx_toolkit-0.0.14/AUTHORS000066400000000000000000000001711226234573700155500ustar00rootroot00000000000000Authors of FASTX toolkit. See also the files THANKS and ChangeLog. Assaf Gordon designed and implemented FASTX toolkit. fastx_toolkit-0.0.14/COPYING000066400000000000000000001033301226234573700155340ustar00rootroot00000000000000 GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 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 Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, our General Public Licenses are intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. 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Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If your software can interact with users remotely through a computer network, you should also make sure that it provides a way for users to get its source. For example, if your program is a web application, its interface could display a "Source" link that leads users to an archive of the code. 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For more information on this, and how to apply and follow the GNU AGPL, see . fastx_toolkit-0.0.14/ChangeLog000066400000000000000000000000001226234573700162410ustar00rootroot00000000000000fastx_toolkit-0.0.14/GALAXY-LICENSE.txt000066400000000000000000000024771226234573700173210ustar00rootroot00000000000000=============== Galaxy License For more information: Galaxy main web: http://g2.bx.psu.edu/ Galaxy license: http://g2.trac.bx.psu.edu/wiki/LICENSE All files under the ./galaxy sub-directory are distributed under the Galaxy license. =============== Copyright (c) 2005 Pennsylvania State University Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. fastx_toolkit-0.0.14/LICENSE000066400000000000000000000005521226234573700155100ustar00rootroot00000000000000FASTX-Toolkit LICENSE ===================== FASTX-Toolkit is distributed under the Affero GPL (AGPL) version 3 or later. See the COPYING file, or . EXCEPT Files under the 'galaxy' sub-direcory are distributed under the same license as Galaxy itself (which is a more permissive, MIT style license). See the GALAXY-LICENSE file. fastx_toolkit-0.0.14/Makefile.am000066400000000000000000000012311226234573700165320ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. EXTRA_DIST = reconf configure README install_galaxy_files.sh SUBDIRS = m4 src doc galaxy scripts build_scripts ACLOCAL_AMFLAGS = -I m4 AUTOMAKE_OPTIONS = dist-bzip2 no-dist-gzip fastx_toolkit-0.0.14/NEWS000066400000000000000000000015471226234573700152070ustar00rootroot00000000000000FASTX toolkit -- History of visible changes. Copyright (C) 2008-2013, Assaf Gordon See the end for copying conditions. Please send FASTX toolkit bug reports to assafgordon@gmail.com. Version 0.0.6 * First public release ------------------------------------------------------- Copying information: Copyright (C) 2008-2013, Assaf Gordon Permission is granted to anyone to make or distribute verbatim copies of this document as received, in any medium, provided that the copyright notice and this permission notice are preserved, thus giving the recipient permission to redistribute in turn. Permission is granted to distribute modified versions of this document, or of portions of it, under the above conditions, provided also that they carry prominent notices stating who last changed them. fastx_toolkit-0.0.14/README000066400000000000000000000216321226234573700153650ustar00rootroot00000000000000FASTX-Toolkit ============= Short Summary =============== The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. More Details ============== Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat (http://www.kentinformatics.com/index.asp), SHRiMP (http://compbio.cs.toronto.edu/shrimp), LastZ (http://www.bx.psu.edu/miller_lab), MAQ (http://maq.sourceforge.net/) And many many others. However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks. Available Tools =============== FASTQ-to-FASTA - Converts a FASTQ file to a FASTA file.. FASTQ-Statistics - scans a FASTQ file, and produces some statistics about the quality and the sequences in the file. FASTQ-Quality-BoxPlot, and FASTQ-Nucleotides-Distribution - Generates charts based on the statistics generated by FASTQ-Statistics. These charts can be used to quickly see the quality of the sequenced library. FASTQ-Quality-Converter - Converts from ASCII to numeric quality scores. FASTQ-Quality-Filter - removes low-quality sequences from FASTQ files. FASTX-Artifacts-Filter - removes some sequencing artifacts from FASTA/Q files. FASTX-Barcode-Splitter - A common practice is to sequence multiple biological samples in the same library (marking each sample using a dedicated barcode). The resulting FASTA/Q file contains intermixed sequences from those samples. This tool separates FASTA/Q files into several individual files, based on the barcodes. FASTX-Clipper - Adapters (aka Linkers) are added to the library (before sequencing), and should be removed from the resulting FASTA/Q file. This tool removes (clips) adapters. FASTA-Clipping-Histogram - After clipping a FASTA file, this tool generates a chart showing the length of the clipped sequences. FASTX-Reverse-Complement - Produces a reverse-complement of FASTA/Q file. If a FASTQ file is given, the quality scores are also reversed. FASTX-Trimmer - Extract sub-seqeunces from FASTA/Q file. Two examples are: Removing barcodes from the 5'-end of all sequences in a FASTQ file; Cutting 7 nucleotides from the 3'-end of all sequences in a FASTA file. Galaxy ====== Galaxy (http://g2.bx.psu.edu) is web-based framework for computational biology. While the programs in the FASTX-Toolkit are command-line based, the package include the necessary files to integrate the tools into a Galaxy server, Allowing users to execute this tools from their web-browser. If you run your own local mirror of a Galaxy server, you can integrate the FASTX-Toolkit into your Galaxy server. Software Requirements ===================== 1. GCC is required to compile most tools. 2. FASTA-Clipping-Histogram tool requires Perl, the "PerlIO::gzip", "GD::Graph::bars" modules. Installing the perl modules can be accomplised by running: $ sudo cpan 'PerlIO::gzip' $ sudo cpan 'GD::Graph::bars' 3. FASTX-Barcode-Splitter requires the GNU Sed program. 4. FASTQ-Quality-Boxplot and FASTQ-Nucleotides-Distribution requires the 'gnuplot' program. Installation ============ To compile to tools, run: $ ./configure $ make To install the tools, run (as root): $ sudo make install This will install the tools into /usr/local/bin. To install the tools to a different location, change the 'configure' step to: $ ./configure --prefix=/DESTINATION/DIRECTORY Command Line Usage ================== Most tools support "-h" argument to show a short help screen. Better documentation is not available at this moment. Some more details and examples are available in the section of the XML tool files (in the 'galaxy' subdirectory). Galaxy Installation =================== Galaxy Installation should be done manually, and requires technical understading of the Galaxy framework. 1. build and install the command line tools (as described above). 2. Make backup of your galaxy installation (better safe than sorry). 3. Run the 'install_galaxy_files.sh' script, and specify the galaxy root directory. This script copies the files from the 'galaxy' sub-directory into your galaxy mirror directory. 4. Manually add the content of ./galaxy/fastx_toolkit_conf.xml file, into your Galaxy's tool_conf.xml 5. Edit [YOUR-GALAXY]/tool-data/fastx_clipper_sequences.txt file, And add your custom adapters/linkers. 6. Modify the "fastx_barcode_splitter_galaxy_wrapper.sh" as explained Below (see section "Special configuration for Barcode-Splitter"). 7. Restart Galaxy. Always make backup of your galaxy server files before trying to install the FASTX-Toolkit. Galaxy Testing ============== The following tools support Galaxy's functional testing: (Run from Galaxy's main directory) $ sh run_functional_tests.sh -id cshl_fastq_qual_conv $ sh run_functional_tests.sh -id cshl_fastq_to_fasta $ sh run_functional_tests.sh -id cshl_fastq_qual_stat $ sh run_functional_tests.sh -id cshl_fastx_trimmer $ sh run_functional_tests.sh -id cshl_fastx_reverse_complement $ sh run_functional_tests.sh -id cshl_fastx_artifacts_filter $ sh run_functional_tests.sh -id cshl_fasta_collapser $ sh run_functional_tests.sh -id cshl_fastx_clipper Special configuration for Barcode-Splitter ========================================== When running the barcode-splitter tool from the command line you specify a prefix direcotry - the output files will be written to that directory (similar to GNU's split program usage). Running the barcode-splittter inside galaxy requires a special hack beacuse (I don't know how to|Galaxy can't) create a variable number of output datasets. The number of required output files is determined by the tool only AFTER reading the barcodes description file. The Galaxy-version of Barcode-Splitter works like this: 1. A FASTA/FASTQ file, and a Barcode description file are fed to the tool. 2. The tool produces a single output dataset (inside galaxy). This output is an HTML file, containing links to the split FASTA files. 3. Users can use the links to get the split FASTA files. (Since Galaxy's 'upload data' tool accepts URLs, this is not a real problem). 4. As the galaxy administrator, you'll have to edit 'fastx_barcode_splitter_galaxy_wrapper.sh' script and change BASEPATH and PUBLICURL to point to a publicly accesibly path on your server. Example: fastx_barcode_splitter_galaxy_wrapper.sh contains: BASEPATH="/media/sdb1/galaxy/barcode_splits/" PUBLICURL="http://tango.cshl.edu/barcode_splits/" When a user runs the barcode splitter tool, the FASTA files will be generated in "/media/sdb1/galaxy/barcode_splits/". The URL "http://tango.cshl.edu/barcode_splits" is set (in an apache server) to serve files from "/media/sdb1/galaxy/barcode_splits/", with the following configuration: Alias /barcode_splits "/media/sdb1/galaxy/barcode_splits/" AllowOverride None Order allow,deny Allow from all Licenses ======== FASTX-Toolkit is distributed under the Affero GPL version 3 or later (AGPLv3), EXCEPT All files under the 'galaxy' sub-directory are distributed under the same license as Galaxy itself (which is an MIT-style license). While IANAL, these licenses basically mean that: 1. You're free to use FASTX-toolkit, 2. You're free to integrate FASTX-toolkit in your Galaxy mirror server (or any other server). 3. You're free to modify the files under 'galaxy', without making your modifications public. 4. If you modify the FASTX-toolkit tools, and make those modifications publicly available (either as downloadable tools, part of another product), or as a web-based server - you must make the modified source code freely available (free as in speech). See the COPYING file for the full Affero GPL. See the GALAXY-LICENSE file for galaxy's license. Please remember: THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. ============= Please send all comments, suggestions, bug reports (or better yet - bug fixes) to assafgordon@gmail.com . fastx_toolkit-0.0.14/THANKS000066400000000000000000000005641226234573700154210ustar00rootroot00000000000000FASTX toolkit THANKS file FASTX toolkit has originally been written by Assaf Gordon. Many people have further contributed to FASTX-Toolkit by reporting problems, suggesting various improvements, or submitting actual code. Here is a list of these people. Help me keep it complete and exempt of errors. Many Hannon-lab members at CSHL (who prefered to remain anonymous). fastx_toolkit-0.0.14/build_scripts/000077500000000000000000000000001226234573700173475ustar00rootroot00000000000000fastx_toolkit-0.0.14/build_scripts/Makefile.am000066400000000000000000000010411226234573700213770ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. EXTRA_DIST = build_on_opensolaris_2009.6.sh \ build_on_linux.sh fastx_toolkit-0.0.14/build_scripts/build_on_linux.sh000077500000000000000000000014221226234573700227170ustar00rootroot00000000000000#!/bin/sh #Tell pkg-config to look for libraries in /usr/local/lib, too. export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH # Configure, with static binaries and target directroy ./configure --enable-static --enable-all-static --prefix="$PWD/build" || exit 1 # build the programs make || exit 1 # Install them to the target directory (doesn't require root) make install || exit 1 # Create a package of the static binaries VERSION=$(grep '#define VERSION' config.h | sed 's/.*"\(.*\)".*/\1/') TARBALL=fastx_toolkit_${VERSION}_binaries_$(uname -s)_$(uname -r)_$(uname -m).tar.bz2 cd build || exit 1 tar -cjvf "../$TARBALL" ./bin/* || exit 1 cd .. echo "Static Binaries are installed in:" echo " $PWD/build/bin" echo echo "Static binaries tarball:" echo " $TARBALL" fastx_toolkit-0.0.14/build_scripts/build_on_opensolaris_2009.6.sh000077500000000000000000000014751226234573700247440ustar00rootroot00000000000000#!/bin/sh export CC=gcc-4.3.2 export CXX=g++-4.3.2 #Tell pkg-config to look for libraries in /usr/local/lib, too. export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH # Configure, with static binaries and target directroy ./configure --enable-static --enable-all-static --prefix="$PWD/build" || exit 1 # build the programs make || exit 1 # Install them to the target directory (doesn't require root) make install || exit 1 # Create a package of the static binaries VERSION=$(grep '#define VERSION' config.h | sed 's/.*"\(.*\)".*/\1/') TARBALL=fastx_toolkit_${VERSION}_binaries_$(uname -s)_$(uname -r)_$(uname -m).tar.bz2 cd build || exit 1 tar -cjvf "../$TARBALL" ./bin/* || exit 1 cd .. echo "Static Binaries are installed in:" echo " $PWD/build/bin" echo echo "Static binaries tarball:" echo " $TARBALL" fastx_toolkit-0.0.14/configure.ac000066400000000000000000000067461226234573700170040ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. AC_INIT([FASTX Toolkit], [0.0.14], [Assaf Gordon assafgordon@gmail.com], [fastx_toolkit]) AC_CONFIG_AUX_DIR(config) AC_CONFIG_MACRO_DIR([m4]) AM_CONFIG_HEADER(config.h) AM_INIT_AUTOMAKE([dist-bzip2]) AC_PROG_CC AC_PROG_CXX AC_PROG_LIBTOOL AX_C_LONG_LONG AX_CXX_HEADER_STDCXX_TR1 AX_CXX_COMPILE_STDCXX_11([noext],[optional]) dnl if test "$ax_cv_cxx_stdcxx_tr1" != yes; then dnl AC_MSG_ERROR([Your version of gcc does not support the 'std::tr1' standard. Recommended gcc version is 4.1.2 or later. Please use a newer gcc version, or try to download the pre-compiled binaries from the fastx-toolkit website.]) dnl fi PKG_CHECK_MODULES([GTEXTUTILS],[gtextutils]) dnl --enable-wall EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror" AC_ARG_ENABLE(wall, [ --enable-wall Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)], [case "${enableval}" in yes) wall=true ;; no) wall=false ;; *) AC_MSG_ERROR(bad value ${enableval} for --enable-wall) ;; esac],[wall=true]) if test "$wall" = "true" then CFLAGS="${CFLAGS} ${EXTRA_CHECKS}" CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}" fi dnl --enable-debug AC_ARG_ENABLE(debug, [ --enable-debug Enable debug mode (default enabled)], [case "${enableval}" in yes) debug=true ;; no) debug=false ;; *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;; esac],[debug=true]) if test "$debug" = "true" then CFLAGS="${CFLAGS} -DDEBUG -g -O1" CXXFLAGS="${CXXFLAGS} -DDEBUG -g -O1" else CFLAGS="${CFLAGS} -O3" CXXFLAGS="${CXXFLAGS} -O3" fi dnl 'all-static' marco copied from subversion's configure.ac dnl Check for --enable-all-static option AC_ARG_ENABLE(all-static, AS_HELP_STRING([--enable-all-static], [Build completely static (standalone) binaries.]), [ if test "$enableval" = "yes" ; then LT_LDFLAGS="-all-static $LT_LDFLAGS" elif test "$enableval" != "no" ; then AC_MSG_ERROR([--enable-all-static doesn't accept argument]) fi ]) AC_SUBST(LT_LDFLAGS) AC_CONFIG_FILES([ Makefile doc/Makefile m4/Makefile src/Makefile src/libfastx/Makefile src/fastx_clipper/Makefile src/fastq_to_fasta/Makefile src/fastx_quality_stats/Makefile src/fastq_quality_converter/Makefile src/fastx_trimmer/Makefile src/fastq_quality_filter/Makefile src/fastq_quality_trimmer/Makefile src/fastx_artifacts_filter/Makefile src/fastx_reverse_complement/Makefile src/fastx_collapser/Makefile src/fastx_uncollapser/Makefile src/seqalign_test/Makefile src/fasta_formatter/Makefile src/fasta_nucleotide_changer/Makefile src/fastx_renamer/Makefile src/fastq_masker/Makefile galaxy/Makefile galaxy/tools/Makefile galaxy/tools/fastx_toolkit/Makefile galaxy/test-data/Makefile galaxy/static/Makefile galaxy/static/fastx_icons/Makefile galaxy/tool-data/Makefile scripts/Makefile build_scripts/Makefile ]) AC_OUTPUT fastx_toolkit-0.0.14/doc/000077500000000000000000000000001226234573700152465ustar00rootroot00000000000000fastx_toolkit-0.0.14/doc/Makefile.am000066400000000000000000000007431226234573700173060ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. fastx_toolkit-0.0.14/galaxy/000077500000000000000000000000001226234573700157665ustar00rootroot00000000000000fastx_toolkit-0.0.14/galaxy/Makefile.am000066400000000000000000000010721226234573700200220ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. SUBDIRS = tools test-data static tool-data EXTRA_DIST = README fastx_toolkit_conf.xml fastx_toolkit-0.0.14/galaxy/README000066400000000000000000000006071226234573700166510ustar00rootroot00000000000000FASTX-Toolkit - Galaxy Files ============================ These files allows easy integration of the FASTX-toolkit tools in the Galaxy framework. Installation ============ See the README file. LICENSE ======= All files under the 'galaxy' sub-directory are licensed under Galaxy's license. see GALAXY-LICENSE file. (The rest of the FASTX-Toolkit files are licensed under AGPLv3 or later). fastx_toolkit-0.0.14/galaxy/fastx_toolkit_conf.xml000066400000000000000000000030061226234573700224060ustar00rootroot00000000000000# # Add the following sections to your Galaxy server's tool_conf.xml file. #
fastx_toolkit-0.0.14/galaxy/static/000077500000000000000000000000001226234573700172555ustar00rootroot00000000000000fastx_toolkit-0.0.14/galaxy/static/Makefile.am000066400000000000000000000007731226234573700213200ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. SUBDIRS = fastx_icons fastx_toolkit-0.0.14/galaxy/static/fastx_icons/000077500000000000000000000000001226234573700215755ustar00rootroot00000000000000fastx_toolkit-0.0.14/galaxy/static/fastx_icons/Makefile.am000066400000000000000000000021171226234573700236320ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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EXTRA_DIST = fastq_qual_conv1a.out \ fastq_qual_conv1.fastq \ fastq_qual_conv1.out \ fastq_qual_conv2.fastq \ fastq_qual_conv2n.out \ fastq_qual_conv2.out \ fastq_qual_filter1a.out \ fastq_qual_filter1b.out \ fastq_qual_filter1.fastq \ fastq_stats1.fastq \ fastq_stats1.out \ fastq_to_fasta1a.out \ fastq_to_fasta1b.out \ fastq_to_fasta1.fastq \ fastx_artifacts1.fasta \ fastx_artifacts1.out \ fastx_artifacts2.fastq \ fastx_artifacts2.out \ fastx_clipper1a.out \ fastx_clipper1.fastq \ fastx_rev_comp1.fasta \ fastx_rev_comp2.fastq \ fastx_reverse_complement1.out \ fastx_reverse_complement2.out \ fastx_trimmer1.fasta \ fastx_trimmer1.out \ fastx_trimmer2.fastq \ fastx_trimmer2.out \ fasta_collapser1.fasta \ fasta_collapser1.out \ fastx_barcode_splitter1.fastq \ fastx_barcode_splitter1.txt \ fastx_barcode_splitter1.out \ fasta_formatter1.fasta \ fasta_formatter1.out \ fasta_formatter2.out \ fasta_nuc_changer1.fasta \ fasta_nuc_changer1.out \ fasta_nuc_changer2.fasta \ fasta_nuc_changer2.out fastx_toolkit-0.0.14/galaxy/test-data/fasta_collapser1.fasta000066400000000000000000000020621226234573700241170ustar00rootroot00000000000000>1 TGTATTTACAATGACTAGAAA >2 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >3 AGTACAAGGACATGC >4 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >5 AGTACAAGGACATGC >6 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >7 AGTACAAGGACATGC >8 AGTACAAGGACATGC >9 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >10 AGTACAAGGACATGC >11 AGTACAAGGACATGC >12 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >13 CGATTGCCGAAGTCTACCA >14 AGTACAAGGACATGC >15 CCTTGTAGTGGATTCTGATGA >16 AGTACAAGGACATGC >17 AGTACAAGGACATGC >18 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >19 AGTACAAGGACATGC >20 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >21 AGTACAAGGACATGC >22 AGTACAAGGACATGC >23 CTGCTGCGATCGGTGTGC >24 AGTACAAGGACATGC >25 ACCATTCGAGCATAC >26 AGTACAAGGACATGC >27 TCAAATTCTAGATTTTTACGG >28 AGTACAAGGACATGC >29 TGATTTCCAGAGCCAAT >30 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >31 TTACCTCACGATATTGTAATA >32 ATGACTTCATCGTCCACCCTTTAGAACT >33 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >34 TTCAACGCCGCCGTGAAC >35 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >36 CTGCTGCGATCGGTGTGC >37 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >38 TTCAACGCCGCCGTGAAC >39 TTCAACGCCGCCGTGAAC >40 CTGCTGCGATCGGTGTGC >41 TTCAACGCCGCCGTGAAC >42 TTCAACGCCGCCGTGAAC fastx_toolkit-0.0.14/galaxy/test-data/fasta_collapser1.out000066400000000000000000000005021226234573700236250ustar00rootroot00000000000000>1-15 AGTACAAGGACATGC >2-11 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >3-5 TTCAACGCCGCCGTGAAC >4-3 CTGCTGCGATCGGTGTGC >5-1 TCAAATTCTAGATTTTTACGG >6-1 ACCATTCGAGCATAC >7-1 TGATTTCCAGAGCCAAT >8-1 TTACCTCACGATATTGTAATA >9-1 TGTATTTACAATGACTAGAAA >10-1 CCTTGTAGTGGATTCTGATGA >11-1 CGATTGCCGAAGTCTACCA >12-1 ATGACTTCATCGTCCACCCTTTAGAACT fastx_toolkit-0.0.14/galaxy/test-data/fasta_formatter1.fasta000066400000000000000000000113051226234573700241360ustar00rootroot00000000000000>Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA GTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTAT ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATC TACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGC AAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTT GATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATA GCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAG AAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACT AAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAA AGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAG AGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCA ACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTC GCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATA CATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATA ATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG GAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAa ggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaag ctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatga taaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt gtttctctcatggtctgtgagagatatagggtagtcccatatacatcttt ctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatca ttttgatgattccagaaccttgcagatgcgagatggtagatgatcaacct tttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccat aactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAG TTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGC CAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAA AAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGA AGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGT GTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAA ATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATT AAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGAT ATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGT GTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATA CTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAG ATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA >Scaffold9309 GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTA TGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAAT TTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATT AGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTT TTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAAC GAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATC GAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAAT ACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAG TTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAA TCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAA TGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt gataatttttttttctttgataatttttttctttttctttaataaatttt ttggataatttttttttggataaatagttcttttttgataattctaataa tttttttatttattttttttttttctataattttttttaaaaaatttatt aatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGAC AATTCAAAAAAAAAAAAAA >Scaffold9310 GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATAC GCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACT TTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGA TGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtg tgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTG ATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgt gcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATT GCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAA AAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAA CGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAG AGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAA GTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtact atgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgca tttgaaagataatactaatttacaacttccctaaaaaaggtggggcttga aaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactt tagggCTATAGAGCCCAAAAGTAATAGTCTTGA >Scaffold11911 TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAA GTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGT ACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttat atCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctc tcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACT TGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT TTGtctctgttcccctctccccccctctctctctctctctctctctctct ctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTG TTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTT AATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAA CTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTA CTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTT CTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTG GACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATA TTA fastx_toolkit-0.0.14/galaxy/test-data/fasta_formatter1.out000066400000000000000000000111531226234573700236500ustar00rootroot00000000000000>Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA >Scaffold9309 GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA >Scaffold9310 GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA >Scaffold11911 TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA fastx_toolkit-0.0.14/galaxy/test-data/fasta_formatter2.out000066400000000000000000000112651226234573700236550ustar00rootroot00000000000000>Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT TCGATATAGTACATGGACACAATTAAATATGATATTGTCT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA >Scaffold9309 GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA >Scaffold9310 GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA >Scaffold11911 TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC TTTGATGCCAATCCAACAATTTTGCATATATTA fastx_toolkit-0.0.14/galaxy/test-data/fasta_nuc_changer1.fasta000066400000000000000000000036341226234573700244150ustar00rootroot00000000000000>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 TGAGGTAGTAGGTTGTATAGTT >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 TCCCTGAGACCTCAAGTGTGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 TGGAATGTAAAGAAGTATGTA >cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 TATCACAGCCAGCTTTGATGTGC >cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 AGGCAGTGTGGTTAGCTGGTTG >cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 TCACCGGGTGGAAACTAGCAGT >cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 TCACCGGGTGAAAATTCGCATG >cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 TCACCGGGTGAACACTTGCAGT >cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 TCACCGGGAGAAAAACTGGAGT >cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 TCACCGGGTGTAAATCAGCTTG >cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 TCACCGGGTGTACATCAGCTAA >cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 TCACCGGGTGAAAAATCACCTA >cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 TCACCGGGTTAACATCTACAGA >cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 TATCACAGTTTACTTGCTGTCGC >cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 TGACTAGAGACACATTCAGCT >cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 TGACTAGAGACACATTCAGCT >cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 TGTCATGGAGTCGCTCTCTTCA >cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 TGTCATGGAGGCGCTCTCTTCA >cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 TGAGGTAGGCTCAGTAGATGCGA >cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 AAGCACCACGAGAAGCTGCAGA >cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 TGATATGTCTGGTATTCTTGGG >cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 TACCCGTAGCTCCTATCCATGTT >cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 CACCCGTACATATGTTTCCGTGCT >cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 CACCCGTACATTTGTTTCCGTGCT >cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 TACCCGTAATCTTCATAATCCGAG fastx_toolkit-0.0.14/galaxy/test-data/fasta_nuc_changer1.out000066400000000000000000000036341226234573700241260ustar00rootroot00000000000000>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 UGAGGUAGUAGGUUGUAUAGUU >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 UCCCUGAGACCUCAAGUGUGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 UGGAAUGUAAAGAAGUAUGUA >cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 UAUCACAGCCAGCUUUGAUGUGC >cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 AGGCAGUGUGGUUAGCUGGUUG >cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 UCACCGGGUGGAAACUAGCAGU >cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 UCACCGGGUGAAAAUUCGCAUG >cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 UCACCGGGUGAACACUUGCAGU >cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 UCACCGGGAGAAAAACUGGAGU >cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 UCACCGGGUGUAAAUCAGCUUG >cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 UCACCGGGUGUACAUCAGCUAA >cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 UCACCGGGUGAAAAAUCACCUA >cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 UCACCGGGUUAACAUCUACAGA >cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 UAUCACAGUUUACUUGCUGUCGC >cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 UGACUAGAGACACAUUCAGCU >cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 UGACUAGAGACACAUUCAGCU >cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 UGUCAUGGAGUCGCUCUCUUCA >cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 UGUCAUGGAGGCGCUCUCUUCA >cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 UGAGGUAGGCUCAGUAGAUGCGA >cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 AAGCACCACGAGAAGCUGCAGA >cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 UGAUAUGUCUGGUAUUCUUGGG >cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 UACCCGUAGCUCCUAUCCAUGUU >cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 CACCCGUACAUAUGUUUCCGUGCU >cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 CACCCGUACAUUUGUUUCCGUGCU >cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 UACCCGUAAUCUUCAUAAUCCGAG fastx_toolkit-0.0.14/galaxy/test-data/fasta_nuc_changer2.fasta000066400000000000000000000036341226234573700244160ustar00rootroot00000000000000>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 UGAGGUAGUAGGUUGUAUAGUU >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 UCCCUGAGACCUCAAGUGUGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 UGGAAUGUAAAGAAGUAUGUA >cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 UAUCACAGCCAGCUUUGAUGUGC >cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 AGGCAGUGUGGUUAGCUGGUUG >cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 UCACCGGGUGGAAACUAGCAGU >cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 UCACCGGGUGAAAAUUCGCAUG >cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 UCACCGGGUGAACACUUGCAGU >cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 UCACCGGGAGAAAAACUGGAGU >cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 UCACCGGGUGUAAAUCAGCUUG >cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 UCACCGGGUGUACAUCAGCUAA >cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 UCACCGGGUGAAAAAUCACCUA >cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 UCACCGGGUUAACAUCUACAGA >cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 UAUCACAGUUUACUUGCUGUCGC >cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 UGACUAGAGACACAUUCAGCU >cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 UGACUAGAGACACAUUCAGCU >cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 UGUCAUGGAGUCGCUCUCUUCA >cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 UGUCAUGGAGGCGCUCUCUUCA >cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 UGAGGUAGGCUCAGUAGAUGCGA >cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 AAGCACCACGAGAAGCUGCAGA >cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 UGAUAUGUCUGGUAUUCUUGGG >cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 UACCCGUAGCUCCUAUCCAUGUU >cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 CACCCGUACAUAUGUUUCCGUGCU >cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 CACCCGUACAUUUGUUUCCGUGCU >cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 UACCCGUAAUCUUCAUAAUCCGAG fastx_toolkit-0.0.14/galaxy/test-data/fasta_nuc_changer2.out000066400000000000000000000036341226234573700241270ustar00rootroot00000000000000>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 TGAGGTAGTAGGTTGTATAGTT >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 TCCCTGAGACCTCAAGTGTGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 TGGAATGTAAAGAAGTATGTA >cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 TATCACAGCCAGCTTTGATGTGC >cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 AGGCAGTGTGGTTAGCTGGTTG >cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 TCACCGGGTGGAAACTAGCAGT >cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 TCACCGGGTGAAAATTCGCATG >cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 TCACCGGGTGAACACTTGCAGT >cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 TCACCGGGAGAAAAACTGGAGT >cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 TCACCGGGTGTAAATCAGCTTG >cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 TCACCGGGTGTACATCAGCTAA >cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 TCACCGGGTGAAAAATCACCTA >cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 TCACCGGGTTAACATCTACAGA >cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 TATCACAGTTTACTTGCTGTCGC >cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 TGACTAGAGACACATTCAGCT >cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 TGACTAGAGACACATTCAGCT >cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 TGTCATGGAGTCGCTCTCTTCA >cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 TGTCATGGAGGCGCTCTCTTCA >cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 TGAGGTAGGCTCAGTAGATGCGA >cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 AAGCACCACGAGAAGCTGCAGA >cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 TGATATGTCTGGTATTCTTGGG >cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 TACCCGTAGCTCCTATCCATGTT >cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 CACCCGTACATATGTTTCCGTGCT >cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 CACCCGTACATTTGTTTCCGTGCT >cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 TACCCGTAATCTTCATAATCCGAG fastx_toolkit-0.0.14/galaxy/test-data/fasta_uncollapser1.fasta000066400000000000000000000005021226234573700244570ustar00rootroot00000000000000>1-15 AGTACAAGGACATGC >2-11 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >3-5 TTCAACGCCGCCGTGAAC >4-3 CTGCTGCGATCGGTGTGC >5-1 TCAAATTCTAGATTTTTACGG >6-1 ACCATTCGAGCATAC >7-1 TGATTTCCAGAGCCAAT >8-1 TTACCTCACGATATTGTAATA >9-1 TGTATTTACAATGACTAGAAA >10-1 CCTTGTAGTGGATTCTGATGA >11-1 CGATTGCCGAAGTCTACCA >12-1 ATGACTTCATCGTCCACCCTTTAGAACT fastx_toolkit-0.0.14/galaxy/test-data/fasta_uncollapser1.out000066400000000000000000000020621226234573700241730ustar00rootroot00000000000000>1 AGTACAAGGACATGC >2 AGTACAAGGACATGC >3 AGTACAAGGACATGC >4 AGTACAAGGACATGC >5 AGTACAAGGACATGC >6 AGTACAAGGACATGC >7 AGTACAAGGACATGC >8 AGTACAAGGACATGC >9 AGTACAAGGACATGC >10 AGTACAAGGACATGC >11 AGTACAAGGACATGC >12 AGTACAAGGACATGC >13 AGTACAAGGACATGC >14 AGTACAAGGACATGC >15 AGTACAAGGACATGC >16 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >17 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >18 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >19 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >20 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >21 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >22 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >23 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >24 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >25 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >26 ATTGCTGCTCGGATGGTCCGGCTGTGCACAC >27 TTCAACGCCGCCGTGAAC >28 TTCAACGCCGCCGTGAAC >29 TTCAACGCCGCCGTGAAC >30 TTCAACGCCGCCGTGAAC >31 TTCAACGCCGCCGTGAAC >32 CTGCTGCGATCGGTGTGC >33 CTGCTGCGATCGGTGTGC >34 CTGCTGCGATCGGTGTGC >35 TCAAATTCTAGATTTTTACGG >36 ACCATTCGAGCATAC >37 TGATTTCCAGAGCCAAT >38 TTACCTCACGATATTGTAATA >39 TGTATTTACAATGACTAGAAA >40 CCTTGTAGTGGATTCTGATGA >41 CGATTGCCGAAGTCTACCA >42 ATGACTTCATCGTCCACCCTTTAGAACT fastx_toolkit-0.0.14/galaxy/test-data/fastq_masker.fastq000066400000000000000000000022721226234573700233770ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_masker.out000066400000000000000000000022721226234573700230700ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACxCAxGACCGAxCCCCCxxxCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 xAATGCxTCxAxTxGxTTxxxxxCxxxxxxxxxxCT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCxGCxxGCGCxTCAGAGAGCCCCCCCCxxxxxxxx +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTxATAATATxGGAGACxxx +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACxxACAATTGGTTAxxxxxxxTAxxxx +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AxxxxxxxCCxxxxxxxxxxxxxxxxxxxxxxxxxx +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGxxxxxxACCCCCCxCCCCCCCCCxxxx +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACxxCAxTTGGTTxxxxxCCxxxTATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCxxxxxxxxxxTxxxxxxx +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_conv1.fastq000066400000000000000000000022721226234573700241650ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACACACACTCATCGTCGTCCCCCG +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACCC +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_conv1.out000066400000000000000000000034441226234573700236600ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC +CSHL_3_FC042AGLLWW:1:2:7:203 33 33 34 30 22 30 33 21 29 32 33 33 30 33 26 33 33 33 34 34 24 5 26 33 34 33 33 33 33 33 33 33 33 29 29 32 @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC +CSHL_3_FC042AGLLWW:1:2:7:33 23 33 33 33 30 33 26 33 33 23 30 21 31 24 33 23 33 33 28 23 13 5 16 30 11 5 26 24 18 16 5 5 5 7 33 33 @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 33 31 13 30 33 28 21 33 33 33 31 13 31 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 22 28 26 21 7 21 21 18 @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 33 30 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 31 21 32 33 33 33 33 33 31 19 31 33 33 33 33 33 22 22 27 @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACACACACTCATCGTCGTCCCCCG +CSHL_3_FC042AGLLWW:1:2:7:292 34 33 34 33 33 33 33 33 33 33 21 13 33 33 33 33 33 33 33 33 33 33 33 28 24 5 21 21 5 16 31 29 21 5 18 5 @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACCC +CSHL_3_FC042AGLLWW:1:2:7:1819 33 28 28 17 22 22 22 12 33 33 12 15 5 24 21 23 21 21 5 11 21 21 12 5 13 21 5 21 21 11 21 12 9 17 13 21 @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 33 33 33 33 33 33 33 33 33 24 21 24 24 5 24 33 33 33 33 33 32 31 26 33 33 33 33 33 33 33 33 33 24 5 24 21 @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:8:624 33 33 27 19 30 32 24 32 33 33 31 29 29 15 15 24 13 21 30 31 27 13 21 31 33 33 33 33 33 33 33 33 33 33 33 33 @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT +CSHL_3_FC042AGLLWW:1:2:8:250 33 33 33 33 33 33 33 33 30 33 33 33 33 33 33 34 34 34 27 11 24 16 5 21 27 18 24 26 30 10 21 11 18 11 24 5 fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_conv1a.out000066400000000000000000000022721226234573700240170ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACACACACTCATCGTCGTCCCCCG +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACCC +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_conv2.fastq000066400000000000000000000060541226234573700241700ustar00rootroot00000000000000@CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:233:1674 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 @CSHL_3_FC0420AGLLKK:2:1:136:448 GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA +CSHL_3_FC0420AGLLKK:2:1:136:448 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 @CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:237:1037 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 @CSHL_3_FC0420AGLLKK:2:1:1601:1525 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1601:1525 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 @CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1805:1464 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 @CSHL_3_FC0420AGLLKK:2:1:1713:528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1713:528 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 @CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA +CSHL_3_FC0420AGLLKK:2:1:126:1087 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 @CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1488:1323 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 @CSHL_3_FC0420AGLLKK:2:1:913:199 GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:913:199 40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 @CSHL_3_FC0420AGLLKK:2:1:1236:1157 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1236:1157 40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 @CSHL_3_FC0420AGLLKK:2:1:928:765 GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC +CSHL_3_FC0420AGLLKK:2:1:928:765 40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 @CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +CSHL_3_FC0420AGLLKK:2:1:727:1020 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 @CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:758:1799 40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 @CSHL_3_FC0420AGLLKK:2:1:1818:550 AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1818:550 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 @CSHL_3_FC0420AGLLKK:2:1:1764:391 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CSHL_3_FC0420AGLLKK:2:1:1764:391 40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_conv2.out000066400000000000000000000040661226234573700236620ustar00rootroot00000000000000@CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:233:1674 hhhhhhhhhhhhhhhhhh`hhhhPTYIUehhP]Z^ @CSHL_3_FC0420AGLLKK:2:1:136:448 GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA +CSHL_3_FC0420AGLLKK:2:1:136:448 hhhhhhhhhhhhhhhhhhhhhhh;MQ\hhHQ[HMJ @CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:237:1037 hhhhhhhhhhhhhhhDhhZchfhFhh@CZ`[NKZK @CSHL_3_FC0420AGLLKK:2:1:1601:1525 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1601:1525 hhhhhhhhhhhhchhLhh^^hhhLdWQXRVYOJbN @CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1805:1464 hhhhhhhhhhhhhhhhhPW\hUhIeMTUGKNNFWJ @CSHL_3_FC0420AGLLKK:2:1:1713:528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1713:528 hhhhhhhhhhhhhhhhhhhhh`hLfOVTQNLJGVK @CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA +CSHL_3_FC0420AGLLKK:2:1:126:1087 hhhhhhhhhhhhhhYhhhhhhh_hhKJWhMLQeQV @CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1488:1323 hhhhhhhhhhhhhhhhhhgV_hhL]V@GLHRGCRI @CSHL_3_FC0420AGLLKK:2:1:913:199 GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:913:199 hhghhhhhhhhhDhhXbTaUd`h;hMUUZQRYNYU @CSHL_3_FC0420AGLLKK:2:1:1236:1157 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1236:1157 hhhhhhhhhhhhhchhhhhahehhhRPTWV_ZJVS @CSHL_3_FC0420AGLLKK:2:1:928:765 GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC +CSHL_3_FC0420AGLLKK:2:1:928:765 hhhhhhhhhhhhhY[hec[hhQh;dKSOSPKLLWK @CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +CSHL_3_FC0420AGLLKK:2:1:727:1020 hhhhhhhhhhhhhhhhhhhhhh^hhXRfaZPWVPR @CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:758:1799 hhhhhhhhchghh[ThQbOhhhhO\QDLJJRNCNK @CSHL_3_FC0420AGLLKK:2:1:1818:550 AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1818:550 hhhhhhhhhhhhhhd`hahhfeh\][VMTSQQMaR @CSHL_3_FC0420AGLLKK:2:1:1764:391 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CSHL_3_FC0420AGLLKK:2:1:1764:391 hhhhhhhhhhhahhhhhXhhhhhLhXNIVO]RKhV fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_conv2n.out000066400000000000000000000060541226234573700240370ustar00rootroot00000000000000@CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:233:1674 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 @CSHL_3_FC0420AGLLKK:2:1:136:448 GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA +CSHL_3_FC0420AGLLKK:2:1:136:448 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 @CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:237:1037 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 @CSHL_3_FC0420AGLLKK:2:1:1601:1525 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1601:1525 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 @CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1805:1464 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 @CSHL_3_FC0420AGLLKK:2:1:1713:528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1713:528 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 @CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA +CSHL_3_FC0420AGLLKK:2:1:126:1087 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 @CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1488:1323 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 @CSHL_3_FC0420AGLLKK:2:1:913:199 GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:913:199 40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 @CSHL_3_FC0420AGLLKK:2:1:1236:1157 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1236:1157 40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 @CSHL_3_FC0420AGLLKK:2:1:928:765 GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC +CSHL_3_FC0420AGLLKK:2:1:928:765 40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 @CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +CSHL_3_FC0420AGLLKK:2:1:727:1020 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 @CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:758:1799 40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 @CSHL_3_FC0420AGLLKK:2:1:1818:550 AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1818:550 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 @CSHL_3_FC0420AGLLKK:2:1:1764:391 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CSHL_3_FC0420AGLLKK:2:1:1764:391 40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_filter1.fastq000066400000000000000000000022721226234573700245050ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_filter1a.out000066400000000000000000000002061226234573700243320ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa fastx_toolkit-0.0.14/galaxy/test-data/fastq_qual_filter1b.out000066400000000000000000000014501226234573700243350ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa fastx_toolkit-0.0.14/galaxy/test-data/fastq_quality_trimmer.fastq000066400000000000000000000022721226234573700253440ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_quality_trimmer.out000066400000000000000000000017741226234573700250430ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGAC +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaa @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCT +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_ @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_Zaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAAT +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^ fastx_toolkit-0.0.14/galaxy/test-data/fastq_stats1.fastq000066400000000000000000000022721226234573700233340ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_stats1.out000066400000000000000000000035271226234573700230310ustar00rootroot00000000000000column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count 1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 9 22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 9 23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 9 24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 9 25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 9 26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 9 27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 9 28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 9 29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 9 30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 9 31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 9 32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 9 33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 9 34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 9 35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 9 36 9 5 33 195 21.67 18 21 32 14 5 33 3 2 1 3 0 9 fastx_toolkit-0.0.14/galaxy/test-data/fastq_to_fasta1.fastq000066400000000000000000000022721226234573700237760ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastq_to_fasta1a.out000066400000000000000000000010321226234573700236210ustar00rootroot00000000000000>CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT >CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC >CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT >CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA >CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA >CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC >CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG >CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA fastx_toolkit-0.0.14/galaxy/test-data/fastq_to_fasta1b.out000066400000000000000000000005501226234573700236260ustar00rootroot00000000000000>1 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT >2 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT >3 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC >4 AATTATTTATTAAATTTTAATAATATGGGAGACACT >5 GGAGAAATACACACAATTGGTTAATCCCCCTATATA >6 AATTCAAACCACCCCAACCCACACACAGAGATACAA >7 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC >8 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG >9 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA fastx_toolkit-0.0.14/galaxy/test-data/fastx_artifacts1.fasta000066400000000000000000000015141226234573700241430ustar00rootroot00000000000000>CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:1601:1525 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA >CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:1713:528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA >CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:1236:1157 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA >CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA >CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:1818:550 AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA >CSHL_3_FC0420AGLLKK:2:1:1764:391 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC fastx_toolkit-0.0.14/galaxy/test-data/fastx_artifacts1.out000066400000000000000000000007541226234573700236610ustar00rootroot00000000000000>CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA >CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC >CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA >CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC fastx_toolkit-0.0.14/galaxy/test-data/fastx_artifacts2.fastq000066400000000000000000000060541226234573700241700ustar00rootroot00000000000000@CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:233:1674 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 @CSHL_3_FC0420AGLLKK:2:1:136:448 GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA +CSHL_3_FC0420AGLLKK:2:1:136:448 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 @CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:237:1037 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 @CSHL_3_FC0420AGLLKK:2:1:1601:1525 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1601:1525 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14 @CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1805:1464 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 @CSHL_3_FC0420AGLLKK:2:1:1713:528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CSHL_3_FC0420AGLLKK:2:1:1713:528 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11 @CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA +CSHL_3_FC0420AGLLKK:2:1:126:1087 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 @CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1488:1323 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 @CSHL_3_FC0420AGLLKK:2:1:913:199 GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:913:199 40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 @CSHL_3_FC0420AGLLKK:2:1:1236:1157 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1236:1157 40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19 @CSHL_3_FC0420AGLLKK:2:1:928:765 GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC +CSHL_3_FC0420AGLLKK:2:1:928:765 40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 @CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +CSHL_3_FC0420AGLLKK:2:1:727:1020 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 @CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:758:1799 40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 @CSHL_3_FC0420AGLLKK:2:1:1818:550 AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA +CSHL_3_FC0420AGLLKK:2:1:1818:550 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18 @CSHL_3_FC0420AGLLKK:2:1:1764:391 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CSHL_3_FC0420AGLLKK:2:1:1764:391 40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22 fastx_toolkit-0.0.14/galaxy/test-data/fastx_artifacts2.out000066400000000000000000000040251226234573700236550ustar00rootroot00000000000000@CSHL_3_FC0420AGLLKK:2:1:233:1674 GTTAGAGGGAATACACCCACTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:233:1674 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30 @CSHL_3_FC0420AGLLKK:2:1:136:448 GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA +CSHL_3_FC0420AGLLKK:2:1:136:448 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10 @CSHL_3_FC0420AGLLKK:2:1:237:1037 GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:237:1037 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11 @CSHL_3_FC0420AGLLKK:2:1:1805:1464 GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1805:1464 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10 @CSHL_3_FC0420AGLLKK:2:1:126:1087 GAGATATTCGAATGCATCATCAGATGGCACCATCA +CSHL_3_FC0420AGLLKK:2:1:126:1087 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22 @CSHL_3_FC0420AGLLKK:2:1:1488:1323 GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:1488:1323 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9 @CSHL_3_FC0420AGLLKK:2:1:913:199 GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:913:199 40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21 @CSHL_3_FC0420AGLLKK:2:1:928:765 GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC +CSHL_3_FC0420AGLLKK:2:1:928:765 40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11 @CSHL_3_FC0420AGLLKK:2:1:727:1020 GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA +CSHL_3_FC0420AGLLKK:2:1:727:1020 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18 @CSHL_3_FC0420AGLLKK:2:1:758:1799 GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC +CSHL_3_FC0420AGLLKK:2:1:758:1799 40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11 fastx_toolkit-0.0.14/galaxy/test-data/fastx_barcode_splitter1.fastq000066400000000000000000000076771226234573700255500ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GATCTAGTAGTAGTAGA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GATCTAGTAGTAGTAGA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GATCTAGTAGTAGTAGA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GATCTAGTAGTAGTAGA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GATCTAGTAGTAGTAGA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTCTAGTAGTAGTAGA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTCTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTCTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTACGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTACTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGTACGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCGTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCGTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCGTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCGTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTCGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTCGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTCTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 ATCTCGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 GGAATGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TAGTTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TAGTTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TAGTTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TAGTTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TAGTTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TAGTTTCTCTATGTACA +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaa @CSHL_3_FC042AGLLWW:1:2:7:203 TGTCTGAGTATACACAT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaafastx_toolkit-0.0.14/galaxy/test-data/fastx_barcode_splitter1.out000066400000000000000000000026631226234573700252270ustar00rootroot00000000000000

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BarcodeCountLocation
BC111http://tango.cshl.edu/barcode_splits/2009-01-19_1719__fastx_barcode_splitter1_fastq__BC1.txt
BC212http://tango.cshl.edu/barcode_splits/2009-01-19_1719__fastx_barcode_splitter1_fastq__BC2.txt
BC39http://tango.cshl.edu/barcode_splits/2009-01-19_1719__fastx_barcode_splitter1_fastq__BC3.txt
BC41http://tango.cshl.edu/barcode_splits/2009-01-19_1719__fastx_barcode_splitter1_fastq__BC4.txt
unmatched9http://tango.cshl.edu/barcode_splits/2009-01-19_1719__fastx_barcode_splitter1_fastq__unmatched.txt
total42
fastx_toolkit-0.0.14/galaxy/test-data/fastx_barcode_splitter1.txt000066400000000000000000000000471226234573700252310ustar00rootroot00000000000000BC1 GATCT BC2 ATCGT BC3 GTGAT BC4 TGTCTfastx_toolkit-0.0.14/galaxy/test-data/fastx_clipper1.fastq000066400000000000000000000022721226234573700236430ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastx_clipper1a.out000066400000000000000000000003241226234573700234710ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCC +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATG +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabb fastx_toolkit-0.0.14/galaxy/test-data/fastx_renamer1.fastq000066400000000000000000000022721226234573700236360ustar00rootroot00000000000000@CSHL_3_FC042AGLLWW:1:2:7:203 GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +CSHL_3_FC042AGLLWW:1:2:7:203 aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CSHL_3_FC042AGLLWW:1:2:7:33 CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CSHL_3_FC042AGLLWW:1:2:7:33 Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @CSHL_3_FC042AGLLWW:1:2:7:169 GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:169 a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @CSHL_3_FC042AGLLWW:1:2:7:1436 AATTATTTATTAAATTTTAATAATATGGGAGACACT +CSHL_3_FC042AGLLWW:1:2:7:1436 a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @CSHL_3_FC042AGLLWW:1:2:7:292 GGAGAAATACACACAATTGGTTAATCCCCCTATATA +CSHL_3_FC042AGLLWW:1:2:7:292 babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @CSHL_3_FC042AGLLWW:1:2:7:1819 AATTCAAACCACCCCAACCCACACACAGAGATACAA +CSHL_3_FC042AGLLWW:1:2:7:1819 a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @CSHL_3_FC042AGLLWW:1:2:7:1875 GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +CSHL_3_FC042AGLLWW:1:2:7:1875 aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @CSHL_3_FC042AGLLWW:1:2:8:624 ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +CSHL_3_FC042AGLLWW:1:2:8:624 aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @CSHL_3_FC042AGLLWW:1:2:8:250 TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +CSHL_3_FC042AGLLWW:1:2:8:250 aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastx_renamer1.out000066400000000000000000000025061226234573700233270ustar00rootroot00000000000000@GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` @CAATGCCTCCAATTGGTTAATCCCCCTATATATACT CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa @GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR @AATTATTTATTAAATTTTAATAATATGGGAGACACT AATTATTTATTAAATTTTAATAATATGGGAGACACT +AATTATTTATTAAATTTTAATAATATGGGAGACACT a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ @GGAGAAATACACACAATTGGTTAATCCCCCTATATA GGAGAAATACACACAATTGGTTAATCCCCCTATATA +GGAGAAATACACACAATTGGTTAATCCCCCTATATA babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE @AATTCAAACCACCCCAACCCACACACAGAGATACAA AATTCAAACCACCCCAACCCACACACAGAGATACAA +AATTCAAACCACCCCAACCCACACACAGAGATACAA a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU @GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU @ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa @TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE fastx_toolkit-0.0.14/galaxy/test-data/fastx_rev_comp1.fasta000066400000000000000000000002151226234573700237720ustar00rootroot00000000000000>CSHL__2_FC042NGABCD:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC >CSHL__2_FC042NGABCD:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC fastx_toolkit-0.0.14/galaxy/test-data/fastx_rev_comp2.fastq000066400000000000000000000006331226234573700240170ustar00rootroot00000000000000@CSHL__2_FC042NGABCD:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +CSHL__2_FC042NGABCD:8:1:120:202 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 @CSHL__2_FC042NGABCD:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC +CSHL__2_FC042NGABCD:8:1:103:1185 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 fastx_toolkit-0.0.14/galaxy/test-data/fastx_reverse_complement1.out000066400000000000000000000002151226234573700255670ustar00rootroot00000000000000>CSHL__2_FC042NGABCD:8:1:120:202 GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT >CSHL__2_FC042NGABCD:8:1:103:1185 GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT fastx_toolkit-0.0.14/galaxy/test-data/fastx_reverse_complement2.out000066400000000000000000000006311226234573700255720ustar00rootroot00000000000000@CSHL__2_FC042NGABCD:8:1:120:202 GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT +CSHL__2_FC042NGABCD:8:1:120:202 8 10 21 -1 10 11 -1 7 3 1 8 40 27 14 40 30 -1 40 20 40 25 40 40 28 40 40 6 40 40 40 40 20 40 40 40 40 @CSHL__2_FC042NGABCD:8:1:103:1185 GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT +CSHL__2_FC042NGABCD:8:1:103:1185 2 30 25 4 2 8 0 10 3 23 12 22 34 15 36 8 14 17 22 9 0 40 22 30 32 40 40 40 31 33 35 40 40 40 40 40 fastx_toolkit-0.0.14/galaxy/test-data/fastx_seqid_uncollapse1.out000066400000000000000000000016531226234573700252320ustar00rootroot0000000000000021 0 0 0 0 0 0 0 - 148-5 22 021 GALNT15 22 1 22 1 21, 1, 1 21 0 0 0 0 0 0 0 - 148-5 22 021 GALNT15 22 1 22 1 21, 1, 1 21 0 0 0 0 0 0 0 - 148-5 22 021 GALNT15 22 1 22 1 21, 1, 1 21 0 0 0 0 0 0 0 - 148-5 22 021 GALNT15 22 1 22 1 21, 1, 1 21 0 0 0 0 0 0 0 - 148-5 22 021 GALNT15 22 1 22 1 21, 1, 1 21 1 0 0 0 0 0 0 - 190-2 22 022 ADDA2 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 190-2 22 022 ADDA2 22 0 22 1 22, 0, 0 21 0 0 0 0 0 0 0 - 253-1 22 021 FORRIL2 22 1 22 1 21, 1, 1 21 1 0 0 0 0 0 0 - 396-1 22 022 JMK446 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 fastx_toolkit-0.0.14/galaxy/test-data/fastx_seqid_uncollapse1.psl000066400000000000000000000004441226234573700252160ustar00rootroot0000000000000021 0 0 0 0 0 0 0 - 148-5 22 021 GALNT15 22 1 22 1 21, 1, 1 21 1 0 0 0 0 0 0 - 190-2 22 022 ADDA2 22 0 22 1 22, 0, 0 21 0 0 0 0 0 0 0 - 253-1 22 021 FORRIL2 22 1 22 1 21, 1, 1 21 1 0 0 0 0 0 0 - 396-1 22 022 JMK446 22 0 22 1 22, 0, 0 21 1 0 0 0 0 0 0 - 463-7 22 022 OPTQTL5 22 0 22 1 22, 0, 0 fastx_toolkit-0.0.14/galaxy/test-data/fastx_trimmer1.fasta000066400000000000000000000002151226234573700236370ustar00rootroot00000000000000>CSHL__2_FC042NGABCD:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC >CSHL__2_FC042NGABCD:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC fastx_toolkit-0.0.14/galaxy/test-data/fastx_trimmer1.out000066400000000000000000000002051226234573700233470ustar00rootroot00000000000000>CSHL__2_FC042NGABCD:8:1:120:202 TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC >CSHL__2_FC042NGABCD:8:1:103:1185 CGATAGATCGGCAGAGCTCGTTTACCGTCTTC fastx_toolkit-0.0.14/galaxy/test-data/fastx_trimmer2.fastq000066400000000000000000000006331226234573700236640ustar00rootroot00000000000000@CSHL__2_FC042NGABCD:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +CSHL__2_FC042NGABCD:8:1:120:202 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 @CSHL__2_FC042NGABCD:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC +CSHL__2_FC042NGABCD:8:1:103:1185 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 fastx_toolkit-0.0.14/galaxy/test-data/fastx_trimmer2.out000066400000000000000000000005321226234573700233530ustar00rootroot00000000000000@CSHL__2_FC042NGABCD:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCC +CSHL__2_FC042NGABCD:8:1:120:202 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 @CSHL__2_FC042NGABCD:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTT +CSHL__2_FC042NGABCD:8:1:103:1185 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 0 9 22 17 14 8 36 15 34 22 12 23 fastx_toolkit-0.0.14/galaxy/test-data/fastx_trimmer_from_end1.fasta000066400000000000000000000003141226234573700255100ustar00rootroot00000000000000>67-3461 TGAGATACATTTGAACATTGAT >68-3451 ACATAGCCTATAAGAA >69-3397 TAGGGAAGTAACACACTGGATT >70-3391 TGAGATCACAGTTTCCACACATTTGGAGGCAACAT >71-3291 TCACAGGATTAGAGTCTGAGCTAT >72-3193 TAGAAATTCAAGCTTTGATGTTTTT fastx_toolkit-0.0.14/galaxy/test-data/fastx_trimmer_from_end1.out000066400000000000000000000002501226234573700252200ustar00rootroot00000000000000>67-3461 TGAGATACATTTGAACATTG >69-3397 TAGGGAAGTAACACACTGGA >70-3391 TGAGATCACAGTTTCCACACATTTGGAGGCAAC >71-3291 TCACAGGATTAGAGTCTGAGCT >72-3193 TAGAAATTCAAGCTTTGATGTTT fastx_toolkit-0.0.14/galaxy/tool-data/000077500000000000000000000000001226234573700176525ustar00rootroot00000000000000fastx_toolkit-0.0.14/galaxy/tool-data/Makefile.am000066400000000000000000000010141226234573700217020ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. EXTRA_DIST = fastx_clipper_sequences.txt fastx_toolkit-0.0.14/galaxy/tool-data/fastx_clipper_sequences.txt000066400000000000000000000004351226234573700253330ustar00rootroot00000000000000# # Adapter/Linker sequences for FASTX-Clipper tool. # # Format: # Adapter Sequence Descriptive name # # Example: # AAATTTGATAAGATA Our-Adapter # # Some adapters can be found here: # http://seqanswers.com/forums/showthread.php?t=198 TGTAGGCC Dummy-Adapter (don't use me) fastx_toolkit-0.0.14/galaxy/tools/000077500000000000000000000000001226234573700171265ustar00rootroot00000000000000fastx_toolkit-0.0.14/galaxy/tools/Makefile.am000066400000000000000000000007731226234573700211710ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. SUBDIRS = fastx_toolkit fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/000077500000000000000000000000001226234573700220205ustar00rootroot00000000000000fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/Makefile.am000066400000000000000000000022001226234573700240460ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. EXTRA_DIST = fastq_quality_converter.xml \ fastq_quality_filter.xml \ fastx_quality_statistics.xml \ fastq_to_fasta.xml \ fastx_artifacts_filter.xml \ fastx_clipper.xml \ fastx_reverse_complement.xml \ fastx_trimmer.xml \ fastx_renamer.xml \ fastx_barcode_splitter.xml fastx_barcode_splitter_galaxy_wrapper.sh \ fastx_nucleotides_distribution.xml \ fastq_quality_boxplot.xml \ fasta_clipping_histogram.xml \ fastx_collapser.xml \ fasta_formatter.xml \ fasta_nucleotide_changer.xml \ fastq_quality_trimmer.xml \ fastx_trimmer_from_end.xml \ fastx_uncollapser.xml \ seqid_uncollapser.xml \ fastx_nucleotides_distribution_line.xml \ fastq_masker.xml fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fasta_clipping_histogram.xml000066400000000000000000000056341226234573700276120ustar00rootroot00000000000000 chart fasta_clipping_histogram.pl $input $outfile **What it does** This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file. **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results. ----- **Output Examples** In the following library, most sequences are 24-mers to 27-mers. This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). .. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png In the following library, most sequences are 19,22 or 23-mers. This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place). .. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png ----- **Input Formats** This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so:: >sequence1 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG >sequence2 GTGTGTGTGGGAAGTTGACACAGTA >sequence3 CCTTGAGATTAACGCTAATCAAGTAAAC If the sequences span over multiple lines:: >sequence1 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG aactggtctttacctTTAAGTTG Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences:: >sequence1 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG ----- **Multiplicity counts (a.k.a reads-count)** If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing). Example 1 - The following FASTA file *does not* have multiplicity counts:: >seq1 GGATCC >seq2 GGTCATGGGTTTAAA >seq3 GGGATATATCCCCACACACACACAC Each sequence is counts as one, to produce the following chart: .. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png Example 2 - The following FASTA file have multiplicity counts:: >seq1-2 GGATCC >seq2-10 GGTCATGGGTTTAAA >seq3-3 GGGATATATCCCCACACACACACAC The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: .. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fasta_formatter.xml000066400000000000000000000057701226234573700257340ustar00rootroot00000000000000 formatter cat '$input' | fasta_formatter -w $width -o '$output' **What it does** This tool re-formats a FASTA file, changing the width of the nucleotides lines. **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line. -------- **Example** Input FASTA file (each nucleotides line is 50 characters long):: >Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG aactggtctttacctTTAAGTTG Output FASTA file (with width=80):: >Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA ATTTTAATGAACATGTAGTAAAAACT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG Output FASTA file (with width=0 => single line):: >Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fasta_nucleotide_changer.xml000066400000000000000000000037521226234573700275510ustar00rootroot00000000000000 converter cat '$input' | fasta_nucleotide_changer $mode -v -o '$output' **What it does** This tool converts RNA FASTA files to DNA (and vice-versa). In **RNA-to-DNA** mode, U's are changed into T's. In **DNA-to-RNA** mode, T's are changed into U's. -------- **Example** Input RNA FASTA file ( from Sanger's mirBase ):: >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 UGAGGUAGUAGGUUGUAUAGUU >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 UCCCUGAGACCUCAAGUGUGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 UGGAAUGUAAAGAAGUAUGUA Output DNA FASTA file (with RNA-to-DNA mode):: >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 TGAGGTAGTAGGTTGTATAGTT >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 TCCCTGAGACCTCAAGTGTGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 TGGAATGTAAAGAAGTATGTA ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastq_masker.xml000066400000000000000000000042311226234573700252220ustar00rootroot00000000000000 (based on quality) cat '$input' | fastq_masker #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -q $cutoff -r '$maskchar' -o '$output' Nucleotides below this quality will be masked Replace low-quality nucleotides with this character. Common values: 'N' or '.' **What it does** This tool masks low-quality nucleotides in a FASTQ file, and replaces them with the specifed mask character (**N** by default). -------- **Example** Input FASTQ file:: @1 TATGGTCAGAAACCATATGC +1 40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 @2 CAGCGAGGCTTTAATGCCAT +2 40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19 @3 CAGCGAGGCTTTAATGCCAT +3 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19 After Masking nucleotides with quality lower than 20 with the character **N**:: @1 TATGGTCAGAAANNNNNNNN +1 40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 @2 CAGCGAGGCTNTNNNNNNNN +2 40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19 @3 CAGCGAGGCNNNNNNNNNNN +3 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastq_quality_boxplot.xml000066400000000000000000000026701226234573700272040ustar00rootroot00000000000000 fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o '$output' **What it does** Creates a boxplot graph for the quality scores in the library. .. class:: infomark **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. ----- **Output Examples** * Black horizontal lines are medians * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) * Whiskers show outlier at max. 1.5*IQR An excellent quality library (median quality is 40 for almost all 36 cycles): .. image:: ../static/fastx_icons/fastq_quality_boxplot_1.png A relatively good quality library (median quality degrades towards later cycles): .. image:: ../static/fastx_icons/fastq_quality_boxplot_2.png A low quality library (median drops quickly): .. image:: ../static/fastx_icons/fastq_quality_boxplot_3.png ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastq_quality_converter.xml000066400000000000000000000063711226234573700275260ustar00rootroot00000000000000 (ASCII-Numeric) cat '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset **What it does** Converts a Solexa FASTQ file to/from numeric or ASCII quality format. .. class:: warningmark Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). ----- FASTQ with Numeric quality scores:: @CSHL__2_FC042AGWWWXX:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +CSHL__2_FC042AGWWWXX:8:1:120:202 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 @CSHL__2_FC042AGWWWXX:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC +CSHL__2_FC042AGWWWXX:8:1:103:1185 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 FASTQ with ASCII quality scores:: @CSHL__2_FC042AGWWWXX:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +CSHL__2_FC042AGWWWXX:8:1:120:202 hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH @CSHL__2_FC042AGWWWXX:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC +CSHL__2_FC042AGWWWXX:8:1:103:1185 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastq_quality_filter.xml000066400000000000000000000051001226234573700267710ustar00rootroot00000000000000 cat '$input' | fastq_quality_filter #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -q $quality -p $percent -v -o '$output' **What it does** This tool filters reads based on quality scores. .. class:: infomark Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. .. class:: infomark Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. -------- Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. **Example**:: @CSHL_4_FC042AGOOII:1:2:214:584 GACAATAAAC +CSHL_4_FC042AGOOII:1:2:214:584 30 30 30 30 30 30 30 30 20 10 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastq_quality_trimmer.xml000066400000000000000000000047641226234573700272020ustar00rootroot00000000000000 cat '$input' | fastq_quality_trimmer #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -t $cutoff -l $minlen -o '$output' Nucleotides below this quality will be trimmed Sequences shorter than this length will be discard. Leave at zero to keep all sequences **What it does** This tool scans the sequence from the end for the first nucleotide to possess the specified minimum quality score. It will then trim (remove nucleotides from) the sequence after this position. After trimming, sequences that are shorter than the minimum length are discarded. -------- **Example** Input Fasta file (with 20 bases in each sequences):: @1 TATGGTCAGAAACCATATGC +1 40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 @2 CAGCGAGGCTTTAATGCCAT +2 40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19 @3 CAGCGAGGCTTTAATGCCAT +3 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19 Trimming with a cutoff of 20, we get the following FASTQ file:: @1 TATGGTCAGAAA +1 40 40 40 40 40 40 40 40 40 40 40 20 @2 CAGCGAGGCTTT +2 40 40 40 40 40 40 40 40 30 20 19 20 @3 CAGCGAGGC +3 40 40 40 40 40 40 40 40 20 Trimming with a cutoff of 20 and a minimum length of 12, we get the following FASTQ file:: @1 TATGGTCAGAAA +1 40 40 40 40 40 40 40 40 40 40 40 20 @2 CAGCGAGGCTTT +2 40 40 40 40 40 40 40 40 30 20 19 20 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastq_to_fasta.xml000066400000000000000000000043251226234573700255440ustar00rootroot00000000000000 converter cat '$input' | fastq_to_fasta #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if $SKIPN $RENAMESEQ -o '$output' -v **What it does** This tool converts data from Solexa format to FASTA format (scroll down for format description). -------- **Example** The following data in Solexa-FASTQ format:: @CSHL_4_FC042GAMMII_2_1_517_596 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +CSHL_4_FC042GAMMII_2_1_517_596 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 Will be converted to FASTA (with 'rename sequence names' = NO):: >CSHL_4_FC042GAMMII_2_1_517_596 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT Will be converted to FASTA (with 'rename sequence names' = YES):: >1 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_artifacts_filter.xml000066400000000000000000000076311226234573700273030ustar00rootroot00000000000000 cat '$input' | fastx_artifacts_filter #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -o '$output' **What it does** This tool filters sequencing artifacts (reads with all but 3 identical bases). -------- **The following is an example of sequences which will be filtered out**:: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_barcode_splitter.xml000066400000000000000000000047611226234573700273040ustar00rootroot00000000000000 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output **What it does** This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria. -------- **Barcode file Format** Barcode files are simple text files. Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. Example:: #This line is a comment (starts with a 'number' sign) BC1 GATCT BC2 ATCGT BC3 GTGAT BC4 TGTCT For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). Sequences matching the barcode will be stored in the appropriate file. One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. The output of this tool is an HTML file, displaying the split counts and the file locations. **Output Example** .. image:: ./static/fastx_icons/barcode_splitter_output_example.png ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh000077500000000000000000000051211226234573700322150ustar00rootroot00000000000000#!/bin/sh # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . # #This is a shell script wrapper for 'fastx_barcode_splitter.pl' # # 1. Output files are saved at the dataset's files_path directory. # # 2. 'fastx_barcode_splitter.pl' outputs a textual table. # This script turns it into pretty HTML with working URL # (so lazy users can just click on the URLs and get their files) if [ "$1x" = "x" ]; then echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 exit 1 fi BARCODE_FILE="$1" FASTQ_FILE="$2" LIBNAME="$3" OUTPUT_PATH="$4" shift 4 # The rest of the parameters are passed to the split program if [ "${OUTPUT_PATH}x" = "x" ]; then echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 exit 1 fi #Sanitize library name, make sure we can create a file with this name LIBNAME=${LIBNAME%.gz} LIBNAME=${LIBNAME%.txt} LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]') if [ ! -r "$FASTQ_FILE" ]; then echo "Error: Input file ($FASTQ_FILE) not found!" >&2 exit 1 fi if [ ! -r "$BARCODE_FILE" ]; then echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 exit 1 fi mkdir -p "$OUTPUT_PATH" if [ ! -d "$OUTPUT_PATH" ]; then echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 exit 1 fi PUBLICURL="" BASEPATH="$OUTPUT_PATH/" #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" PREFIX="$BASEPATH""${LIBNAME}__" SUFFIX=".txt" RESULTS=`gzip -cdf "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` if [ $? != 0 ]; then echo "error" fi # # Convert the textual tab-separated table into simple HTML table, # with the local path replaces with a valid URL echo "" echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' i
s|\t||g a<\/td><\/tr> ' echo "

" echo "

" fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_clipper.xml000066400000000000000000000070331226234573700254100ustar00rootroot00000000000000 adapter sequences cat '$input' | fastx_clipper #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS use this for hairpin barcoding. keep at 0 unless you know what you're doing. **What it does** This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. -------- **Clipping Illustration:** .. image:: ../static/fastx_icons/fastx_clipper_illustration.png **Clipping Example:** .. image:: ../static/fastx_icons/fastx_clipper_example.png **In the above example:** * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_collapser.xml000066400000000000000000000036161226234573700257410ustar00rootroot00000000000000 sequences cat '$input' | fastx_collapser #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -o '$output' **What it does** This tool collapses identical sequences in a FASTQ or FASTA file into a single sequence. -------- **Example** Example Input File (Sequence "ATAT" appears multiple times):: >CSHL_2_FC0042AGLLOO_1_1_605_414 TGCG >CSHL_2_FC0042AGLLOO_1_1_537_759 ATAT >CSHL_2_FC0042AGLLOO_1_1_774_520 TGGC >CSHL_2_FC0042AGLLOO_1_1_742_502 ATAT >CSHL_2_FC0042AGLLOO_1_1_781_514 TGAG >CSHL_2_FC0042AGLLOO_1_1_757_487 TTCA >CSHL_2_FC0042AGLLOO_1_1_903_769 ATAT >CSHL_2_FC0042AGLLOO_1_1_724_499 ATAT Example Output file:: >1-1 TGCG >2-4 ATAT >3-1 TGGC >4-1 TGAG >5-1 TTCA .. class:: infomark Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. The following output:: >2-4 ATAT means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_nucleotides_distribution.xml000066400000000000000000000031731226234573700310700ustar00rootroot00000000000000 fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o '$output' **What it does** Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. .. class:: infomark **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. ----- **Output Examples** The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_nucleotides_distribution_line.xml000066400000000000000000000020121226234573700320660ustar00rootroot00000000000000 fastx_nucleotide_distribution_line_graph.sh -i '$input' -o '$output' **What it does** Creates a line and points graph for the nucleotide distribution in the Solexa library. .. class:: infomark **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. ----- **Output Examples** .. image:: ../static/fastx_icons/fastq_nucleotides_distribution_line_graph.png ------ This tool was created by Oliver Tam, based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_quality_statistics.xml000066400000000000000000000123351226234573700277150ustar00rootroot00000000000000 cat '$input' | fastx_quality_stats #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -o '$output' **What it does** Creates quality statistics report for the given Solexa/FASTQ library. .. class:: infomark **TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools. ----- **The output file will contain the following fields:** * column = column number (1 to 36 for a 36-cycles read FASTQ file) * count = number of bases found in this column. * min = Lowest quality score value found in this column. * max = Highest quality score value found in this column. * sum = Sum of quality score values for this column. * mean = Mean quality score value for this column. * Q1 = 1st quartile quality score. * med = Median quality score. * Q3 = 3rd quartile quality score. * IQR = Inter-Quartile range (Q3-Q1). * lW = 'Left-Whisker' value (for boxplotting). * rW = 'Right-Whisker' value (for boxplotting). * A_Count = Count of 'A' nucleotides found in this column. * C_Count = Count of 'C' nucleotides found in this column. * G_Count = Count of 'G' nucleotides found in this column. * T_Count = Count of 'T' nucleotides found in this column. * N_Count = Count of 'N' nucleotides found in this column. **Output Example**:: column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 4 6362991 -5 40 247654797 38.92 40 40 40 0 40 40 1683197 1410855 1722633 1546306 0 5 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 6 6362991 -5 40 248499903 39.05 40 40 40 0 40 40 1598956 1236081 1568608 1959346 0 7 6362991 -4 40 247719760 38.93 40 40 40 0 40 40 1692667 1822140 1496741 1351443 0 8 6362991 -5 40 245745205 38.62 40 40 40 0 40 40 2230936 1343260 1529928 1258867 0 9 6362991 -5 40 245766735 38.62 40 40 40 0 40 40 1702064 1306257 1336511 2018159 0 10 6362991 -5 40 245089706 38.52 40 40 40 0 40 40 1519917 1446370 1450995 1945709 0 11 6362991 -5 40 242641359 38.13 40 40 40 0 40 40 1717434 1282975 1387804 1974778 0 12 6362991 -5 40 242026113 38.04 40 40 40 0 40 40 1662872 1202041 1519721 1978357 0 13 6362991 -5 40 238704245 37.51 40 40 40 0 40 40 1549965 1271411 1973291 1566681 1643 14 6362991 -5 40 235622401 37.03 40 40 40 0 40 40 2101301 1141451 1603990 1515774 475 15 6362991 -5 40 230766669 36.27 40 40 40 0 40 40 2344003 1058571 1440466 1519865 86 16 6362991 -5 40 224466237 35.28 38 40 40 2 35 40 2203515 1026017 1474060 1651582 7817 17 6362991 -5 40 219990002 34.57 34 40 40 6 25 40 1522515 1125455 2159183 1555765 73 18 6362991 -5 40 214104778 33.65 30 40 40 10 15 40 1479795 2068113 1558400 1249337 7346 19 6362991 -5 40 212934712 33.46 30 40 40 10 15 40 1432749 1231352 1769799 1920093 8998 20 6362991 -5 40 212787944 33.44 29 40 40 11 13 40 1311657 1411663 2126316 1513282 73 21 6362991 -5 40 211369187 33.22 28 40 40 12 10 40 1887985 1846300 1300326 1318380 10000 22 6362991 -5 40 213371720 33.53 30 40 40 10 15 40 542299 3446249 516615 1848190 9638 23 6362991 -5 40 221975899 34.89 36 40 40 4 30 40 347679 1233267 926621 3855355 69 24 6362991 -5 40 194378421 30.55 21 40 40 19 -5 40 433560 674358 3262764 1992242 67 25 6362991 -5 40 199773985 31.40 23 40 40 17 -2 40 944760 325595 1322800 3769641 195 26 6362991 -5 40 179404759 28.20 17 34 40 23 -5 40 3457922 156013 1494664 1254293 99 27 6362991 -5 40 163386668 25.68 13 28 40 27 -5 40 1392177 281250 3867895 821491 178 28 6362991 -5 40 156230534 24.55 12 25 40 28 -5 40 907189 981249 4174945 299437 171 29 6362991 -5 40 163236046 25.65 13 28 40 27 -5 40 1097171 3418678 1567013 280008 121 30 6362991 -5 40 151309826 23.78 12 23 40 28 -5 40 3514775 2036194 566277 245613 132 31 6362991 -5 40 141392520 22.22 10 21 40 30 -5 40 1569000 4571357 124732 97721 181 32 6362991 -5 40 143436943 22.54 10 21 40 30 -5 40 1453607 4519441 38176 351107 660 33 6362991 -5 40 114269843 17.96 6 14 30 24 -5 40 3311001 2161254 155505 734297 934 34 6362991 -5 40 140638447 22.10 10 20 40 30 -5 40 1501615 1637357 18113 3205237 669 35 6362991 -5 40 138910532 21.83 10 20 40 30 -5 40 1532519 3495057 23229 1311834 352 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_quality_statistics_ng.xml000066400000000000000000000307111226234573700303770ustar00rootroot00000000000000 (improved) cat '$input' | fastx_quality_stats #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -N -o '$output' **What it does** Creates quality statistics report for the given Solexa/FASTQ library. .. class:: warningmark The output format is different than the old quality statistics tool. It can't be used for the quality-chart and nucleotide distribution tools (without further processing) ----- **The output file will contain the following fields:** * cycle = cycle number (1 to 36 for a 36-cycles read solexa file) * max-count = maximum number of bases (in all cycles) For each nucleotide type of each cycle (ALL/A/C/G/T/N), the following columns are generated: * count = number of bases found in this column. * min = Lowest quality score value found in this column. * max = Highest quality score value found in this column. * sum = Sum of quality score values for this column. * mean = Mean quality score value for this column. * Q1 = 1st quartile quality score. * med = Median quality score. * Q3 = 3rd quartile quality score. * IQR = Inter-Quartile range (Q3-Q1). * lW = 'Left-Whisker' value (for boxplotting). * rW = 'Right-Whisker' value (for boxplotting). (see column list at the bottom of this page) ----- **Output Example**:: cycle max_count ALL_count ALL_min ALL_max ALL_sum ALL_mean ALL_Q1 ALL_med ALL_Q3 ALL_IQR ALL_lW ALL_rW A_count A_min A_max A_sum A_mean A_Q1 A_med A_Q3 A_IQR A_lW A_rW C_count C_min C_max C_sum C_mean C_Q1 C_med C_Q3 C_IQR C_lW C_rW G_count G_min G_max G_sum G_mean G_Q1 G_med G_Q3 G_IQR G_lW G_rW T_count T_min T_max T_sum T_mean T_Q1 T_med T_Q3 T_IQR T_lW T_rW N_count N_min N_max N_sum N_mean N_Q1 N_med N_Q3 N_IQR N_lW N_rW 1 2827201 2827201 5 34 86622739 30.64 33 33 33 0 33 33 31337 5 34 841248 26.85 23 30 33 10 8 34 9269 5 34 154582 16.68 5 12 30 25 5 34 2095406 5 34 64401991 30.73 33 33 33 0 33 33 689133 5 34 21214602 30.78 33 33 33 0 33 33 2056 5 13 10316 5.02 5 5 5 0 5 5 2 2827201 2827201 5 34 81416729 28.80 27 33 33 6 18 34 1860337 5 34 56188709 30.20 33 33 33 0 33 33 21274 5 34 420221 19.75 11 21 30 19 5 34 862406 5 34 22835654 26.48 21 32 33 12 5 34 81979 5 34 1964575 23.96 17 26 33 16 5 34 1205 5 24 7570 6.28 5 5 5 0 5 5 3 2827201 2827201 5 34 89142476 31.53 33 33 34 1 32 34 18121 5 34 203489 11.23 5 5 15 10 5 30 45699 5 34 944362 20.66 5 26 33 28 5 34 79472 5 34 859251 10.81 5 5 12 7 5 22 2682082 5 34 87126165 32.48 33 33 34 1 32 34 1827 5 18 9209 5.04 5 5 5 0 5 5 4 2827201 2827201 5 34 90033575 31.85 33 34 34 1 32 34 172281 5 34 2905831 16.87 5 11 33 28 5 34 2597111 5 34 85653490 32.98 33 34 34 1 32 34 24461 5 34 643275 26.30 23 33 33 10 8 34 32749 5 34 827798 25.28 17 33 33 16 5 34 599 5 21 3181 5.31 5 5 5 0 5 5 5 2827201 2827201 5 34 89641650 31.71 33 33 34 1 32 34 26774 5 34 476388 17.79 5 13 33 28 5 34 58691 5 34 891506 15.19 5 5 32 27 5 34 54916 5 34 714335 13.01 5 5 24 19 5 34 2685062 5 34 87550414 32.61 33 33 34 1 32 34 1758 5 21 9007 5.12 5 5 5 0 5 5 6 2827201 2827201 5 34 84595812 29.92 29 33 33 4 23 34 1204450 5 34 36229599 30.08 29 33 33 4 23 34 463119 5 34 13924930 30.07 30 33 33 3 26 34 712076 5 34 21093763 29.62 28 33 33 5 21 34 447508 5 34 13347178 29.83 29 33 33 4 23 34 48 5 21 342 7.12 5 5 7 2 5 10 7 2827201 2827201 5 34 81404399 28.79 26 33 33 7 16 34 912751 5 34 26241597 28.75 26 33 33 7 16 34 540022 5 34 15843612 29.34 28 33 33 5 21 34 701269 5 34 19699830 28.09 26 32 33 7 16 34 672893 5 34 19617405 29.15 27 33 33 6 18 34 266 5 24 1955 7.35 5 5 7 2 5 10 8 2827201 2827201 5 34 83714332 29.61 28 33 33 5 21 34 809852 5 34 23610246 29.15 27 33 33 6 18 34 563842 5 34 17062600 30.26 30 33 33 3 26 34 650887 5 34 18848062 28.96 27 33 33 6 18 34 802551 5 34 24192911 30.15 30 33 33 3 26 34 69 5 24 513 7.43 5 5 5 0 5 5 9 2827201 2827201 5 34 83974872 29.70 28 33 33 5 21 34 834129 5 34 24483965 29.35 27 33 33 6 18 34 567059 5 34 17270502 30.46 30 33 33 3 26 34 620453 5 34 17917829 28.88 26 33 33 7 16 34 805499 5 34 24302177 30.17 30 33 33 3 26 34 61 5 26 399 6.54 5 5 5 0 5 5 10 2827201 2827201 5 34 83278375 29.46 27 33 33 6 18 34 896783 5 34 26245652 29.27 27 33 33 6 18 34 551055 5 34 16628773 30.18 30 33 33 3 26 34 648328 5 34 18502443 28.54 26 33 33 7 16 34 730957 5 34 21900963 29.96 30 33 33 3 26 34 78 5 21 544 6.97 5 5 7 2 5 10 11 2827201 2827201 5 34 82511316 29.18 27 33 33 6 18 34 857880 5 34 24789241 28.90 27 33 33 6 18 34 642205 5 34 19342469 30.12 30 33 33 3 26 34 655942 5 34 18484775 28.18 26 31 33 7 16 34 671046 5 34 19893945 29.65 28 33 33 5 21 34 128 5 24 886 6.92 5 5 5 0 5 5 12 2827201 2827201 5 34 83171736 29.42 27 33 33 6 18 34 826807 5 34 24025084 29.06 27 33 33 6 18 34 586948 5 34 17775697 30.28 30 33 33 3 26 34 636734 5 34 17999923 28.27 26 31 33 7 16 34 776614 5 34 23370369 30.09 30 33 33 3 26 34 98 5 18 663 6.77 5 5 5 0 5 5 13 2827201 2827201 5 34 82829608 29.30 27 33 33 6 18 34 822607 5 34 23762719 28.89 27 33 33 6 18 34 644718 5 34 19458385 30.18 30 33 33 3 26 34 591437 5 34 16607859 28.08 26 31 33 7 16 34 768323 5 34 22999812 29.94 30 33 33 3 26 34 116 5 24 833 7.18 5 5 7 2 5 10 14 2827201 2827201 5 34 82345826 29.13 27 33 33 6 18 34 798164 5 34 22982673 28.79 26 33 33 7 16 34 649845 5 34 19506688 30.02 30 33 33 3 26 34 608966 5 34 16892044 27.74 24 31 33 9 11 34 770051 5 34 22963200 29.82 29 33 33 4 23 34 175 5 24 1221 6.98 5 5 5 0 5 5 15 2827201 2827201 5 34 82462892 29.17 27 33 33 6 18 34 831167 5 34 23971929 28.84 26 33 33 7 16 34 613017 5 34 18416386 30.04 30 33 33 3 26 34 621149 5 34 17284205 27.83 24 31 33 9 11 34 761767 5 34 22789700 29.92 29 33 33 4 23 34 101 5 18 672 6.65 5 5 5 0 5 5 16 2827201 2827201 5 34 82526664 29.19 27 33 33 6 18 34 824933 5 34 23753705 28.79 26 33 33 7 16 34 610126 5 34 18388479 30.14 30 33 33 3 26 34 612088 5 34 16999148 27.77 24 31 33 9 11 34 779925 5 34 23384436 29.98 30 33 33 3 26 34 129 5 24 896 6.95 5 5 5 0 5 5 17 2827201 2827201 5 34 82610038 29.22 27 33 33 6 18 34 819008 5 34 23665033 28.89 27 33 33 6 18 34 618277 5 34 18651436 30.17 30 33 33 3 26 34 597414 5 34 16501609 27.62 24 30 33 9 11 34 792381 5 34 23791076 30.02 30 33 33 3 26 34 121 5 21 884 7.31 5 5 5 0 5 5 18 2827201 2827201 5 34 82402647 29.15 27 33 33 6 18 34 815170 5 34 23471377 28.79 26 33 33 7 16 34 615913 5 34 18527086 30.08 30 33 33 3 26 34 607020 5 34 16707257 27.52 24 30 33 9 11 34 788977 5 34 23695988 30.03 30 33 33 3 26 34 121 5 24 939 7.76 5 5 11 6 5 20 19 2827201 2827201 5 34 82124647 29.05 27 33 33 6 18 34 799663 5 34 22872641 28.60 26 32 33 7 16 34 628535 5 34 18876510 30.03 30 33 33 3 26 34 610246 5 34 16776560 27.49 24 30 33 9 11 34 788629 5 34 23598027 29.92 29 33 33 4 23 34 128 5 27 909 7.10 5 5 5 0 5 5 20 2827201 2827201 5 34 81985110 29.00 27 33 33 6 18 34 797587 5 34 22834667 28.63 26 32 33 7 16 34 636494 5 34 19081110 29.98 30 33 33 3 26 34 603916 5 34 16456404 27.25 24 30 33 9 11 34 789056 5 34 23611835 29.92 29 33 33 4 23 34 148 5 27 1094 7.39 5 5 7 2 5 10 21 2827201 2827201 5 34 81789492 28.93 27 33 33 6 18 34 794078 5 34 22654429 28.53 26 32 33 7 16 34 636334 5 34 19008271 29.87 29 33 33 4 23 34 614943 5 34 16761297 27.26 24 30 33 9 11 34 781661 5 34 23364202 29.89 29 33 33 4 23 34 185 5 27 1293 6.99 5 5 5 0 5 5 22 2827201 2827201 5 34 81451811 28.81 27 33 33 6 18 34 789032 5 34 22366485 28.35 26 31 33 7 16 34 645777 5 34 19277917 29.85 29 33 33 4 23 34 608030 5 34 16404902 26.98 23 29 33 10 8 34 784198 5 34 23401407 29.84 29 33 33 4 23 34 164 5 24 1100 6.71 5 5 5 0 5 5 23 2827201 2827201 5 34 80945146 28.63 26 32 33 7 16 34 786207 5 34 22128593 28.15 26 31 33 7 16 34 647440 5 34 19187231 29.64 28 33 33 5 21 34 607663 5 34 16274550 26.78 22 29 33 11 6 34 785744 5 34 23353803 29.72 29 33 33 4 23 34 147 5 24 969 6.59 5 5 5 0 5 5 24 2827201 2827201 5 34 80501327 28.47 26 32 33 7 16 34 786929 5 34 22067207 28.04 26 31 33 7 16 34 645831 5 34 19042366 29.49 28 33 33 5 21 34 612772 5 34 16261175 26.54 22 29 33 11 6 34 781496 5 34 23129334 29.60 28 33 33 5 21 34 173 5 26 1245 7.20 5 5 5 0 5 5 25 2827201 2827201 5 34 79714527 28.20 26 31 33 7 16 34 782000 5 34 21701186 27.75 24 30 33 9 11 34 644171 5 34 18796511 29.18 27 33 33 6 18 34 617490 5 34 16226119 26.28 22 28 33 11 6 34 783396 5 34 22989588 29.35 27 33 33 6 18 34 144 5 26 1123 7.80 5 5 11 6 5 20 26 2827201 2827201 5 34 77523225 27.42 24 31 33 9 11 34 783881 5 34 21162231 27.00 24 30 33 9 11 34 645075 5 34 18368273 28.47 27 33 33 6 18 34 617885 5 34 15635967 25.31 21 27 33 12 5 34 779368 5 34 22349766 28.68 27 33 33 6 18 34 992 5 27 6988 7.04 5 5 5 0 5 5 27 2827201 2827201 5 34 76792679 27.16 24 31 33 9 11 34 788575 5 34 21113021 26.77 23 30 33 10 8 34 638456 5 34 18023093 28.23 26 32 33 7 16 34 624665 5 34 15600176 24.97 21 27 33 12 5 34 774483 5 34 22049478 28.47 27 32 33 6 18 34 1022 5 27 6911 6.76 5 5 5 0 5 5 28 2827201 2827201 5 34 76446203 27.04 24 30 33 9 11 34 783001 5 34 20828394 26.60 22 30 33 11 6 34 639424 5 34 17921638 28.03 26 32 33 7 16 34 621361 5 34 15437055 24.84 21 27 33 12 5 34 782313 5 34 22251729 28.44 27 32 33 6 18 34 1102 5 26 7387 6.70 5 5 5 0 5 5 29 2827201 2827201 5 34 75869397 26.84 24 30 33 9 11 34 777718 5 34 20485923 26.34 22 30 33 11 6 34 645283 5 34 18004108 27.90 26 31 33 7 16 34 627295 5 34 15440771 24.61 21 27 33 12 5 34 775728 5 34 21930783 28.27 26 32 33 7 16 34 1177 5 27 7812 6.64 5 5 5 0 5 5 30 2827201 2827201 5 34 75137420 26.58 22 30 33 11 6 34 779313 5 34 20336426 26.10 22 29 33 11 6 34 646974 5 34 17887122 27.65 24 31 33 9 11 34 626980 5 34 15205903 24.25 19 26 33 14 5 34 772774 5 34 21699992 28.08 26 31 33 7 16 34 1160 5 27 7977 6.88 5 5 5 0 5 5 31 2827201 2827201 5 34 74256817 26.27 22 30 33 11 6 34 780211 5 34 20171360 25.85 21 29 33 12 5 34 645371 5 34 17606830 27.28 24 31 33 9 11 34 629456 5 34 14997599 23.83 18 26 33 15 5 34 771023 5 34 21473316 27.85 26 31 33 7 16 34 1140 5 27 7712 6.76 5 5 5 0 5 5 32 2827201 2827201 5 34 73624704 26.04 22 29 33 11 6 34 776741 5 34 19802248 25.49 21 28 33 12 5 34 642994 5 34 17408712 27.07 24 30 33 9 11 34 631699 5 34 14925494 23.63 18 26 32 14 5 34 774316 5 34 21478972 27.74 26 31 33 7 16 34 1451 5 27 9278 6.39 5 5 5 0 5 5 33 2827201 2827201 5 34 72833249 25.76 21 29 33 12 5 34 775426 5 34 19509710 25.16 21 27 33 12 5 34 644177 5 34 17265182 26.80 24 30 33 9 11 34 627490 5 34 14612407 23.29 18 26 31 13 5 34 778476 5 34 21435400 27.54 24 31 33 9 11 34 1632 5 27 10550 6.46 5 5 5 0 5 5 34 2827201 2827201 5 34 71937995 25.44 21 28 33 12 5 34 772803 5 34 19226676 24.88 21 27 33 12 5 34 647127 5 34 17098061 26.42 22 30 33 11 6 34 628686 5 34 14382900 22.88 17 24 31 14 5 34 777289 5 34 21221307 27.30 24 30 33 9 11 34 1296 5 27 9051 6.98 5 5 5 0 5 5 35 2827201 2827201 5 34 70604895 24.97 21 27 33 12 5 34 769554 5 34 18722160 24.33 19 27 32 13 5 34 643915 5 34 16662802 25.88 21 28 33 12 5 34 627642 5 34 14115224 22.49 17 24 30 13 5 34 784712 5 34 21095775 26.88 24 30 33 9 11 34 1378 5 27 8934 6.48 5 5 5 0 5 5 36 2827201 2827201 5 34 71705284 25.36 21 28 33 12 5 34 775278 5 34 18770248 24.21 18 27 33 15 5 34 634906 5 34 16703972 26.31 22 30 33 11 6 34 630819 5 34 14421307 22.86 17 24 31 14 5 34 784826 5 34 21800547 27.78 26 32 33 7 16 34 1372 5 27 9210 6.71 5 5 5 0 5 5 ----- All columns:: cycle max_count ALL_count ALL_min ALL_max ALL_sum ALL_mean ALL_Q1 ALL_med ALL_Q3 ALL_IQR ALL_lW ALL_rW A_count A_min A_max A_sum A_mean A_Q1 A_med A_Q3 A_IQR A_lW A_rW C_count C_min C_max C_sum C_mean C_Q1 C_med C_Q3 C_IQR C_lW C_rW G_count G_min G_max G_sum G_mean G_Q1 G_med G_Q3 G_IQR G_lW G_rW T_count T_min T_max T_sum T_mean T_Q1 T_med T_Q3 T_IQR T_lW T_rW N_count N_min N_max N_sum N_mean N_Q1 N_med N_Q3 N_IQR N_lW N_rW ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_renamer.xml000066400000000000000000000040601226234573700254000ustar00rootroot00000000000000 cat '$input' | fastx_renamer #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -n $TYPE -o '$output' -v **What it does** This tool renames the sequence identifiers in a FASTQ/A file. .. class:: infomark Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc). -------- **Example** The following Solexa-FASTQ file:: @CSHL_4_FC042GAMMII_2_1_517_596 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +CSHL_4_FC042GAMMII_2_1_517_596 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 Renamed to **nucleotides sequence**:: @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 Renamed to **numeric counter**:: @1 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +1 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_reverse_complement.xml000066400000000000000000000033321226234573700276460ustar00rootroot00000000000000 cat '$input' | fastx_reverse_complement #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -o '$output' **What it does** This tool reverse-complements each sequence in a library. If the library is a FASTQ, the quality-scores are also reversed. -------- **Example** Input FASTQ file:: @CSHL_1_FC42AGWWWXX:8:1:3:740 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA +CSHL_1_FC42AGWWWXX:8:1:3:740 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26 Output FASTQ file:: @CSHL_1_FC42AGWWWXX:8:1:3:740 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA +CSHL_1_FC42AGWWWXX:8:1:3:740 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_trimmer.xml000066400000000000000000000041101226234573700254220ustar00rootroot00000000000000 to fixed length cat '$input' | fastx_trimmer #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -f $first -l $last -o '$output' **What it does** This tool trims (cut nucleotides from) sequences in a FASTA/Q file. -------- **Example** Input Fasta file (with 36 bases in each sequences):: >1-1 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC >2-1 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: >1-1 TATGGTCAGAAACCATATGCA >2-1 CAGCGAGGCTTTAATGCCATT Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: >1-1 TCAGA >2-1 AGGCT ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_trimmer_from_end.xml000066400000000000000000000040171226234573700273010ustar00rootroot00000000000000 of sequences cat '$input' | fastx_trimmer #if $input.ext == "fastqsanger": -Q 33 #elif $input.ext == "fastq": -Q 64 #end if -v -t $trimnum -m $minlen -o '$output' This will trim from the end of the sequences Sequences shorter than this length will be discarded **What it does** This tool trims (cut nucleotides from) sequences in a FASTQ/FASTA file from the 3' end. .. class:: infomark When trimming a FASTQ file, the quality scores will be trimmed appropriately (to the same length of the corresponding sequence). -------- **Example** Input Fasta file:: >1-1 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC >2-1 CAGCGAGGCTTTAATGCCATT Trimming 5 nucleotides from the end, and discarding sequences shorter than 10 , we get the following FASTA file:: >1-1 TATGGTCAGAAACCATATGCAGAGCCTGTAG >2-1 CAGCGAGGCTTTAATG Trimming 10 nucleotides from the end, and discarding sequences shorter than 15 , we get the following FASTA file:: >1-1 TATGGTCAGAAACCATATGCAGAGCC ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/fastx_uncollapser.xml000066400000000000000000000025661226234573700263070ustar00rootroot00000000000000 sequences cat '$input' | fastx_uncollapser -v -o '$output' **What it does** This tool uncollapses a previously-collapsed FASTA file. It reads each collapsed sequence and generates multiple sequences based on the collapsed read count. -------- **Example** Example Input - a collapsed FASTA file (Sequence "ATAT" has four collapsed reads):: >1-1 TGCG >2-4 ATAT Example Output - uncollapsed FASTA file (Sequence "ATAT" now appears as 4 separate sequences):: >1 TGCG >2 ATAT >3 ATAT >4 ATAT >5 ATAT .. class:: infomark The original sequence id (with the read counts) are discarded, with the sequence given a numerical name. ----- This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/galaxy/tools/fastx_toolkit/seqid_uncollapser.xml000066400000000000000000000050501226234573700262560ustar00rootroot00000000000000 containing collapsed sequence IDs cat '$input' | fastx_uncollapser -c $idcol -v -o '$output' This column contains the sequence id from a collapsed FASTA file in the form of "(seq number)-(read count)" (e.g. 15-4). Use 10 if you're analyzing BLAT output **What it does** This tool reads a row (in a table) containing a collapsed sequence ID, and duplicates the . .. class:: warningmark You must specify the column containing the collapsed sequence ID (e.g. 15-4). -------- **Example Input File** The following input file contains two collapsed sequence identifiers at column 10: *84-2* and *87-5* (meaning the first has multiplicity-count of 2 and the second has multiplicity count of 5):: 23 0 0 0 0 0 0 0 + 84-2 ... 22 0 0 0 0 0 0 0 + 87-5 ... **Output Example** After **uncollapsing** (on column 10), the line of the first sequence-identifier is repeated *twice*, and the line of the second sequence-identifier is repeated *five* times:: 23 0 0 0 0 0 0 0 + 84-2 ... 23 0 0 0 0 0 0 0 + 84-2 ... 22 0 0 0 0 0 0 0 + 87-5 ... 22 0 0 0 0 0 0 0 + 87-5 ... 22 0 0 0 0 0 0 0 + 87-5 ... 22 0 0 0 0 0 0 0 + 87-5 ... 22 0 0 0 0 0 0 0 + 87-5 ... Uncollapsing a text file allows analsys of collapsed FASTA files to be used with any tool which doesn't 'understand' collapsed multiplicity counts. .. class:: infomark See the *Collapse* tool in the *FASTA Manipulation* category for more details about collapsing FASTA files. ----- This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit-0.0.14/install_galaxy_files.sh000077500000000000000000000064531226234573700212450ustar00rootroot00000000000000#!/bin/sh # # Arguments check and suage information # SRC="." DEST="$1" if [ -z "$DEST" ]; then cat< # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # Install m4 macros in this directory m4datadir = $(datadir)/aclocal # List your m4 macros here m4macros = ax_c_long_long.m4 \ ax_cxx_compile_stdcxx_11.m4 \ ax_cxx_header_stdcxx_tr1.m4 # The following is boilerplate m4data_DATA = $(m4macros) EXTRA_DIST = $(m4data_DATA) fastx_toolkit-0.0.14/m4/ax_c_long_long.m4000066400000000000000000000021411226234573700202310ustar00rootroot00000000000000# =========================================================================== # http://www.nongnu.org/autoconf-archive/ax_c_long_long.html # =========================================================================== # # SYNOPSIS # # AX_C_LONG_LONG # # DESCRIPTION # # Provides a test for the existence of the long long int type and defines # HAVE_LONG_LONG if it is found. # # LICENSE # # Copyright (c) 2008 Caolan McNamara # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice # and this notice are preserved. This file is offered as-is, without any # warranty. #serial 4 AU_ALIAS([AC_C_LONG_LONG], [AX_C_LONG_LONG]) AC_DEFUN([AX_C_LONG_LONG], [AC_CACHE_CHECK(for long long int, ac_cv_c_long_long, [if test "$GCC" = yes; then ac_cv_c_long_long=yes else AC_TRY_COMPILE(,[long long int i;], ac_cv_c_long_long=yes, ac_cv_c_long_long=no) fi]) if test $ac_cv_c_long_long = yes; then AC_DEFINE(HAVE_LONG_LONG, 1, [compiler understands long long]) fi ]) fastx_toolkit-0.0.14/m4/ax_cxx_compile_stdcxx_11.m4000066400000000000000000000107631226234573700221720ustar00rootroot00000000000000# ============================================================================ # http://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html # ============================================================================ # # SYNOPSIS # # AX_CXX_COMPILE_STDCXX_11([ext|noext],[mandatory|optional]) # # DESCRIPTION # # Check for baseline language coverage in the compiler for the C++11 # standard; if necessary, add switches to CXXFLAGS to enable support. # # The first argument, if specified, indicates whether you insist on an # extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g. # -std=c++11). If neither is specified, you get whatever works, with # preference for an extended mode. # # The second argument, if specified 'mandatory' or if left unspecified, # indicates that baseline C++11 support is required and that the macro # should error out if no mode with that support is found. If specified # 'optional', then configuration proceeds regardless, after defining # HAVE_CXX11 if and only if a supporting mode is found. # # LICENSE # # Copyright (c) 2008 Benjamin Kosnik # Copyright (c) 2012 Zack Weinberg # Copyright (c) 2013 Roy Stogner # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice # and this notice are preserved. This file is offered as-is, without any # warranty. #serial 3 m4_define([_AX_CXX_COMPILE_STDCXX_11_testbody], [ template struct check { static_assert(sizeof(int) <= sizeof(T), "not big enough"); }; typedef check> right_angle_brackets; int a; decltype(a) b; typedef check check_type; check_type c; check_type&& cr = static_cast(c); auto d = a; ]) AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [dnl m4_if([$1], [], [], [$1], [ext], [], [$1], [noext], [], [m4_fatal([invalid argument `$1' to AX_CXX_COMPILE_STDCXX_11])])dnl m4_if([$2], [], [ax_cxx_compile_cxx11_required=true], [$2], [mandatory], [ax_cxx_compile_cxx11_required=true], [$2], [optional], [ax_cxx_compile_cxx11_required=false], [m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX_11])])dnl AC_LANG_PUSH([C++])dnl ac_success=no AC_CACHE_CHECK(whether $CXX supports C++11 features by default, ax_cv_cxx_compile_cxx11, [AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])], [ax_cv_cxx_compile_cxx11=yes], [ax_cv_cxx_compile_cxx11=no])]) if test x$ax_cv_cxx_compile_cxx11 = xyes; then ac_success=yes fi m4_if([$1], [noext], [], [dnl if test x$ac_success = xno; then for switch in -std=gnu++11 -std=gnu++0x; do cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx11_$switch]) AC_CACHE_CHECK(whether $CXX supports C++11 features with $switch, $cachevar, [ac_save_CXXFLAGS="$CXXFLAGS" CXXFLAGS="$CXXFLAGS $switch" AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])], [eval $cachevar=yes], [eval $cachevar=no]) CXXFLAGS="$ac_save_CXXFLAGS"]) if eval test x\$$cachevar = xyes; then CXXFLAGS="$CXXFLAGS $switch" ac_success=yes break fi done fi]) m4_if([$1], [ext], [], [dnl if test x$ac_success = xno; then for switch in -std=c++11 -std=c++0x; do cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx11_$switch]) AC_CACHE_CHECK(whether $CXX supports C++11 features with $switch, $cachevar, [ac_save_CXXFLAGS="$CXXFLAGS" CXXFLAGS="$CXXFLAGS $switch" AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])], [eval $cachevar=yes], [eval $cachevar=no]) CXXFLAGS="$ac_save_CXXFLAGS"]) if eval test x\$$cachevar = xyes; then CXXFLAGS="$CXXFLAGS $switch" ac_success=yes break fi done fi]) AC_LANG_POP([C++]) if test x$ax_cxx_compile_cxx11_required = xtrue; then if test x$ac_success = xno; then AC_MSG_ERROR([*** A compiler with support for C++11 language features is required.]) fi else if test x$ac_success = xno; then HAVE_CXX11=0 AC_MSG_NOTICE([No compiler with C++11 support was found]) else HAVE_CXX11=1 AC_DEFINE(HAVE_CXX11,1, [define if the compiler supports basic C++11 syntax]) fi AC_SUBST(HAVE_CXX11) fi ]) fastx_toolkit-0.0.14/m4/ax_cxx_header_stdcxx_tr1.m4000066400000000000000000000024401226234573700222500ustar00rootroot00000000000000# =========================================================================== # http://www.nongnu.org/autoconf-archive/ax_cxx_header_stdcxx_tr1.html # =========================================================================== # # SYNOPSIS # # AX_CXX_HEADER_STDCXX_TR1 # # DESCRIPTION # # Check for library coverage of the TR1 standard. # # LICENSE # # Copyright (c) 2008 Benjamin Kosnik # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice # and this notice are preserved. This file is offered as-is, without any # warranty. ## ## Modified by A. Gordon (assafgordon@gmail.com), 1-Feb-2010 ## Removed unused header files (which can't be found on some TR1 gcc-4.2.4 on CentOS 5.4) ## #serial 5 AU_ALIAS([AC_CXX_HEADER_STDCXX_TR1], [AX_CXX_HEADER_STDCXX_TR1]) AC_DEFUN([AX_CXX_HEADER_STDCXX_TR1], [ AC_CACHE_CHECK(for ISO C++ TR1 include files, ax_cv_cxx_stdcxx_tr1, [AC_LANG_SAVE AC_LANG_CPLUSPLUS AC_TRY_COMPILE([ #include ],, ax_cv_cxx_stdcxx_tr1=yes, ax_cv_cxx_stdcxx_tr1=no) AC_LANG_RESTORE ]) if test "$ax_cv_cxx_stdcxx_tr1" = yes; then AC_DEFINE(STDCXX_TR1_HEADERS,,[Define if ISO C++ TR1 header files are present. ]) fi ]) fastx_toolkit-0.0.14/reconf000077500000000000000000000012631226234573700157050ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. #!/bin/sh rm -f config.cache mkdir -p config echo "- libtoolize." libtoolize -i echo "- aclocal." aclocal -I m4 echo "- autoconf." autoconf echo "- autoheader." autoheader echo "- automake." automake -a exit fastx_toolkit-0.0.14/scripts/000077500000000000000000000000001226234573700161705ustar00rootroot00000000000000fastx_toolkit-0.0.14/scripts/Makefile.am000066400000000000000000000016271226234573700202320ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_SCRIPTS = fastx_barcode_splitter.pl \ fastx_nucleotide_distribution_graph.sh \ fastx_nucleotide_distribution_line_graph.sh \ fastq_quality_boxplot_graph.sh \ fasta_clipping_histogram.pl EXTRA_DIST = fastx_barcode_splitter.pl \ fastx_nucleotide_distribution_graph.sh \ fastx_nucleotide_distribution_line_graph.sh \ fastq_quality_boxplot_graph.sh \ fasta_clipping_histogram.pl fastx_toolkit-0.0.14/scripts/fasta_clipping_histogram.pl000077500000000000000000000053271226234573700235770ustar00rootroot00000000000000#!/usr/bin/perl # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . use strict; use warnings; use GD::Graph::bars; use Data::Dumper; use PerlIO::gzip; if (scalar @ARGV==0) { print<$ARGV[1]") or die "Cannot create output file $ARGV[1]\n"; binmode OUT; my %histogram ; while (my $name = ) { my $sequence = ; chomp $sequence; my $sequence_length = length($sequence); my $count; if ( index($name, "-")==-1 ) { #Assume this file is not collapsed, just count each seqeunce as 1 $count = 1 ; } else { #Assume file is collapsed (that is - sequence-ID has two numbers with a separating dash) ($count) = $name =~ /^\>[^-]+\-(\d+)$/ ; # If the match failed, treat this fasta as not collapsed; $count = 1 if not defined $count ; } $histogram{$sequence_length} += $count ; } #Textual Output if (0) { print "Length\tCount\n"; foreach my $length_key ( sort { $a <=> $b } keys %histogram ) { print $length_key,"\t", $histogram{$length_key},"\n"; } exit 0; } ## Build the data as required by GD::Graph::bars. ## Data list has two items (each item is itself a list) ## 1. a list of x-axis labels (these are the keys from the histogram) ## 2. a list of values my @data = ( [ sort { $a <=> $b } keys %histogram ], [ map { $histogram{$_} } sort { $a <=> $b } keys %histogram ] ) ; my $graph = new GD::Graph::bars (1000,800); $graph->set( x_label => 'Length', y_label => 'Amount', title => 'Sequences lengths Distribution (after clipping)', bar_spacing => 10, transparent => 0, t_margin => 10, y_tick_number => 20, y_long_ticks => 1, ) or die $graph->error; $graph->plot(\@data) or die $graph->error; print OUT $graph->gd->png; close IN; close OUT; fastx_toolkit-0.0.14/scripts/fastq_quality_boxplot_graph.sh000077500000000000000000000124171226234573700243520ustar00rootroot00000000000000#!/usr/bin/env bash # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . function usage() { echo "Solexa-Quality BoxPlot plotter" echo "Generates a solexa quality score box-plot graph " echo echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]" echo echo " [-p] - Generate PostScript (.PS) file. Default is PNG image." echo " [-i INPUT.TXT] - Input file. Should be the output of \"solexa_quality_statistics\" program." echo " [-o OUTPUT] - Output file name. default is STDOUT." echo " [-t TITLE] - Title (usually the solexa file name) - will be plotted on the graph." echo exit } # # Input Data columns: #pos cnt min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count # As produced by "solexa_quality_statistics" program TITLE="" # default title is empty FILENAME="" OUTPUTTERM="set term png size 2048,768" # default output terminal is "PNG" OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout" while getopts ":t:i:o:ph" Option do case $Option in # w ) CMD=$OPTARG; FILENAME="PIMSLogList.txt"; TARGET="logfiles"; ;; t ) TITLE="for $OPTARG" ;; i ) FILENAME=$OPTARG ;; o ) OUTPUTFILE="$OPTARG" ;; p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 8" ;; h ) usage ;; * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;; esac done shift $(($OPTIND - 1)) if [ "$FILENAME" == "" ]; then usage fi if [ ! -r "$FILENAME" ]; then echo "Error: can't open input file ($1)." >&2 exit 1 fi ## ## Input validation ## Too many users (in galaxy) try to plot a FASTQ file ## (without using the 'fastq statistics' tool first). ## ## gnuplot's error in that case is crypt, and support emails are annoying. ## ## try to detect FASTA/FASTQ input, and give a detailed, easy-to-understand warning. ## ## AWK_FASTX_DETECTION=' NR==1 && $0 ~ /^>/ { fasta_id = 1 } NR==1 && $0 ~ /^@/ { fastq_id = 1 } NR==2 && $0 ~ /^[ACGT][ACGT]*$/ { nucleotides = 1 } NR>3 { exit } END { if ( fasta_id && nucleotides ) { print "FASTA" } if ( fastq_id && nucleotides ) { print "FASTQ" } }' INPUT_TYPE=$(awk "$AWK_FASTX_DETECTION" "$FILENAME") if [ "x$INPUT_TYPE" = "xFASTA" ] ; then #this doesn't even make sense: FASTA files don't contain any quality scores cat>&2<&2<&2< "$OUTPUTFILE" fastx_toolkit-0.0.14/scripts/fastx_barcode_splitter.pl000077500000000000000000000331661226234573700232730ustar00rootroot00000000000000#!/usr/bin/perl # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . use strict; use warnings; use IO::Handle; use Data::Dumper; use Getopt::Long; use Carp; ## ## This program splits a FASTQ/FASTA file into several smaller files, ## Based on barcode matching. ## ## run with "--help" for usage information ## ## Assaf Gordon , 11sep2008 # Forward declarations sub load_barcode_file ($); sub parse_command_line ; sub match_sequences ; sub mismatch_count($$) ; sub print_results; sub open_and_detect_input_format; sub read_record; sub write_record($); sub usage(); # Global flags and arguments, # Set by command line argumens my $barcode_file ; my $barcodes_at_eol = 0 ; my $barcodes_at_bol = 0 ; my $exact_match = 0 ; my $allow_partial_overlap = 0; my $allowed_mismatches = 1; my $newfile_suffix = ''; my $newfile_prefix ; my $quiet = 0 ; my $debug = 0 ; my $fastq_format = 1; # Global variables # Populated by 'create_output_files' my %filenames; my %files; my %counts = ( 'unmatched' => 0 ); my $barcodes_length; my @barcodes; my $input_file_io; # The Four lines per record in FASTQ format. # (when using FASTA format, only the first two are used) my $seq_name; my $seq_bases; my $seq_name2; my $seq_qualities; # # Start of Program # parse_command_line ; load_barcode_file ( $barcode_file ) ; open_and_detect_input_format; match_sequences ; print_results unless $quiet; # # End of program # sub parse_command_line { my $help; usage() if (scalar @ARGV==0); my $result = GetOptions ( "bcfile=s" => \$barcode_file, "eol" => \$barcodes_at_eol, "bol" => \$barcodes_at_bol, "exact" => \$exact_match, "prefix=s" => \$newfile_prefix, "suffix=s" => \$newfile_suffix, "quiet" => \$quiet, "partial=i" => \$allow_partial_overlap, "debug" => \$debug, "mismatches=i" => \$allowed_mismatches, "help" => \$help ) ; usage() if ($help); die "Error: barcode file not specified (use '--bcfile [FILENAME]')\n" unless defined $barcode_file; die "Error: prefix path/filename not specified (use '--prefix [PATH]')\n" unless defined $newfile_prefix; if ($barcodes_at_bol == $barcodes_at_eol) { die "Error: can't specify both --eol & --bol\n" if $barcodes_at_eol; die "Error: must specify either --eol or --bol\n" ; } die "Error: invalid for value partial matches (valid values are 0 or greater)\n" if $allow_partial_overlap<0; $allowed_mismatches = 0 if $exact_match; die "Error: invalid value for mismatches (valid values are 0 or more)\n" if ($allowed_mismatches<0); die "Error: partial overlap value ($allow_partial_overlap) bigger than " . "max. allowed mismatches ($allowed_mismatches)\n" if ($allow_partial_overlap > $allowed_mismatches); exit unless $result; } # # Read the barcode file # sub load_barcode_file ($) { my $filename = shift or croak "Missing barcode file name"; open BCFILE,"<$filename" or die "Error: failed to open barcode file ($filename)\n"; while () { next if m/^#/; chomp; my ($ident, $barcode) = split ; $barcode = uc($barcode); # Sanity checks on the barcodes die "Error: bad data at barcode file ($filename) line $.\n" unless defined $barcode; die "Error: bad barcode value ($barcode) at barcode file ($filename) line $.\n" unless $barcode =~ m/^[AGCT]+$/; die "Error: bad identifier value ($ident) at barcode file ($filename) line $. (must be alphanumeric)\n" unless $ident =~ m/^\w+$/; die "Error: badcode($ident, $barcode) is shorter or equal to maximum number of " . "mismatches ($allowed_mismatches). This makes no sense. Specify fewer mismatches.\n" if length($barcode)<=$allowed_mismatches; $barcodes_length = length($barcode) unless defined $barcodes_length; die "Error: found barcodes in different lengths. this feature is not supported yet.\n" unless $barcodes_length == length($barcode); push @barcodes, [$ident, $barcode]; if ($allow_partial_overlap>0) { foreach my $i (1 .. $allow_partial_overlap) { substr $barcode, ($barcodes_at_bol)?0:-1, 1, ''; push @barcodes, [$ident, $barcode]; } } } close BCFILE; if ($debug) { print STDERR "barcode\tsequence\n"; foreach my $barcoderef (@barcodes) { my ($ident, $seq) = @{$barcoderef}; print STDERR $ident,"\t", $seq ,"\n"; } } } # Create one output file for each barcode. # (Also create a file for the dummy 'unmatched' barcode) sub create_output_files { my %barcodes = map { $_->[0] => 1 } @barcodes; #generate a uniq list of barcode identifiers; $barcodes{'unmatched'} = 1 ; foreach my $ident (keys %barcodes) { my $new_filename = $newfile_prefix . $ident . $newfile_suffix; $filenames{$ident} = $new_filename; open my $file, ">$new_filename" or die "Error: failed to create output file ($new_filename)\n"; $files{$ident} = $file ; } } sub match_sequences { my %barcodes = map { $_->[0] => 1 } @barcodes; #generate a uniq list of barcode identifiers; $barcodes{'unmatched'} = 1 ; #reset counters foreach my $ident ( keys %barcodes ) { $counts{$ident} = 0; } create_output_files; # Read file FASTQ file # split accotding to barcodes while ( read_record ) { chomp $seq_bases; print STDERR "sequence $seq_bases: \n" if $debug; my $best_barcode_mismatches_count = $barcodes_length; my $best_barcode_ident = undef; #Try all barcodes, find the one with the lowest mismatch count foreach my $barcoderef (@barcodes) { my ($ident, $barcode) = @{$barcoderef}; # Get DNA fragment (in the length of the barcodes) # The barcode will be tested only against this fragment # (no point in testing the barcode against the whole sequence) my $sequence_fragment; if ($barcodes_at_bol) { $sequence_fragment = substr $seq_bases, 0, $barcodes_length; } else { $sequence_fragment = substr $seq_bases, - $barcodes_length; } my $mm = mismatch_count($sequence_fragment, $barcode) ; # if this is a partial match, add the non-overlap as a mismatch # (partial barcodes are shorter than the length of the original barcodes) $mm += ($barcodes_length - length($barcode)); if ( $mm < $best_barcode_mismatches_count ) { $best_barcode_mismatches_count = $mm ; $best_barcode_ident = $ident ; } } $best_barcode_ident = 'unmatched' if ( (!defined $best_barcode_ident) || $best_barcode_mismatches_count>$allowed_mismatches) ; print STDERR "sequence $seq_bases matched barcode: $best_barcode_ident\n" if $debug; $counts{$best_barcode_ident}++; #get the file associated with the matched barcode. #(note: there's also a file associated with 'unmatched' barcode) my $file = $files{$best_barcode_ident}; write_record($file); } } #Quickly calculate hamming distance between two strings # #NOTE: Strings must be same length. # returns number of different characters. #see http://www.perlmonks.org/?node_id=500235 sub mismatch_count($$) { length( $_[ 0 ] ) - ( ( $_[ 0 ] ^ $_[ 1 ] ) =~ tr[\0][\0] ) } sub print_results { print "Barcode\tCount\tLocation\n"; my $total = 0 ; foreach my $ident (sort keys %counts) { print $ident, "\t", $counts{$ident},"\t",$filenames{$ident},"\n"; $total += $counts{$ident}; } print "total\t",$total,"\n"; } sub read_record { $seq_name = $input_file_io->getline(); return undef unless defined $seq_name; # End of file? $seq_bases = $input_file_io->getline(); die "Error: bad input file, expecting line with sequences\n" unless defined $seq_bases; # If using FASTQ format, read two more lines if ($fastq_format) { $seq_name2 = $input_file_io->getline(); die "Error: bad input file, expecting line with sequence name2\n" unless defined $seq_name2; $seq_qualities = $input_file_io->getline(); die "Error: bad input file, expecting line with quality scores\n" unless defined $seq_qualities; } return 1; } sub write_record($) { my $file = shift; croak "Bad file handle" unless defined $file; print $file $seq_name; print $file $seq_bases,"\n"; #if using FASTQ format, write two more lines if ($fastq_format) { print $file $seq_name2; print $file $seq_qualities; } } sub open_and_detect_input_format { $input_file_io = new IO::Handle; die "Failed to open STDIN " unless $input_file_io->fdopen(fileno(STDIN),"r"); # Get the first characeter, and push it back my $first_char = $input_file_io->getc(); $input_file_io->ungetc(ord $first_char); if ($first_char eq '>') { # FASTA format $fastq_format = 0 ; print STDERR "Detected FASTA format\n" if $debug; } elsif ($first_char eq '@') { # FASTQ format $fastq_format = 1; print STDERR "Detected FASTQ format\n" if $debug; } else { die "Error: unknown file format. First character = '$first_char' (expecting > or \@)\n"; } } sub usage() { print<. usage() { echo "FASTA/Q Nucleotide Distribution Plotter" echo echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]" echo echo " [-p] - Generate PostScript (.PS) file. Default is PNG image." echo " [-i INPUT.TXT] - Input file. Should be the output of \"fastx_quality_statistics\" program." echo " [-o OUTPUT] - Output file name. default is STDOUT." echo " [-t TITLE] - Title - will be plotted on the graph." echo exit } # # Input Data columns: #pos cnt min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count # As produced by "fastq_quality_statistics" program TITLE="" # default title is empty FILENAME="" OUTPUTTERM="set term png size 1048,768" # default output terminal is "PNG" OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout" while getopts ":t:i:o:ph" Option do case $Option in t ) TITLE="for $OPTARG" ;; i ) FILENAME=$OPTARG ;; o ) OUTPUTFILE="$OPTARG" ;; p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 8" ;; h ) usage ;; * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;; esac done shift $(($OPTIND - 1)) if [ -z "$FILENAME" ]; then usage fi if [ ! -r "$FILENAME" ]; then echo "Error: can't open input file ($1)." >&2 exit 1 fi ## ## Input validation ## Too many users (in galaxy) try to plot a FASTQ file ## (without using the 'fastq statistics' tool first). ## ## gnuplot's error in that case is crypt, and support emails are annoying. ## ## try to detect FASTA/FASTQ input, and give a detailed, easy-to-understand warning. ## ## AWK_FASTX_DETECTION=' NR==1 && $0 ~ /^>/ { fasta_id = 1 } NR==1 && $0 ~ /^@/ { fastq_id = 1 } NR==2 && $0 ~ /^[ACGT][ACGT]*$/ { nucleotides = 1 } NR>3 { exit } END { if ( fasta_id && nucleotides ) { print "FASTA" } if ( fastq_id && nucleotides ) { print "FASTQ" } }' INPUT_TYPE=$(awk "$AWK_FASTX_DETECTION" "$FILENAME") if [ "x$INPUT_TYPE" = "xFASTA" ] ; then #this doesn't even make sense: FASTA files don't contain any quality scores cat>&2<&2<&2< "$OUTPUTFILE" fastx_toolkit-0.0.14/scripts/fastx_nucleotide_distribution_line_graph.sh000077500000000000000000000137001226234573700270570ustar00rootroot00000000000000#!/usr/bin/env bash # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . # # # This script was modified by Oliver Tam (tam@cshl.edu) usage() { echo "FASTA/Q Nucleotide Distribution Plotter" echo echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]" echo echo " [-p] - Generate PostScript (.PS) file. Default is PNG image." echo " [-i INPUT.TXT] - Input file. Should be the output of \"fastx_quality_statistics\" program." echo " [-o OUTPUT] - Output file name. default is STDOUT." echo " [-t TITLE] - Title - will be plotted on the graph." echo exit } # # Input Data columns: #pos cnt min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count # As produced by "fastq_quality_statistics" program TITLE="" # default title is empty FILENAME="" OUTPUTTERM="set term png size 1048,768" # default output terminal is "PDF" OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout" while getopts ":t:i:o:ph" Option do case $Option in t ) TITLE="for $OPTARG" ;; i ) FILENAME=$OPTARG ;; o ) OUTPUTFILE="$OPTARG" ;; p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 8" ;; h ) usage ;; * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;; esac done shift $(($OPTIND - 1)) if [ -z "$FILENAME" ]; then usage fi if [ ! -r "$FILENAME" ]; then echo "Error: can't open input file ($1)." >&2 exit 1 fi ## ## Input validation ## Too many users (in galaxy) try to plot a FASTQ file ## (without using the 'fastq statistics' tool first). ## ## gnuplot's error in that case is crypt, and support emails are annoying. ## ## try to detect FASTA/FASTQ input, and give a detailed, easy-to-understand warning. ## ## AWK_FASTX_DETECTION=' NR==1 && $0 ~ /^>/ { fasta_id = 1 } NR==1 && $0 ~ /^@/ { fastq_id = 1 } NR==2 && $0 ~ /^[ACGT][ACGT]*$/ { nucleotides = 1 } NR>3 { exit } END { if ( fasta_id && nucleotides ) { print "FASTA" } if ( fastq_id && nucleotides ) { print "FASTQ" } }' INPUT_TYPE=$(awk "$AWK_FASTX_DETECTION" "$FILENAME") if [ "x$INPUT_TYPE" = "xFASTA" ] ; then #this doesn't even make sense: FASTA files don't contain any quality scores cat>&2<&2<&2< "$OUTPUTFILE" fastx_toolkit-0.0.14/src/000077500000000000000000000000001226234573700152705ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/Makefile.am000066400000000000000000000015171226234573700173300ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. SUBDIRS = libfastx \ fastx_clipper \ fastx_trimmer \ fastx_quality_stats \ fastq_quality_converter \ fastq_to_fasta \ fastq_quality_filter \ fastq_quality_trimmer \ fastx_artifacts_filter \ fastx_reverse_complement \ fastx_collapser \ fastx_uncollapser \ seqalign_test \ fasta_formatter \ fasta_nucleotide_changer \ fastx_renamer \ fastq_masker fastx_toolkit-0.0.14/src/fasta_formatter/000077500000000000000000000000001226234573700204515ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fasta_formatter/Makefile.am000066400000000000000000000013371226234573700225110ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fasta_formatter AM_CPPFLAGS = $(CC_WARNINGS) $(GTEXTUTILS_CFLAGS) \ -I$(top_srcdir)/src/libfastx LDADD = $(GTEXTUTILS_LIBS) ../libfastx/libfastx.a $(LT_LDFLAGS) fasta_formatter_SOURCES = fasta_formatter.cpp \ sequence_writers.h fastx_toolkit-0.0.14/src/fasta_formatter/fasta_formatter.cpp000066400000000000000000000121401226234573700243340ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "sequence_writers.h" #include "config.h" using namespace std; string input_filename; string output_filename; bool flag_output_empty_sequences = false ; bool flag_output_tabular = false ; int flag_requested_output_width = 0 ; const char* usage_string= "usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e]\n" \ "Part of " PACKAGE_STRING " by assafgordon@gmail.com\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ " [-w N] = max. sequence line width for output FASTA file.\n" \ " When ZERO (the default), sequence lines will NOT be wrapped -\n" \ " all nucleotides of each sequences will appear on a single \n" \ " line (good for scripting).\n" \ " [-t] = Output tabulated format (instead of FASTA format).\n" \ " Sequence-Identifiers will be on first column,\n" \ " Nucleotides will appear on second column (as single line).\n" \ " [-e] = Output empty sequences (default is to discard them).\n" \ " Empty sequences are ones who have only a sequence identifier,\n" \ " but not actual nucleotides.\n" \ "\n" \ "Input Example:\n" \ " >MY-ID\n" \ " AAAAAGGGGG\n" \ " CCCCCTTTTT\n" \ " AGCTN\n" \ "\n" \ "Output example with unlimited line width [-w 0]:\n" \ " >MY-ID\n" \ " AAAAAGGGGGCCCCCTTTTTAGCTN\n" \ "\n" \ "Output example with max. line width=7 [-w 7]:\n" \ " >MY-ID\n" \ " AAAAAGG\n" \ " GGGTTTT\n" \ " TCCCCCA\n" \ " GCTN\n" \ "\n" \ "Output example with tabular output [-t]:\n" \ " MY-ID AAAAAGGGGGCCCCCTTTTAGCTN\n" \ "\n" \ "example of empty sequence:\n" \ "(will be discarded unless [-e] is used)\n" \ " >REGULAR-SEQUENCE-1\n" \ " AAAGGGTTTCCC\n" \ " >EMPTY-SEQUENCE\n" \ " >REGULAR-SEQUENCE-2\n" \ " AAGTAGTAGTAGTAGT\n" \ " GTATTTTATAT\n" \ "\n" \ "\n"; void usage() { printf("%s",usage_string); exit(0); } void parse_command_line(int argc, char* argv[]) { int opt; while ( (opt = getopt(argc, argv, "i:o:hw:te") ) != -1 ) { //Parse the default options switch(opt) { case 'h': usage(); case 'i': input_filename = optarg; break; case 'o': output_filename = optarg; break; case 'w': flag_requested_output_width = atoi(optarg); if ( flag_requested_output_width < 0 ) errx(1,"Invalid value (%s) for requested width [-w]", optarg); break ; case 't': flag_output_tabular = true ; break; case 'e': flag_output_empty_sequences = true; break; default: exit(1); } } } int main(int argc, char* argv[]) { ios::sync_with_stdio(false); parse_command_line(argc, argv); InputStreamWrapper input ( input_filename ) ; OutputStreamWrapper output ( output_filename ); TextLineReader reader ( input.stream() ) ; /* * Use the writer according to the user's request */ SequencesWriter * pWriter = NULL ; if ( flag_output_tabular ) { pWriter = new TabulatedFastaWriter ( output.stream() ) ; } else { if ( flag_requested_output_width == 0 ) pWriter = new SingleLineFastaWriter ( output.stream() ) ; else pWriter = new MultiLineFastaWriter ( output.stream(), flag_requested_output_width ) ; } if (!flag_output_empty_sequences) { EmptySequencesFilter *filter = new EmptySequencesFilter ( pWriter ) ; pWriter = filter ; } /* * FASTA read/process/write loop */ int max_length = 0 ; string sequence_id ; string sequence_bases ; bool first_line = true ; while ( reader.next_line() ) { const string &line = reader.line_string(); if ( line.length()==0 ) continue; if ( line[0] == '>' ) { //Got new sequence identifier - print previous sequence if (first_line) first_line = false; else pWriter->write ( sequence_id, sequence_bases ) ; // Start new sequence sequence_id = line ; sequence_bases.clear(); sequence_bases.resize ( max_length * 2 ) ; } else { //Got sequence nucleotides sequence_bases += line ; } } //Write the last sequence pWriter->write ( sequence_id, sequence_bases ) ; delete pWriter; } fastx_toolkit-0.0.14/src/fasta_formatter/sequence_writers.h000066400000000000000000000057131226234573700242170ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #ifndef __SEQUENCE_WRITERS__ #define __SEQUENCE_WRITERS__ #include #include class SequencesWriter { public: virtual ~SequencesWriter() {} virtual void write ( const std::string& sequence_id, const std::string& sequence_bases ) = 0 ; }; class EmptySequencesFilter : public SequencesWriter { private: SequencesWriter* upstream ; public: EmptySequencesFilter ( SequencesWriter * _upstream ) : upstream(_upstream) {} ~EmptySequencesFilter() { delete upstream; } virtual void write ( const std::string & sequence_id, const std::string& sequence_bases) { if ( !sequence_bases.empty() ) upstream->write ( sequence_id, sequence_bases ) ; } }; class SingleLineFastaWriter : public SequencesWriter { private: std::ostream& ostrm ; public: SingleLineFastaWriter ( std::ostream& output_stream ) : ostrm ( output_stream ) { } virtual void write ( const std::string & sequence_id, const std::string& sequence_bases ) { ostrm << sequence_id << std::endl; if ( !sequence_bases.empty() ) ostrm << sequence_bases << std::endl ; } }; class MultiLineFastaWriter : public SequencesWriter { private: std::ostream& ostrm ; size_t max_width ; public: MultiLineFastaWriter ( std::ostream& output_stream, size_t _max_width ) : ostrm ( output_stream ), max_width ( _max_width ) { } virtual void write ( const std::string & sequence_id, const std::string& sequence_bases ) { ostrm << sequence_id << std::endl; if ( !sequence_bases.empty() ) { size_t start = 0 ; while ( (sequence_bases.length() - start) >= max_width ) { ostrm << sequence_bases.substr ( start, max_width ) << std::endl; start += max_width ; } if ( sequence_bases.length() - start > 0 ) ostrm << sequence_bases.substr ( start ) << std::endl ; } } }; class TabulatedFastaWriter : public SequencesWriter { private: std::ostream& ostrm ; public: TabulatedFastaWriter ( std::ostream& output_stream ) : ostrm ( output_stream ) { } virtual void write ( const std::string & sequence_id, const std::string& sequence_bases ) { ostrm << sequence_id.substr(1) ; if ( !sequence_bases.empty() ) { ostrm << "\t" ; ostrm << sequence_bases ; } ostrm << std::endl; } }; #endif fastx_toolkit-0.0.14/src/fasta_nucleotide_changer/000077500000000000000000000000001226234573700222705ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fasta_nucleotide_changer/Makefile.am000066400000000000000000000013241226234573700243240ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fasta_nucleotide_changer AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fasta_nucleotide_changer_SOURCES = fasta_nucleotide_changer.c fasta_nucleotide_changer_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fasta_nucleotide_changer/fasta_nucleotide_changer.c000066400000000000000000000072371226234573700274450ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" #define MAX_ADAPTER_LEN 100 const char* usage= "usage: fasta_nucleotide_changer [-h] [-z] [-v] [-i INFILE] [-o OUTFILE] [-r] [-d]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-v] = Verbose mode. Prints a short summary.\n" \ " with [-o], summary is printed to STDOUT.\n" \ " Otherwise, summary is printed to STDERR.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ " [-r] = DNA-to-RNA mode - change T's into U's.\n" \ " [-d] = RNA-to-DNA mode - change U's into T's.\n" \ "\n"; int flag_dna_mode = 0; int flag_rna_mode = 0; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused))* optarg) { switch(optc) { case 'd': flag_dna_mode = 1 ; break; case 'r': flag_rna_mode = 1 ; break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { size_t i; char nuc_from ; char nuc_to; size_t changes_count=0 ; fastx_parse_cmdline(argc, argv, "rd", parse_program_args); if ( !flag_dna_mode && !flag_rna_mode ) errx(1,"Please specify either RNA mode (-r) or DNA mode (-d)" ); if ( flag_dna_mode && flag_rna_mode ) errx(1,"RNA mode (-r) and DNA mode (-d) can not be used together." ); if ( flag_dna_mode ) { nuc_from = 'U'; nuc_to = 'T'; } if ( flag_rna_mode ) { nuc_from = 'T'; nuc_to = 'U'; } fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N | ALLOW_U, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_FASTA, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { for (i=0; i < strlen(fastx.nucleotides) ; i++) { if ( fastx.nucleotides[i] == nuc_to ) { errx(1,"Error: found '%c' nucleotide on line %lld. (input should not contain '%c' nucleotides in %s mode)", nuc_to, fastx.input_line_number, nuc_to,(flag_dna_mode)?"RNA-to-DNA":"DNA-to-RNA" ); } if ( fastx.nucleotides[i] == nuc_from ) { fastx.nucleotides[i] = nuc_to ; changes_count++; } } fastx_write_record(&fastx); } if ( verbose_flag() ) { fprintf(get_report_file(), "Mode: %s\n", (flag_dna_mode)?"RNA-to-DNA":"DNA-to-RNA" ) ; fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; fprintf(get_report_file(), "Nucleotides changed: %zu\n", changes_count ) ; } return 0; } fastx_toolkit-0.0.14/src/fastq_masker/000077500000000000000000000000001226234573700177505ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastq_masker/Makefile.am000066400000000000000000000012441226234573700220050ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastq_masker AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastq_masker_SOURCES = fastq_masker.c fastq_masker_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastq_masker/fastq_masker.c000066400000000000000000000076421226234573700226050ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" const char* usage= "usage: fastq_masker [-h] [-v] [-q N] [-r C] [-z] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-q N] = Quality threshold - nucleotides with lower quality will be masked\n" \ " Default is 10.\n" \ " [-r C] = Replace low-quality nucleotides with character C. Default is 'N'\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTQ input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTQ output file. default is STDOUT.\n" \ " [-v] = Verbose - report number of sequences.\n" \ " If [-o] is specified, report will be printed to STDOUT.\n" \ " If [-o] is not specified (and output goes to STDOUT),\n" \ " report will be printed to STDERR.\n" \ "\n"; int min_quality_threshold=10; char mask_character='N'; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'q': if (optarg==NULL) errx(1, "[-q] parameter requires an argument value"); min_quality_threshold = atoi(optarg); if (min_quality_threshold<-40) errx(1,"Invalid minimum length value (-q %s)", optarg); break; case 'r': if (optarg==NULL) errx(1, "[-r] parameter requires an argument value"); if (strlen(optarg)!=1) errx(1, "[-r] parameter requires a single character as value"); mask_character = optarg[0]; break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { int i ; size_t masked_reads_count=0; size_t masked_nucleotides_count=0; fastx_parse_cmdline(argc, argv, "q:r:", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { int masked = 0; //Scan each sequence - backwards for ( i=0; i<(int)strlen(fastx.nucleotides); ++i ) { if ( fastx.quality[i] < min_quality_threshold ) { fastx.nucleotides[i] = mask_character ; masked = 1; ++masked_nucleotides_count; } } if (masked) masked_reads_count += get_reads_count(&fastx); fastx_write_record(&fastx); } // //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Minimum Quality Threshold: %d\n", min_quality_threshold); fprintf(get_report_file(), "Low-quality nucleotides replaced with '%c'\n", mask_character); fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; fprintf(get_report_file(), "Masked reads: %zu\n", masked_reads_count ) ; fprintf(get_report_file(), "Masked nucleotides: %zu\n", masked_nucleotides_count ) ; } return 0; } fastx_toolkit-0.0.14/src/fastq_quality_converter/000077500000000000000000000000001226234573700222455ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastq_quality_converter/Makefile.am000066400000000000000000000013201226234573700242750ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastq_quality_converter AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastq_quality_converter_SOURCES = fastq_quality_converter.c fastq_quality_converter_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastq_quality_converter/fastq_quality_converter.c000066400000000000000000000050261226234573700273710ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" const char* usage= "usage: fastq_quality_converter [-h] [-a] [-n] [-z] [-i INFILE] [-f OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-a] = Output ASCII quality scores (default).\n" \ " [-n] = Output numeric quality scores.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA output file. default is STDOUT.\n" \ "\n"; FASTX fastx; int flag_output_ascii = 1; int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused)) *optarg) { switch(optc) { case 'a': //this is the default, nothing to change break; case 'n': flag_output_ascii = 0 ; break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "an", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), flag_output_ascii ? OUTPUT_FASTQ_ASCII_QUAL : OUTPUT_FASTQ_NUMERIC_QUAL, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { fastx_write_record(&fastx); } //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastq_quality_filter/000077500000000000000000000000001226234573700215235ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastq_quality_filter/Makefile.am000066400000000000000000000013041226234573700235550ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastq_quality_filter AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastq_quality_filter_SOURCES = fastq_quality_filter.c fastq_quality_filter_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastq_quality_filter/fastq_quality_filter.c000066400000000000000000000120101226234573700261140ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" #define MAX_ADAPTER_LEN 100 const char* usage= "usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-q N] = Minimum quality score to keep.\n" \ " [-p N] = Minimum percent of bases that must have [-q] quality.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ " [-v] = Verbose - report number of sequences.\n" \ " If [-o] is specified, report will be printed to STDOUT.\n" \ " If [-o] is not specified (and output goes to STDOUT),\n" \ " report will be printed to STDERR.\n" \ "\n"; #define DO_NOT_TRIM_LAST_BASE (0) int min_quality=0; int min_percent=0; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'q': if (optarg==NULL) errx(1, "[-q] parameter requires an argument value"); min_quality = strtoul(optarg,NULL,10); break; case 'p': if (optarg==NULL) errx(1, "[-l] parameter requires an argument value"); min_percent = strtoul(optarg,NULL,10); if (min_percent<=0 || min_percent>100) errx(1,"Invalid percent value (-p %s)", optarg); break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int get_index_of_nth_element(int *array, int array_size, int n) { int pos; //Find the first nono-empty index pos = 0 ; while ( pos < array_size && array[pos]==0 ) pos++; #if 0 fprintf(stderr,"n=%d\n", n); for (i=0; i< array_size; i++) { if (array[i] != 0) fprintf(stderr, "[%d]=%d ", i + MIN_QUALITY_VALUE, array[i]) ; } fprintf(stderr,"\n"); #endif if (pos == array_size) errx(1,"bug: got empty array at %s:%d", __FILE__, __LINE__); while (n > 0) { if (array[pos] > n) break; n -= array[pos]; pos++; while (array[pos]==0 && pos < array_size) pos++; } return pos; } int get_percentile_quality(const FASTX *fastx, int percentile) { size_t i; int count=0; int quality_values[QUALITY_VALUES_RANGE]; memset(quality_values, 0, sizeof(quality_values)); for (i=0; i< strlen(fastx->nucleotides); i++) { count++; quality_values[ fastx->quality[i] - MIN_QUALITY_VALUE ] ++ ; } i = get_index_of_nth_element(quality_values, QUALITY_VALUES_RANGE, (count * (100-percentile) / 100)); //printf(" n = %d, i = %d, i+MIN_QUAL_VALUE=%d\n", // (count*(100-percentile)/100), i, i+MIN_QUALITY_VALUE) ; return i + MIN_QUALITY_VALUE ; } int main(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "q:p:", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { #if 0 fprintf(stderr, "%s\n", fastx.nucleotides ) ; for (i=0; i= min_quality) { fastx_write_record(&fastx); } else { // fprintf(stderr, "%s\n", fastx.nucleotides ) ; // fprintf(stderr, "value = %d\n", value ) ; } } // //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Quality cut-off: %d\n", min_quality); fprintf(get_report_file(), "Minimum percentage: %d\n", min_percent); fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; size_t discarded = num_input_reads(&fastx) - num_output_reads(&fastx) ; fprintf(get_report_file(), "discarded %zu (%zu%%) low-quality reads.\n", discarded, (discarded*100)/( num_input_reads(&fastx) ) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastq_quality_trimmer/000077500000000000000000000000001226234573700217155ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastq_quality_trimmer/Makefile.am000066400000000000000000000013101226234573700237440ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastq_quality_trimmer AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastq_quality_trimmer_SOURCES = fastq_quality_trimmer.c fastq_quality_trimmer_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastq_quality_trimmer/fastq_quality_trimmer.c000066400000000000000000000077431226234573700265210ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" const char* usage= "usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-t N] = Quality threshold - nucleotides with lower \n" \ " quality will be trimmed (from the end of the sequence).\n" \ " [-l N] = Minimum length - sequences shorter than this (after trimming)\n" \ " will be discarded. Default = 0 = no minimum length. \n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTQ input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTQ output file. default is STDOUT.\n" \ " [-v] = Verbose - report number of sequences.\n" \ " If [-o] is specified, report will be printed to STDOUT.\n" \ " If [-o] is not specified (and output goes to STDOUT),\n" \ " report will be printed to STDERR.\n" \ "\n"; int min_quality_threshold=0; int min_length=0; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'l': if (optarg==NULL) errx(1, "[-l] parameter requires an argument value"); min_length = strtoul(optarg,NULL,10); if (min_length<0) errx(1,"Invalid minimum length value (-l %s)", optarg); break; case 't': if (optarg==NULL) errx(1, "[-t] parameter requires an argument value"); min_quality_threshold = strtol(optarg,NULL,10); break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { int i ; fastx_parse_cmdline(argc, argv, "t:l:", parse_program_args); if ( min_quality_threshold == 0 ) errx(1, "Missing minimum quality threshold value (-t)" ) ; fastx_init_reader(&fastx, get_input_filename(), FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { //Scan each sequence - backwards for ( i=(int)strlen(fastx.nucleotides)-1 ; i >=0 ; i-- ) { if ( fastx.quality[i] < min_quality_threshold ) fastx.nucleotides[i] = 0 ; else break ; } if ( i>=0 && i+1 >= min_length ) fastx_write_record(&fastx); } // //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Minimum Quality Threshold: %d\n", min_quality_threshold); if ( min_length > 0 ) fprintf(get_report_file(), "Minimum Length: %d\n", min_length); else fprintf(get_report_file(), "No minimum Length\n"); fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; size_t discarded = num_input_reads(&fastx) - num_output_reads(&fastx) ; fprintf(get_report_file(), "discarded %zu (%zu%%) too-short reads.\n", discarded, (discarded*100)/( num_input_reads(&fastx) ) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastq_to_fasta/000077500000000000000000000000001226234573700202665ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastq_to_fasta/Makefile.am000066400000000000000000000012541226234573700223240ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastq_to_fasta AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastq_to_fasta_SOURCES = fastq_to_fasta.c fastq_to_fasta_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastq_to_fasta/fastq_to_fasta.c000066400000000000000000000064551226234573700234420ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" const char* usage= "usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-r] = Rename sequence identifiers to numbers.\n" \ " [-n] = keep sequences with unknown (N) nucleotides.\n" \ " Default is to discard such sequences.\n" \ " [-v] = Verbose - report number of sequences.\n" \ " If [-o] is specified, report will be printed to STDOUT.\n" \ " If [-o] is not specified (and output goes to STDOUT),\n" \ " report will be printed to STDERR.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA output file. default is STDOUT.\n" \ "\n"; FASTX fastx; int flag_rename_seqid = 0; int flag_discard_N = 1 ; int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused)) *optarg) { switch(optc) { case 'n': flag_discard_N = 0 ; break; case 'r': flag_rename_seqid = 1; break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "rn", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_FASTA, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { //See if the input sequence contained 'N' nucleotides if ( flag_discard_N && (strchr(fastx.nucleotides,'N') != NULL)) continue; if ( flag_rename_seqid ) snprintf(fastx.name, sizeof(fastx.name), "%zu", num_output_reads(&fastx)+1) ; fastx_write_record(&fastx); } //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; if ( flag_discard_N ) { size_t discarded = num_input_reads(&fastx) - num_output_reads(&fastx) ; fprintf(get_report_file(), "discarded %zu (%zu%%) low-quality reads.\n", discarded, (discarded*100)/( num_input_reads(&fastx) ) ) ; } } return 0; } fastx_toolkit-0.0.14/src/fastx_artifacts_filter/000077500000000000000000000000001226234573700220225ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_artifacts_filter/Makefile.am000066400000000000000000000013141226234573700240550ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_artifacts_filter AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_artifacts_filter_SOURCES = fastx_artifacts_filter.c fastx_artifacts_filter_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_artifacts_filter/fastx_artifacts_filter.c000066400000000000000000000071611226234573700267250ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" #define MAX_ADAPTER_LEN 100 const char* usage= "usage: fastx_artifacts_filter [-h] [-v] [-z] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-v] = Verbose - report number of processed reads.\n" \ " If [-o] is specified, report will be printed to STDOUT.\n" \ " If [-o] is not specified (and output goes to STDOUT),\n" \ " report will be printed to STDERR.\n" \ "\n"; #define DO_NOT_TRIM_LAST_BASE (0) FASTX fastx; int parse_commandline(int argc, char* argv[]) { return fastx_parse_cmdline(argc, argv, "", NULL); } int artifact_sequence(const FASTX *fastx) { int n_count=0; int a_count=0; int c_count=0; int t_count=0; int g_count=0; int total_count=0; int max_allowed_different_bases = 3 ; int i=0; while (1) { if (fastx->nucleotides[i]==0) break; total_count++; switch(fastx->nucleotides[i]) { case 'A': a_count++; break; case 'C': c_count++; break; case 'G': g_count++; break; case 'T': t_count++; break; case 'N': n_count++; break; default: errx(1, __FILE__":%d: invalid nucleotide value (%c) at position %d", __LINE__, fastx->nucleotides[i], i ) ; } i++; } //Rules for artifacts if ( a_count>=(total_count-max_allowed_different_bases) || c_count>=(total_count-max_allowed_different_bases) || g_count>=(total_count-max_allowed_different_bases) || t_count>=(total_count-max_allowed_different_bases) ) return 1; return 0; } int main(int argc, char* argv[]) { parse_commandline(argc, argv); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { if ( artifact_sequence(&fastx) ) { } else { fastx_write_record(&fastx); } } //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; size_t discarded = num_input_reads(&fastx) - num_output_reads(&fastx) ; fprintf(get_report_file(), "discarded %zu (%zu%%) artifact reads.\n", discarded, (discarded*100)/( num_input_reads(&fastx) ) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastx_clipper/000077500000000000000000000000001226234573700201335ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_clipper/Makefile.am000066400000000000000000000012521226234573700221670ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_clipper AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_clipper_SOURCES = fastx_clipper.cpp fastx_clipper_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_clipper/fastx_clipper.cpp000066400000000000000000000251461226234573700235120ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include #include #include "sequence_alignment.h" #include #include #include #include "fastx.h" #include "fastx_args.h" #define MAX_ADAPTER_LEN 100 const char* usage= "usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).\n" \ " [-l N] = discard sequences shorter than N nucleotides. default is 5.\n" \ " [-d N] = Keep the adapter and N bases after it.\n" \ " (using '-d 0' is the same as not using '-d' at all. which is the default).\n" \ " [-c] = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).\n" \ " [-C] = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).\n" \ " [-k] = Report Adapter-Only sequences.\n" \ " [-n] = keep sequences with unknown (N) nucleotides. default is to discard such sequences.\n" \ " [-v] = Verbose - report number of sequences.\n" \ " If [-o] is specified, report will be printed to STDOUT.\n" \ " If [-o] is not specified (and output goes to STDOUT),\n" \ " report will be printed to STDERR.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-D] = DEBUG output.\n" \ " [-M N] = require minimum adapter alignment length of N.\n" \ " If less than N nucleotides aligned with the adapter - don't clip it." \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ "\n"; //Default adapter - Dummy sequence char adapter[MAX_ADAPTER_LEN]="CCTTAAGG"; unsigned int min_length=5; int discard_unknown_bases=1; int keep_delta=0; int discard_non_clipped=0; int discard_clipped=0; int show_adapter_only=0; int debug = 0 ; int minimum_adapter_length = 0; //Statistics for verbose report unsigned int count_input=0 ; unsigned int count_discarded_too_short=0; // see [-l N] option unsigned int count_discarded_adapter_at_index_zero=0; //empty sequences (after clipping) unsigned int count_discarded_no_adapter_found=0; // see [-c] option unsigned int count_discarded_adapter_found=0; // see [-C] option unsigned int count_discarded_N=0; // see [-n] FASTX fastx; HalfLocalSequenceAlignment align; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'M': if (optarg==NULL) errx(1, "[-M] parameter requires an argument value"); minimum_adapter_length = atoi(optarg); if (minimum_adapter_length<=0) errx(1,"Invalid minimum adapter length (-M %s)", optarg); break; case 'k': show_adapter_only=1; break; case 'D': debug++; break ; case 'c': discard_non_clipped = 1; break; case 'C': discard_clipped = 1 ; break ; case 'd': if (optarg==NULL) errx(1, "[-d] parameter requires an argument value"); keep_delta = strtoul(optarg,NULL,10); if (keep_delta<0) errx(1,"Invalid number bases to keep (-d %s)", optarg); break; case 'a': strncpy(adapter,optarg,sizeof(adapter)-1); //TODO: //if (!valid_sequence_string(adapter)) // errx(1,"Invalid adapter string (-a %s)", adapter); break ; case 'l': if (optarg==NULL) errx(1,"[-l] parameter requires an argument value"); min_length = strtoul(optarg, NULL, 10); break; case 'n': discard_unknown_bases = 0 ; break; default: errx(1,"Unknown argument (%c)", optc ) ; } return 1; } int parse_commandline(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "M:kDCcd:a:s:l:n", parse_program_args); if (keep_delta>0) keep_delta += strlen(adapter); return 1; } int adapter_cutoff_index ( const SequenceAlignmentResults& alignment_results ) __attribute__ ((const)); int adapter_cutoff_index ( const SequenceAlignmentResults& alignment_results ) { #if 0 int mismatches = alignment_results.mismatches ; //The adapter(=target) is expected to align from the first base. //If the start is not zero (=not aligned from first base), //count each skipped base as a mismatch mismatches += alignment_results.target_start ; //The adapter is expected to align up to the end //of the adapter(=target), or the end of the query. //If it doesn't, count the un-aligned bases as mismatches int missing_from_query_end = (alignment_results.query_size - alignment_results.query_end-1); int missing_from_target_end = (alignment_results.target_size - alignment_results.target_end-1); int missing_from_end = std::min(missing_from_query_end, missing_from_target_end); mismatches += missing_from_end ; std::cout << "Missing from start = " << alignment_results.target_start << " Missing from end = " << missing_from_end << " mismatches = " << mismatches << std::endl; if (mismatches > max_mismatches) return -1; return alignment_results.query_start; #endif int alignment_size = alignment_results.neutral_matches + alignment_results.matches + alignment_results.mismatches + alignment_results.gaps ; //No alignment at all? if (alignment_size==0) return -1; if (minimum_adapter_length>0 && alignment_size 5 && alignment_results.target_start == 0 && (alignment_results.matches * 100 / alignment_size ) >= 75 ) { //printf("--2\n"); return alignment_results.query_start ; } if ( alignment_size > 11 && (alignment_results.matches * 100 / alignment_size ) >= 80 ) { //printf("--2\n"); return alignment_results.query_start ; } // //Be very lenient regarding alignments at the end of the query sequence if ( alignment_results.query_end >= alignment_results.query_size-2 && alignment_size <= 5 && alignment_results.matches >= 3) { //printf("--3\n"); return alignment_results.query_start ; } return -1; } int main(int argc, char* argv[]) { int i; int reads_count; parse_commandline(argc, argv); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { reads_count = get_reads_count(&fastx); #if 0 std::string query = std::string(fastx.nucleotides) + std::string( strlen(adapter), 'N' ); std::string target= std::string( strlen(fastx.nucleotides), 'N' ) + std::string(adapter); #else std::string query = std::string(fastx.nucleotides) ; std::string target= std::string(adapter); #endif align.align( query, target ) ; if (debug>1) align.print_matrix(); if (debug>0) align.results().print(); count_input+= reads_count; //Find the best match with the adapter i = adapter_cutoff_index ( align.results() ) ; if (i!=-1 && i>0) { i += keep_delta; //Just trim the string after this position fastx.nucleotides[i] = 0 ; } if (i==0) { // empty sequence ? (in which the adapter was found at index 0) count_discarded_adapter_at_index_zero += reads_count; if (show_adapter_only) fastx_write_record(&fastx); continue; } if (strlen(fastx.nucleotides) < min_length) { // too-short sequence ? count_discarded_too_short += reads_count; continue; } if ( (i==-1) && discard_non_clipped ) { // adapter not found (i.e. sequence was not clipped) ? count_discarded_no_adapter_found += reads_count; continue ; } if ( (i>0) && discard_clipped ) { // adapter found, and user requested to keep only non-clipped sequences count_discarded_adapter_found += reads_count; continue; } if ( (discard_unknown_bases && strchr(fastx.nucleotides,'N')!=NULL ) ) { // contains unknown bases (after clipping) ? count_discarded_N += reads_count; continue; } if (!show_adapter_only) { //none of the above condition matched, so print this sequence. fastx_write_record(&fastx); } } // //Print verbose report if ( verbose_flag() ) { fprintf(get_report_file(), "Clipping Adapter: %s\n", adapter ); fprintf(get_report_file(), "Min. Length: %d\n", min_length) ; if (discard_clipped) fprintf(get_report_file(), "Clipped reads - discarded.\n" ) ; if (discard_non_clipped) fprintf(get_report_file(), "Non-Clipped reads - discarded.\n" ) ; fprintf(get_report_file(), "Input: %u reads.\n", count_input ) ; fprintf(get_report_file(), "Output: %u reads.\n", count_input - count_discarded_too_short - count_discarded_no_adapter_found - count_discarded_adapter_found - count_discarded_N - count_discarded_adapter_at_index_zero ) ; fprintf(get_report_file(), "discarded %u too-short reads.\n", count_discarded_too_short ) ; fprintf(get_report_file(), "discarded %u adapter-only reads.\n", count_discarded_adapter_at_index_zero ); if (discard_non_clipped) fprintf(get_report_file(), "discarded %u non-clipped reads.\n", count_discarded_no_adapter_found ); if (discard_clipped) fprintf(get_report_file(), "discarded %u clipped reads.\n", count_discarded_adapter_found ); if (discard_unknown_bases) fprintf(get_report_file(), "discarded %u N reads.\n", count_discarded_N ); } return 0; } fastx_toolkit-0.0.14/src/fastx_collapser/000077500000000000000000000000001226234573700204615ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_collapser/Makefile.am000066400000000000000000000013041226234573700225130ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_collapser AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_collapser_SOURCES = fastx_collapser.cpp \ std_hash.h fastx_collapser_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_collapser/fastx_collapser.cpp000066400000000000000000000102371226234573700243610ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "config.h" #include "fastx.h" #include "fastx_args.h" using namespace std; const char* usage= "usage: fastx_collapser [-h] [-v] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-v] = verbose: print short summary of input/output counts\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ "\n"; FASTX fastx; #if HAVE_CXX11 == 1 /* compiler supports -std=cxx11 - use */ #include std::unordered_map collapsed_sequences; #else #ifdef STDCXX_TR1_HEADERS /* fallback - compiler suppots 'tr1' headers - use them */ #include std::tr1::unordered_map collapsed_sequences; #else /* Worse fallback - use map instead of unordered_map */ #include std::map collapsed_sequences; #endif #endif std::list< pair > sorted_collapsed_sequences ; struct PrintCollapsedSequence { size_t counter; size_t total_reads ; ostream &output ; PrintCollapsedSequence( ostream& _output ) : counter(0), total_reads(0), output(_output) {} void operator() ( const std::pair & sequence ) { counter++; total_reads += sequence.second ; output << ">" << counter << "-" << sequence.second << endl << sequence.first << endl ; } }; bool sort_by_abundance_count ( const pair & sequence1, const pair& sequence2 ) { return sequence1.second < sequence2.second ; } int main(int argc, char* argv[]) { ofstream output_file ; fastx_parse_cmdline(argc, argv, "", NULL ); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); bool use_stdout = true; if ( strcmp(get_output_filename(), "-")!=0 ) { use_stdout = false; output_file.open(get_output_filename()); if (!output_file) errx(1,"Failed to create output file (%s)", get_output_filename() ); } ostream& real_output = (use_stdout) ? cout : output_file ; while ( fastx_read_next_record(&fastx) ) { collapsed_sequences[string(fastx.nucleotides)]+= get_reads_count(&fastx); } copy ( collapsed_sequences.begin(), collapsed_sequences.end(), back_inserter(sorted_collapsed_sequences) ) ; sorted_collapsed_sequences.sort ( sort_by_abundance_count ) ; PrintCollapsedSequence stats = for_each ( sorted_collapsed_sequences.rbegin(), sorted_collapsed_sequences.rend(), PrintCollapsedSequence(real_output) ) ; /* This (in)sanity check prevents collapsing an already-collapsed FASTA file, so skip it for now */ /* if (stats.total_reads != num_input_reads(&fastx)) errx(1,"Internal error: stats.total_reads (%zu) != num_input_reads(&fastx) (%zu).\n", stats.total_reads, num_input_reads(&fastx) ); */ if ( verbose_flag() ) { fprintf(get_report_file(), "Input: %zu sequences (representing %zu reads)\n", num_input_sequences(&fastx), num_input_reads(&fastx)); fprintf(get_report_file(), "Output: %zu sequences (representing %zu reads)\n", stats.counter, stats.total_reads); } return 0; } fastx_toolkit-0.0.14/src/fastx_collapser/std_hash.h000066400000000000000000000040521226234573700224300ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #ifndef __STD_HASH__ #define __STD_HASH__ /* * Centralized place to load std::hash_map * * GCC needs the following hacks... * Other compilers/systems might require different hacks */ #include #include namespace std { using namespace __gnu_cxx; struct std_string_hash { size_t operator()( const std::string& x ) const { //printf("std_string_hash: hashing '%s'\n", x.c_str()); return hash< const char* >()( x.c_str() ); } }; /* * 'eqstr' and 'hash_map' usage is based on http://www.sgi.com/tech/stl/hash_map.html */ struct eqstr { bool operator()(const char* s1, const char* s2) const { return strcmp(s1, s2) == 0; } }; typedef hash_map< const char*, int, hash< const char* >, eqstr > hash_map_charptr_to_int; typedef hash_map< string, int, std_string_hash > hash_map_string_to_int; typedef hash_set < string, std_string_hash > hash_set_string ; } #endif fastx_toolkit-0.0.14/src/fastx_quality_stats/000077500000000000000000000000001226234573700214035ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_quality_stats/Makefile.am000066400000000000000000000013001226234573700234310ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_quality_stats AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_quality_stats_SOURCES = fastx_quality_stats.c fastx_quality_stats_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_quality_stats/fastx_quality_stats.c000066400000000000000000000326421226234573700256710ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "chomp.h" #include "fastx.h" #include "fastx_args.h" #ifndef MAX #define MAX(a,b) (((a) > (b)) ? (a) : (b)) #endif #ifndef MIN #define MIN(a,b) (((a) < (b)) ? (a) : (b)) #endif #define MAX_SEQUENCE_LENGTH (2000) //that's pretty arbitrary... should be enough for now const char* usage= "usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-i INFILE] = FASTQ input file. default is STDIN.\n" \ " [-o OUTFILE] = TEXT output file. default is STDOUT.\n" \ " [-N] = New output format (with more information per nucleotide/cycle).\n" \ "\n"\ "The *OLD* output TEXT file will have the following fields (one row per column):\n" \ " column = column number (1 to 36 for a 36-cycles read solexa file)\n" \ " count = number of bases found in this column.\n" \ " min = Lowest quality score value found in this column.\n" \ " max = Highest quality score value found in this column.\n" \ " sum = Sum of quality score values for this column.\n" \ " mean = Mean quality score value for this column.\n" \ " Q1 = 1st quartile quality score.\n" \ " med = Median quality score.\n" \ " Q3 = 3rd quartile quality score.\n" \ " IQR = Inter-Quartile range (Q3-Q1).\n" \ " lW = 'Left-Whisker' value (for boxplotting).\n" \ " rW = 'Right-Whisker' value (for boxplotting).\n" \ " A_Count = Count of 'A' nucleotides found in this column.\n" \ " C_Count = Count of 'C' nucleotides found in this column.\n" \ " G_Count = Count of 'G' nucleotides found in this column.\n" \ " T_Count = Count of 'T' nucleotides found in this column.\n" \ " N_Count = Count of 'N' nucleotides found in this column.\n" \ " max-count = max. number of bases (in all cycles)\n" \ "\n" \ "\n" \ "The *NEW* output format:\n" \ " cycle (previously called 'column') = cycle number\n" \ " max-count\n" \ " For each nucleotide in the cycle (ALL/A/C/G/T/N):\n" " count = number of bases found in this column.\n" \ " min = Lowest quality score value found in this column.\n" \ " max = Highest quality score value found in this column.\n" \ " sum = Sum of quality score values for this column.\n" \ " mean = Mean quality score value for this column.\n" \ " Q1 = 1st quartile quality score.\n" \ " med = Median quality score.\n" \ " Q3 = 3rd quartile quality score.\n" \ " IQR = Inter-Quartile range (Q3-Q1).\n" \ " lW = 'Left-Whisker' value (for boxplotting).\n" \ " rW = 'Right-Whisker' value (for boxplotting).\n" \ "\n"\ "\n"; ; FILE* outfile; int new_output_format = 0 ; /* Information for each column in the solexa file. ("Column" here refers to the number of reads in the file, usually 36) */ typedef enum { ALL = 0, A = 1, C = 2, G = 3, T = 4, N = 5, NUC_INDEX_SIZE=6 } NUCLEOTIDE_INDEX ; char* nucleotide_index_name[NUC_INDEX_SIZE] = { "ALL","A","C","G","T","N" } ; //Lookup table to convert from ASCII character A/C/G/T to NUCLEOTIDE_INDEX. //Initialized in init_values(). int nuc_to_index[256]; //Information for each nucleotide of each cycle struct nucleotide_data { int min; int max; int count; unsigned long long sum; //Instead of keeping a sorted array of all the quality values (which is needed to find the median value), //We keep the values in this array. similar to "Couting Sort" array in "Introduction to Algorithms", page 169. //Each time we encounter a quality value number (in the range of MIN_QUALITY_VALUE to MAX_QUALITY_VALUE), //we increment the count in the corresponding index of this array. int bases_values_count[QUALITY_VALUES_RANGE]; }; //Information for each cycle struct cycle_data { struct nucleotide_data nucleotide[NUC_INDEX_SIZE]; }; int sequences_count; struct cycle_data cycles[MAX_SEQUENCE_LENGTH]; FASTX fastx; void init_values() { int i,j; bzero ( nuc_to_index, sizeof(nuc_to_index) ) ; nuc_to_index['A'] = A ; nuc_to_index['a'] = A ; nuc_to_index['C'] = C ; nuc_to_index['c'] = C ; nuc_to_index['G'] = G ; nuc_to_index['g'] = G ; nuc_to_index['T'] = T ; nuc_to_index['t'] = T ; nuc_to_index['N'] = N ; nuc_to_index['n'] = N ; sequences_count=0; bzero ( &cycles, sizeof(cycles) ); for (i=0;i= MAX_SEQ_LINE_LENGTH) errx(1, "Internal error: sequence too long (on line %llu). Hard-coded max. length is %d", fastx.input_line_number, MAX_SEQ_LINE_LENGTH ) ; //for each base in the sequence... for (index=0; indexMAX_SEQUENCE_LENGTH) { fprintf(stderr,"Internal error at get_nth_value, cycle=%d, nucleotide=%d\n", cycle, nucleotide); exit(1); } if (n==0) return cycles[cycle].nucleotide[nucleotide].min; if (n<0 || n>=cycles[cycle].nucleotide[nucleotide].count) { fprintf(stderr,"Internal error at get_nth_value (cycle=%d, nucleotide=%d, n=%d), count_values[%d]=%d\n", cycle, nucleotide, n, cycle, cycles[cycle].nucleotide[nucleotide].count ) ; exit(1); } pos = 0 ; while (n > 0) { if (cycles[cycle].nucleotide[nucleotide].bases_values_count[pos] > n) break; n -= cycles[cycle].nucleotide[nucleotide].bases_values_count[pos]; pos++; while (cycles[cycle].nucleotide[nucleotide].bases_values_count[pos]==0) pos++; } return pos + MIN_QUALITY_VALUE ; } void print_nucleotide_statistics_header(const char *nuc_name) { const char* headers[] = { "count", "min", "max", "sum", "mean", "Q1", "med", "Q3", "IQR", "lW", "rW", NULL }; const char** header = headers; while ( *header != NULL ) { fprintf(outfile,"\t%s_%s", nuc_name, *header); header++; } } /* print quality statistics (for one nucleotide) in new format */ void print_nucleotide_statistics(int cycle, int nuc_index) { int Q1,Q3,IQR; int LeftWisker, RightWisker; Q1 = get_nth_value ( cycle, nuc_index, cycles[cycle].nucleotide[nuc_index].count / 4 ); Q3 = get_nth_value ( cycle, nuc_index, cycles[cycle].nucleotide[nuc_index].count * 3 / 4 ); IQR = Q3 - Q1 ; if ( (Q1 - IQR*3/2) < cycles[cycle].nucleotide[nuc_index].min ) LeftWisker = cycles[cycle].nucleotide[nuc_index].min; else LeftWisker = (Q1 - IQR*3/2); //TODO - make sure there's an observed value at this point if ( (Q3 + IQR*3/2) > cycles[cycle].nucleotide[nuc_index].max ) RightWisker = cycles[cycle].nucleotide[nuc_index].max; else RightWisker = (Q3 + IQR*3/2); //TODO - make sure there's an observed value at this point fprintf(outfile,"\t%d\t%d\t%d\t%lld\t", cycles[cycle].nucleotide[nuc_index].count, cycles[cycle].nucleotide[nuc_index].min, cycles[cycle].nucleotide[nuc_index].max, cycles[cycle].nucleotide[nuc_index].sum); fprintf(outfile,"%3.2f\t%d\t%d\t%d\t", ((double)cycles[cycle].nucleotide[nuc_index].sum)/((double)cycles[cycle].nucleotide[nuc_index].count), Q1, get_nth_value ( cycle, nuc_index, cycles[cycle].nucleotide[nuc_index].count / 2 ), Q3); fprintf(outfile,"%d\t%d\t%d", IQR, LeftWisker, RightWisker ); } void print_statistics() { int nuc ; int cycle ; int max_count ; fprintf(outfile,"cycle\tmax_count"); for ( nuc = 0 ;nuc < NUC_INDEX_SIZE ; ++nuc ) print_nucleotide_statistics_header( nucleotide_index_name[nuc] ) ; fprintf(outfile,"\n"); //Maximum number of bases (out of all cycles/columns). //it is always equal to the count of the first column //(since all reads have a base at the first column, // but some might not have base at later columns (if they were clipped) ) max_count = cycles[0].nucleotide[ALL].count ; for (cycle=0;cycle cycles[i].nucleotide[ALL].max ) RightWisker = cycles[i].nucleotide[ALL].max; else RightWisker = (Q3 + IQR*3/2); //TODO - make sure there's an observed value at this point //Column number fprintf(outfile,"%d\t", i+1); fprintf(outfile,"%d\t%d\t%d\t%lld\t", cycles[i].nucleotide[ALL].count, cycles[i].nucleotide[ALL].min, cycles[i].nucleotide[ALL].max, cycles[i].nucleotide[ALL].sum); fprintf(outfile,"%3.2f\t%d\t%d\t%d\t", ((double)cycles[i].nucleotide[ALL].sum)/((double)cycles[i].nucleotide[ALL].count), Q1, get_nth_value ( i, ALL, cycles[i].nucleotide[ALL].count / 2 ), Q3); fprintf(outfile,"%d\t%d\t%d\t", IQR, LeftWisker, RightWisker ); fprintf(outfile,"%d\t%d\t%d\t%d\t%d\t", cycles[i].nucleotide[A].count, cycles[i].nucleotide[C].count, cycles[i].nucleotide[G].count, cycles[i].nucleotide[T].count, cycles[i].nucleotide[N].count); //Maximum number of bases (out of all cycles/columns). //it is always equal to the count of the first column //(since all reads have a base at the first column, // but some might not have base at later columns (if they were clipped) ) fprintf(outfile,"%d\n", cycles[0].nucleotide[ALL].count ) ; } } int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused))* optarg) { switch(optc) { case 'N': new_output_format = 1 ; break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } void parse_commandline(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "N", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); if (strcmp( get_output_filename(), "-" ) == 0 ) { outfile = stdout; } else { outfile = fopen(get_output_filename(), "w+"); if (outfile==NULL) err(1,"Failed to create output file (%s)", get_output_filename()); } } int main(int argc, char* argv[]) { parse_commandline(argc,argv); init_values(); read_file(); if ( new_output_format ) print_statistics(); else print_old_statistics(); return 0; } fastx_toolkit-0.0.14/src/fastx_renamer/000077500000000000000000000000001226234573700201265ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_renamer/Makefile.am000066400000000000000000000012501226234573700221600ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_renamer AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_renamer_SOURCES = fastx_renamer.c fastx_renamer_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_renamer/fastx_renamer.c000066400000000000000000000060771226234573700231420ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" const char* usage= "usage: fastx_renamer [-n TYPE] [-h] [-z] [-v] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-n TYPE] = rename type:\n" \ " SEQ - use the nucleotides sequence as the name.\n" \ " COUNT - use simply counter as the name.\n" \ " [-h] = This helpful help screen.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ "\n"; enum RENAME_TYPE { SEQ, COUNT }; enum RENAME_TYPE rename_type; unsigned int counter = 1 ; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'n': if (optarg==NULL) errx(1, "[-n] parameter requires an argument value"); if (strncmp(optarg,"SEQ",3)==0) { rename_type = SEQ ; } else if (strncmp(optarg,"COUNT",5)==0) { rename_type = COUNT ; counter = 1 ; } else errx(1,"Uknown rename type [-n]: '%s'", optarg); break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "n:", parse_program_args); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { switch(rename_type) { case SEQ: strncpy(fastx.name, fastx.nucleotides, sizeof(fastx.name)); strncpy(fastx.name2, fastx.nucleotides, sizeof(fastx.name2)); break; case COUNT: snprintf(fastx.name, sizeof(fastx.name),"%u",counter); strncpy(fastx.name2, fastx.name, sizeof(fastx.name2)); counter++; break; default: errx(1,"Internal error: rename_type = %d", (int)rename_type); } fastx_write_record(&fastx); } if ( verbose_flag() ) { fprintf(get_report_file(), "Renamed: %zu reads.\n", num_input_reads(&fastx) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastx_reverse_complement/000077500000000000000000000000001226234573700223735ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_reverse_complement/Makefile.am000066400000000000000000000013241226234573700244270ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_reverse_complement AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_reverse_complement_SOURCES = fastx_reverse_complement.c fastx_reverse_complement_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_reverse_complement/fastx_reverse_complement.c000066400000000000000000000063211226234573700276440ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" const char* usage= "usage: fastx_reverse_complement [-h] [-r] [-z] [-v] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ "\n"; FASTX fastx; char reverse_complement_base ( const char input ) { switch(input) { case 'N': return 'N'; case 'n': return 'n'; case 'A': return 'T'; case 'T': return 'A'; case 'G': return 'C'; case 'C': return 'G'; case 'a': return 't'; case 't': return 'a'; case 'g': return 'c'; case 'c': return 'g'; default: errx(1,"Invalid nucleotide value (%c) in reverse_complement_base()", input ); } return '0'; //should not get here - just to please the compiler } void reverse_complement_fastx(FASTX* pFASTX) { int i,j ; int length = strlen(pFASTX->nucleotides); char temp_nuc; int temp_qual; for (i=0;inucleotides[i] = reverse_complement_base ( pFASTX->nucleotides[i] ) ; i = 0 ; j = length - 1 ; while ( i < j ) { //Swap the nucleotides temp_nuc = pFASTX->nucleotides[i] ; pFASTX->nucleotides[i] = pFASTX->nucleotides[j] ; pFASTX->nucleotides[j] = temp_nuc; //Swap the quality scores if (pFASTX->read_fastq) { temp_qual = pFASTX->quality[i]; pFASTX->quality[i] = pFASTX->quality[j]; pFASTX->quality[j] = temp_qual ; } //Advance to next position i++; j--; } } int main(int argc, char* argv[]) { fastx_parse_cmdline(argc, argv, "", NULL); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { reverse_complement_fastx(&fastx); fastx_write_record(&fastx); } if ( verbose_flag() ) { fprintf(get_report_file(), "Printing Reverse-Complement Sequences.\n" ); fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastx_trimmer/000077500000000000000000000000001226234573700201545ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_trimmer/Makefile.am000066400000000000000000000012501226234573700222060ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_trimmer AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx fastx_trimmer_SOURCES = fastx_trimmer.c fastx_trimmer_LDADD = ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_toolkit-0.0.14/src/fastx_trimmer/fastx_trimmer.c000066400000000000000000000123271226234573700232110ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "fastx.h" #include "fastx_args.h" #define MAX_ADAPTER_LEN 100 const char* usage= "usage: fastx_trimmer [-h] [-f N] [-l N] [-t N] [-m MINLEN] [-z] [-v] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-f N] = First base to keep. Default is 1 (=first base).\n" \ " [-l N] = Last base to keep. Default is entire read.\n" \ " [-t N] = Trim N nucleotides from the end of the read.\n" \ " '-t' can not be used with '-l' and '-f'.\n" \ " [-m MINLEN] = With [-t], discard reads shorter than MINLEN.\n" " [-z] = Compress output with GZIP.\n" \ " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \ "\n"; #define DO_NOT_TRIM_LAST_BASE (0) int keep_first_base=1; int keep_last_base=DO_NOT_TRIM_LAST_BASE; unsigned int trim_last_bases=0; unsigned int minimum_length=0; int trim_by_position=0; int trim_from_end=0; FASTX fastx; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'f': if (optarg==NULL) errx(1, "[-f] parameter requires an argument value"); keep_first_base = strtoul(optarg,NULL,10); if (keep_first_base<=0 || keep_first_base>=MAX_SEQ_LINE_LENGTH) errx(1,"Invalid number bases to keep (-f %s)", optarg); trim_by_position=1; break; case 'l': if (optarg==NULL) errx(1, "[-l] parameter requires an argument value"); keep_last_base = strtoul(optarg,NULL,10); if (keep_last_base<=0 || keep_last_base>=MAX_SEQ_LINE_LENGTH) errx(1,"Invalid number bases to keep (-l %s)", optarg); trim_by_position=1; break; case 't': if (optarg==NULL) errx(1, "[-t] parameter requires an argument value"); trim_last_bases = strtoul(optarg,NULL,10); if (trim_last_bases<=0 || trim_last_bases>=MAX_SEQ_LINE_LENGTH) errx(1,"Invalid number bases to trim (-t %s)", optarg); trim_from_end=1; break; case 'm': if (optarg==NULL) errx(1, "[-t] parameter requires an argument value"); minimum_length = strtoul(optarg,NULL,10); if (minimum_length<=0 || minimum_length>=MAX_SEQ_LINE_LENGTH) errx(1,"Invalid minimum length value (-m %s)", optarg); break; default: errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; } return 1; } int main(int argc, char* argv[]) { size_t i; fastx_parse_cmdline(argc, argv, "l:f:t:m:", parse_program_args); //validate command line arguments if (trim_by_position && trim_from_end) errx(1,"[-t], [-f] and [-l] options can not be used together. Use [-t] or [-l,-f]"); fastx_init_reader(&fastx, get_input_filename(), FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); while ( fastx_read_next_record(&fastx) ) { if (keep_last_base != DO_NOT_TRIM_LAST_BASE) { fastx.nucleotides[keep_last_base] = 0 ; } if (keep_first_base != 1) { if ( strlen(fastx.nucleotides) < (size_t)keep_first_base ) //sequence too short - remove it continue ; for (i=0; i < strlen(fastx.nucleotides)-keep_first_base+1 ; i++) { fastx.nucleotides[i] = fastx.nucleotides[i+keep_first_base-1]; fastx.quality[i] = fastx.quality[i+keep_first_base-1]; } fastx.nucleotides[i] = 0 ; } if (trim_last_bases>0) { if (strlen(fastx.nucleotides) <= trim_last_bases) continue; i = strlen(fastx.nucleotides) - trim_last_bases; if (i < minimum_length) continue; fastx.nucleotides[i] = 0; fastx.quality[i] = 0 ; } //none of the above condition matched, so print this sequence. fastx_write_record(&fastx); } if ( verbose_flag() ) { if (keep_first_base!=1 || keep_last_base!=DO_NOT_TRIM_LAST_BASE) fprintf(get_report_file(), "Trimming: base %d to %d\n", keep_first_base, keep_last_base ) ; if (trim_last_bases) { fprintf(get_report_file(), "Trimming %d bases from the end of the reads\n", trim_last_bases); if ( minimum_length ) fprintf(get_report_file(), "Discarding reads shorter than %d bases\n", minimum_length); } fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; } return 0; } fastx_toolkit-0.0.14/src/fastx_uncollapser/000077500000000000000000000000001226234573700210245ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/fastx_uncollapser/Makefile.am000066400000000000000000000013171226234573700230620ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. bin_PROGRAMS = fastx_uncollapser AM_CPPFLAGS = \ $(CC_WARNINGS) \ $(GTEXTUTILS_CFLAGS) \ -I$(top_srcdir)/src/libfastx LDADD = $(GTEXTUTILS_LIBS) ../libfastx/libfastx.a $(LT_LDFLAGS) fastx_uncollapser_SOURCES = fastx_uncollapser.cpp fastx_toolkit-0.0.14/src/fastx_uncollapser/fastx_uncollapser.cpp000066400000000000000000000135551226234573700252750ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "config.h" #include "fastx.h" #include "fastx_args.h" using namespace std; const char* usage= "usage: fasta_uncollapser [-c N] [-h] [-v] [-i INFILE] [-o OUTFILE]\n" \ "Part of " PACKAGE_STRING " by A. Gordon (assafgordon@gmail.com)\n" \ "\n" \ " [-h] = This helpful help screen.\n" \ " [-v] = verbose: print short summary of input/output counts\n" \ " [-c N] = Assume input is a tabular file (not FASTA file),\n" \ " And the collapsed identifier (e.g. '1-1000') is on column N.\n" \ " [-i INFILE] = FASTA/Tabular input file. default is STDIN.\n" \ " [-o OUTFILE] = FASTA/Tabular output file. default is STDOUT.\n" \ "\n"; size_t collapsed_identifier_column = 0; int parse_program_args(int __attribute__((unused)) optind, int optc, char* optarg) { switch(optc) { case 'c': if (optarg==NULL) errx(1, "[-c] parameter requires an argument value"); collapsed_identifier_column = strtoul(optarg,NULL,10); if (collapsed_identifier_column<=0) errx(1,"Invalid column number (-c %s)", optarg); break; default: errx(1,"Internal error: unknown option '%c'",optc); } return 1; } void uncollapse_fasta_file() { FASTX fastx; fastx_init_reader(&fastx, get_input_filename(), FASTA_ONLY, ALLOW_N, REQUIRE_UPPERCASE, get_fastq_ascii_quality_offset() ); fastx_init_writer(&fastx, get_output_filename(), OUTPUT_SAME_AS_INPUT, compress_output_flag()); size_t seqid=1; while ( fastx_read_next_record(&fastx) ) { int count = get_reads_count(&fastx); for (int i=0;i0 && *endptr==0 ) //value converted successfuly, without surplus character? return count; return 1; } void uncollapse_tabular_file() { ios::sync_with_stdio(false); size_t input_count=0; size_t output_count=0; string input_file(get_input_filename()); if (input_file=="-") input_file=""; string output_file(get_output_filename()); if (output_file=="-") output_file=""; InputStreamWrapper input(input_file); OutputStreamWrapper output(output_file); TextLineReader reader(input.stream()); ostream &os = output.stream(); // size_t seqid=1; while (reader.next_line()) { ++input_count; vector tokens; //Split input line into fields String_Tokenize(reader.line_string(), back_inserter(tokens), "\t"); if (tokens.size()1) { prefix_fields = join(tokens.begin(),tokens.begin()+(collapsed_identifier_column-1),"\t"); prefix_fields += "\t"; } std::string suffix_fields; if (collapsed_identifier_column. */ #include "chomp.h" /* Chomp - Removes CR/LF from given string. Input - string - NULL terminated string. WILL BE MODIFIED! Output - None Remarks - The first CR (ASCII 13) or LF (ASCII 10) found in the string will be replaced with a NULL - Effectively chomping the string. */ void chomp(char *string) { while (*string != 0) { if (*string==13 || *string==10) { *string = 0 ; return; } string++; } return ; } fastx_toolkit-0.0.14/src/libfastx/chomp.h000066400000000000000000000015501226234573700203640ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #ifndef __CHOMP_H__ #define __CHOMP_H__ void chomp(char *string); #endif fastx_toolkit-0.0.14/src/libfastx/fastx.c000066400000000000000000000344261226234573700204060ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include #include "chomp.h" #include "fastx.h" /* valid_sequence_string - check validity of a given sequence string. input - sequence - NULL terminated string to be validated. Output - 1 (true) - The given sequence is valid - contained only A/C/G/N/T characters. 0 (false) - The given string contained invalid characeters. Remark - sequences with unknown (N) bases are considered VALID. */ static int validate_nucleotides_string(int allowed_nucleotides[256], const char* seq) { int match = 1 ; while (*seq != '\0' && match) { unsigned char c = *seq; match &= allowed_nucleotides[ c ]; seq++; } return match; } static void create_lookup_table(FASTX *pFASTX) { int i; for (i=0; i<256; i++) pFASTX->allowed_nucleotides[i] = 0 ; pFASTX->allowed_nucleotides['A'] = 1; pFASTX->allowed_nucleotides['C'] = 1; pFASTX->allowed_nucleotides['G'] = 1; pFASTX->allowed_nucleotides['T'] = 1; if (pFASTX->allow_N) pFASTX->allowed_nucleotides['N'] = 1; if (pFASTX->allow_U) pFASTX->allowed_nucleotides['U'] = 1; if (pFASTX->allow_lowercase) { pFASTX->allowed_nucleotides['a'] = 1; pFASTX->allowed_nucleotides['c'] = 1; pFASTX->allowed_nucleotides['g'] = 1; pFASTX->allowed_nucleotides['t'] = 1; if (pFASTX->allow_N) pFASTX->allowed_nucleotides['n'] = 1; if (pFASTX->allow_U) pFASTX->allowed_nucleotides['u'] = 1; } } static void detect_input_format(FASTX *pFASTX) { //Get the first character in the file, //and put it right back int c = fgetc(pFASTX->input); ungetc(c, pFASTX->input); switch(c) { case '>': /* FASTA file */ if ( pFASTX->allow_input_filetype==FASTQ_ONLY ) errx(1,"input file (%s) is FASTA, but only FASTQ input is allowed.", pFASTX->input_file_name); pFASTX->read_fastq = 0 ; break; case '@': /* FASTQ file */ if ( pFASTX->allow_input_filetype==FASTA_ONLY ) errx(1,"input file (%s) is FASTQ, but only FASTA input is allowed.", pFASTX->input_file_name); pFASTX->read_fastq = 1; break; case -1: /* EOF as first character - no input */ errx(1, "Premature End-Of-File (filename ='%s')", pFASTX->input_file_name); break; default: errx(1, "input file (%s) has unknown file format (not FASTA or FASTQ), first character = %c (%d)", pFASTX->input_file_name, c,c); } } static void convert_ascii_quality_score_line(const char* ascii_quality_scores, FASTX *pFASTX) { size_t i; if (strlen(ascii_quality_scores) != strlen(pFASTX->nucleotides)) errx(1,"number of quality values (%zu) doesn't match number of nucleotides (%zu) on line %lld", strlen(ascii_quality_scores), strlen(pFASTX->nucleotides), pFASTX->input_line_number); for (i=0; iquality[i] = (int) (ascii_quality_scores[i] - pFASTX->fastq_ascii_quality_offset ) ; if (pFASTX->quality[i] < -15 || pFASTX->quality[i] > 93) errx(1, "Invalid quality score value (char '%c' ord %d quality value %d) on line %lld", ascii_quality_scores[i], ascii_quality_scores[i], pFASTX->quality[i], pFASTX->input_line_number ); } } static void convert_numeric_quality_score_line ( const char* numeric_quality_line, FASTX *pFASTX ) { size_t index; const char *quality_tok; char *endptr; int quality_value; index=0; quality_tok = numeric_quality_line; do { //read the quality score as an integer value quality_value = strtol(quality_tok, &endptr, 10); if (endptr == quality_tok) errx(1,"Error: invalid quality score data on line %lld (quality_tok = \"%s\"", pFASTX->input_line_number ,quality_tok); if (quality_value > 93 || quality_value < -15) errx(1, "invalid quality score value (%d) in line %lld.", quality_value, pFASTX->input_line_number); //convert it ASCII (as per solexa's encoding) pFASTX->quality[index] = quality_value; index++; quality_tok = endptr; } while (quality_tok != NULL && *quality_tok!='\0') ; if (index != strlen(pFASTX->nucleotides)) { errx(1,"number of quality values (%zu) doesn't match number of nucleotides (%zu) on line %lld", index, strlen(pFASTX->nucleotides), pFASTX->input_line_number ); } } void fastx_init_reader(FASTX *pFASTX, const char* filename, ALLOWED_INPUT_FILE_TYPES allowed_input_filetype, ALLOWED_INPUT_BASES allow_bases, ALLOWED_INPUT_CASE allow_lowercase, int fastq_ascii_quality_offset) { if (pFASTX==NULL) errx(1,"Internal error: pFASTX==NULL (%s:%d)", __FILE__,__LINE__); memset(pFASTX, 0, sizeof(FASTX)); if (strncmp(filename,"-",1)==0) { pFASTX->input = stdin; } else { pFASTX->input = fopen(filename, "r"); if (pFASTX->input==NULL) err(1, "failed to open input file '%s'", filename); } strncpy(pFASTX->input_file_name, filename, sizeof(pFASTX->input_file_name)-1); pFASTX->allow_input_filetype = allowed_input_filetype; pFASTX->allow_lowercase = allow_lowercase; pFASTX->allow_N = ((allow_bases & ALLOW_N)!=0) ; pFASTX->allow_U = ((allow_bases & ALLOW_U)!=0) ; pFASTX->fastq_ascii_quality_offset = fastq_ascii_quality_offset ; create_lookup_table(pFASTX); detect_input_format(pFASTX); } int open_output_file(const char* filename) { int fd ; if (strncmp(filename,"-", 6)==0) { fd = STDOUT_FILENO; } else { fd = open(filename, O_CREAT | O_WRONLY | O_TRUNC, 0666 ); if (fd==-1) err(1, "Failed to create output file (%s)", filename); } return fd; } int open_output_compressor(FASTX __attribute__((unused)) *pFASTX, const char* filename) { int fd; pid_t child_pid; int parent_pipe[2]; if (pipe(parent_pipe)!=0) err(1,"pipe (for gzip) failed"); child_pid = fork(); if (child_pid>0) { /* The parent process */ fd = parent_pipe[1]; close(parent_pipe[0]); return fd; } /* The child process */ //the compressor's STDIN is the pipe from the parent dup2(parent_pipe[0], STDIN_FILENO); close(parent_pipe[1]); //the compressor's STDOUT is the output file //(which can be the parent's STDOUT, too) fd = open_output_file(filename); dup2(fd, STDOUT_FILENO); //Run GZIP execlp("gzip","gzip",(char*)NULL); //Should never get here... err(1,"execlp(gzip) failed"); return 0; //just to please the compiler } void fastx_init_writer(FASTX *pFASTX, const char *filename, OUTPUT_FILE_TYPE output_type, int compress_output) { int fd; if (pFASTX==NULL) errx(1,"Internal error: pFASTX==NULL (%s:%d)", __FILE__,__LINE__); if (pFASTX->input==NULL) errx(1,"Internal error: pFASTX not initialized (%s:%d)", __FILE__, __LINE__); pFASTX->compress_output = compress_output; if (pFASTX->compress_output) fd = open_output_compressor(pFASTX, filename); else fd = open_output_file(filename); pFASTX->output = fdopen(fd,"w"); if (pFASTX->output==NULL) err(1,"fdopen failed"); switch(output_type) { case OUTPUT_FASTA: pFASTX->write_fastq = 0 ; pFASTX->output_sequence_id_prefix = '>'; break ; case OUTPUT_FASTQ_ASCII_QUAL: if (! pFASTX->read_fastq) errx(1,"Can't output FASTQ when input is FASTA."); pFASTX->write_fastq = 1; pFASTX->write_fastq_ascii = 1; pFASTX->output_sequence_id_prefix = '@'; break ; case OUTPUT_FASTQ_NUMERIC_QUAL: if (! pFASTX->read_fastq) errx(1,"Can't output FASTQ when input is FASTA."); pFASTX->write_fastq = 1; pFASTX->write_fastq_ascii = 0; pFASTX->output_sequence_id_prefix = '@'; break ; case OUTPUT_SAME_AS_INPUT: pFASTX->write_fastq = pFASTX->read_fastq; //Assume we're writing ASCII format, pFASTX->write_fastq_ascii = 1 ; //But set this flag and the real format will be determined //when we actually read the FASTQ record pFASTX->copy_input_fastq_format_to_output = 1; pFASTX->output_sequence_id_prefix = (pFASTX->write_fastq) ? '@' : '>'; break; default: errx(1, __FILE__ ":%d: Unknown output_type (%d)", __LINE__, output_type ) ; } } int fastx_read_next_record(FASTX *pFASTX) { char temp_qual[MAX_SEQ_LINE_LENGTH+1]; temp_qual[MAX_SEQ_LINE_LENGTH] = 0; if (pFASTX==NULL) errx(1,"Internal error: pFASTX==NULL (%s:%d)", __FILE__,__LINE__); pFASTX->input_line_number++; if (fgets(pFASTX->dummy_read_id_buffer, MAX_SEQ_LINE_LENGTH, pFASTX->input) == NULL) return 0; //assume end-of-file, if we couldn't read the first line of the foursome chomp(pFASTX->name); // quick sanity check - // FASTQ files should start with '@' in the identifier line // FASTA files should start with '>' in the identifier line if ( pFASTX->read_fastq && (pFASTX->input_sequence_id_prefix[0] != '@' ) ) errx(1,"Invalid input: expecting FASTQ prefix character '@' on line %lld. Is this a valid FASTQ file?\n", pFASTX->input_line_number) ; if ( !pFASTX->read_fastq && (pFASTX->input_sequence_id_prefix[0] != '>') ) { //Extra friendly check, warn users if they fed us a multiline FASTA file if ( validate_nucleotides_string ( pFASTX->allowed_nucleotides, pFASTX->input_sequence_id_prefix ) ) errx(1,"Invalid input: This looks like a multi-line FASTA file.\n" \ "Line %lld contains a nucleotides string instead of a '>' prefix.\n" \ "FASTX-Toolkit can't handle multi-line FASTA files.\n" \ "Please use the FASTA-Formatter tool to convert this file into a single-line FASTA.\n", pFASTX->input_line_number) ; // Otherwise, assume it's just bad input file errx(1,"Invalid input: expecting FASTA prefix character '>' on line %lld. Is this a valid FASTA file?\n", pFASTX->input_line_number) ; } //for the rest of the lines, if they don't appear, it's an error pFASTX->input_line_number++; if (fgets(pFASTX->nucleotides, MAX_SEQ_LINE_LENGTH, pFASTX->input) == NULL) errx(1,"Failed to read complete record, missing 2nd line (nucleotides), on line %lld\n", pFASTX->input_line_number); chomp(pFASTX->nucleotides); /* Disallow empty nucleotide strings */ if (strlen(pFASTX->nucleotides)==0) errx(1,"found empty nucleotide sequence on line %lld\n",pFASTX->input_line_number); if (!validate_nucleotides_string(pFASTX->allowed_nucleotides, pFASTX->nucleotides)) errx(1,"found invalid nucleotide sequence (%s) on line %lld\n", pFASTX->nucleotides,pFASTX->input_line_number); if (pFASTX->read_fastq) { pFASTX->input_line_number++; if (fgets(pFASTX->dummy_read_id2_buffer, MAX_SEQ_LINE_LENGTH, pFASTX->input) == NULL) errx(1,"Failed to read complete record, missing 3rd line (name-2), on line %lld\n", pFASTX->input_line_number); pFASTX->input_line_number++; if (fgets(temp_qual, sizeof(temp_qual), pFASTX->input) == NULL) errx(1,"Failed to read complete record, missing 4th line (quality), on line %lld\n", pFASTX->input_line_number); chomp(pFASTX->name2); chomp(temp_qual); if (strlen(temp_qual) == strlen(pFASTX->nucleotides)) { //Assume this is an ASCII quality score line, convert it to values convert_ascii_quality_score_line ( temp_qual, pFASTX ) ; pFASTX->read_fastq_ascii = 1 ; } else { //Assume this is a numeric quality score line, convert it to values convert_numeric_quality_score_line ( temp_qual, pFASTX ) ; pFASTX->read_fastq_ascii = 0 ; } //Copy the input format to the output format flag if (pFASTX->copy_input_fastq_format_to_output) { pFASTX->write_fastq_ascii = pFASTX->read_fastq_ascii; } } pFASTX->num_input_sequences++; pFASTX->num_input_reads += get_reads_count(pFASTX); return 1; } static void write_ascii_qual_string(FASTX *pFASTX, int length) { int i; int rc; for (i=0; ioutput, "%c", pFASTX->quality[i] + pFASTX->fastq_ascii_quality_offset ) ; if (rc<=0) err(1,"writing quality scores failed"); } rc = fprintf(pFASTX->output, "\n"); if (rc<=0) err(1,"writing quality scores failed"); } static void write_numeric_qual_string(FASTX *pFASTX, int length) { int i; int rc; for (i=0; ioutput, "%d", pFASTX->quality[i] ) ; if (rc<=0) err(1,"writing quality scores failed"); if (ioutput," "); if (rc<=0) err(1,"writing quality scores failed"); } } rc = fprintf(pFASTX->output, "\n"); if (rc<=0) err(1,"writing quality scores failed"); } void fastx_write_record(FASTX *pFASTX) { int len; int rc; if (pFASTX==NULL) errx(1,"Internal error: pFASTX==NULL (%s:%d)", __FILE__,__LINE__); rc = fprintf(pFASTX->output, "%c%s\n", pFASTX->output_sequence_id_prefix, pFASTX->name ) ; if (rc<=0) err(1,"writing sequence identifier failed"); rc = fprintf(pFASTX->output, "%s\n", pFASTX->nucleotides); if (rc<=0) err(1,"writing nucleotides failed"); if (pFASTX->write_fastq) { rc = fprintf(pFASTX->output, "+%s\n", pFASTX->name2 ) ; if (rc<=0) err(1,"writing 2nd sequence identifier failed"); len = strlen(pFASTX->nucleotides); if (pFASTX->write_fastq_ascii) write_ascii_qual_string(pFASTX, len); else write_numeric_qual_string(pFASTX, len); } pFASTX->num_output_sequences++; pFASTX->num_output_reads += get_reads_count(pFASTX); } int get_reads_count(const FASTX *pFASTX) { char *dash = NULL ; //FASTQ files are never collapsed (at least not in Gordon's Galaxy) if (pFASTX->read_fastq) return 1; dash = strchr(pFASTX->name,'-'); // minus character wasn't found- // this sequence is most probably not collapsed if (dash==NULL) return 1; int count = atoi(dash+1); if (count>0) return count; return 1; } size_t num_input_sequences(const FASTX *pFASTX) { return pFASTX->num_input_sequences; } size_t num_input_reads(const FASTX *pFASTX) { return pFASTX->num_input_reads; } size_t num_output_sequences(const FASTX *pFASTX) { return pFASTX->num_output_sequences; } size_t num_output_reads(const FASTX *pFASTX) { return pFASTX->num_output_reads; } fastx_toolkit-0.0.14/src/libfastx/fastx.h000066400000000000000000000111131226234573700203770ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #ifndef __FASTX_HEADER__ #define __FASTX_HEADER__ #ifdef __cplusplus extern "C" { #endif /* for PATH_MAX */ #include #define MIN_QUALITY_VALUE (-50) #define MAX_QUALITY_VALUE 50 #define QUALITY_VALUES_RANGE (MAX_QUALITY_VALUE-MIN_QUALITY_VALUE) #ifndef MAX_SEQ_LINE_LENGTH #define MAX_SEQ_LINE_LENGTH (25000) #endif typedef enum { FASTA_ONLY=0, FASTA_OR_FASTQ=1, FASTQ_ONLY=2 } ALLOWED_INPUT_FILE_TYPES; typedef enum { DISALLOW_N=0, ALLOW_N=1, ALLOW_U=2 } ALLOWED_INPUT_BASES; typedef enum { REQUIRE_UPPERCASE=0, ALLOW_LOWERCASE=1 } ALLOWED_INPUT_CASE; typedef enum { OUTPUT_FASTA=0, OUTPUT_FASTQ_ASCII_QUAL=1, OUTPUT_FASTQ_NUMERIC_QUAL=2, OUTPUT_SAME_AS_INPUT=3 } OUTPUT_FILE_TYPE; #pragma pack(1) typedef struct { /* Record data - common for FASTA/FASTQ */ union { struct { char input_sequence_id_prefix[1]; //DON'T touch this - this hack will read the entire name into the variable 'name', //leaving the prefix ('>' or '@') in 'input_sequence_id_name'. char name[MAX_SEQ_LINE_LENGTH+1]; }; char dummy_read_id_buffer[MAX_SEQ_LINE_LENGTH+2]; }; char nucleotides[MAX_SEQ_LINE_LENGTH+1]; /* Record data - only for FASTQ */ union { struct { char input_name2_prefix[1]; //same hack as 'input_sequence_id_prefix' char name2[MAX_SEQ_LINE_LENGTH+1]; }; char dummy_read_id2_buffer[MAX_SEQ_LINE_LENGTH+2]; }; int quality[MAX_SEQ_LINE_LENGTH+1]; //note: this is NOT ascii values, but numerical values // numeric quality scores and ASCII quality scores // are automatically converted to numbers (-15 to 93) /* Configuration */ int allow_input_filetype; // 0 = Allow only FASTA int allow_N; // 1 = N is valid nucleotide, 0 = only A/G/C/T are valid int allow_U; // 1 = U is a valid nucleotide int allow_lowercase; int read_fastq; // 1 = Input is FASTQ (only if allow_input_fastq==1) int read_fastq_ascii; // 1 = Input is FASTQ with ASCII quality scores (0 = with numeric quality scores) int write_fastq; // 0 = Write only FASTA (regardless of input type) int write_fastq_ascii; // 1 = Write ASCII quality scores, 0 = write numeric quality scores int compress_output; // 1 = pass output through GZIP int copy_input_fastq_format_to_output ; // 1 = copy 'read_fastq_ascii' to 'write_fastq_ascii' // so that the output format is the same as the input int fastq_ascii_quality_offset ; // When reading FASTQ with ASCII quality values, subtract this value to get 'real' numeric quality score; /* Internal data */ int allowed_nucleotides[256]; //quick lookup table for valid input char output_sequence_id_prefix; // '>' or '@', depending on the requested output type char input_file_name[PATH_MAX]; //in linux, PATH_MAX is defined in unsigned long long input_line_number; char output_file_name[PATH_MAX]; //in linux, PATH_MAX is defined in size_t num_input_sequences; size_t num_output_sequences; size_t num_input_reads; size_t num_output_reads; FILE* input; FILE* output; } FASTX ; void fastx_init_reader(FASTX *pFASTX, const char* filename, ALLOWED_INPUT_FILE_TYPES allowed_input_filetype, ALLOWED_INPUT_BASES allow_bases, ALLOWED_INPUT_CASE allow_lowercase, int fastq_ascii_quality_offset); // If the sequence identifier is collapsed (= "N-N") returns the reads_count, // otherwise, returns 1 int get_reads_count(const FASTX *pFASTX); void fastx_init_writer(FASTX *pFASTX, const char* filename, OUTPUT_FILE_TYPE output_type, int compress_output); int fastx_read_next_record(FASTX *pFASTX); void fastx_write_record(FASTX *pFASTX); size_t num_input_sequences(const FASTX *pFASTX); size_t num_input_reads(const FASTX *pFASTX); size_t num_output_sequences(const FASTX *pFASTX); size_t num_output_reads(const FASTX *pFASTX); #ifdef __cplusplus } #endif #endif fastx_toolkit-0.0.14/src/libfastx/fastx_args.c000066400000000000000000000057611226234573700214220ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #include #include #include #include #include #include #include #include "fastx_args.h" /* * Each program should specify its own usage string */ extern char* usage; /* * globals.. yuck * * some day this will be a stand alone class */ const char* input_filename = "-"; const char* output_filename = "-"; int verbose = 0; int compress_output = 0 ; int fastq_ascii_quality_offset = 33 ; FILE* report_file; int get_fastq_ascii_quality_offset() { return fastq_ascii_quality_offset; } const char* get_input_filename() { return input_filename; } const char* get_output_filename() { return output_filename; } int verbose_flag() { return verbose; } int compress_output_flag() { return compress_output ; } FILE* get_report_file() { return report_file; } int fastx_parse_cmdline( int argc, char* argv[], const char* program_options, parse_argument_func program_parse_args ) { int opt; char combined_options_string[100]; strcpy(combined_options_string, "Q:zhvi:o:"); strcat(combined_options_string, program_options); report_file = stderr ; //since the default output is STDOUT, the report goes by default to STDERR while ( (opt = getopt(argc, argv, combined_options_string) ) != -1 ) { // Parse the program's custom options if ( strchr(program_options, opt) != NULL ) { if (!program_parse_args(optind, opt, optarg)) return 0; continue; } //Parse the default options switch(opt) { case 'h': printf("%s", usage); exit(1); case 'v': verbose = 1 ; break ; case 'z': compress_output = 1 ; break ; case 'i': if (optarg==NULL) errx(1,"[-i] option requires FILENAME argument"); input_filename = optarg; break; case 'o': if (optarg==NULL) errx(1,"[-o] option requires FILENAME argument"); output_filename = optarg; //The user specified a specific output file, so the report can go to STDOUT report_file = stdout; break; case 'Q': if (optarg==NULL) errx(1,"[-Q] option requires VALUE argument"); fastq_ascii_quality_offset = atoi(optarg); break; default: printf("use '-h' for usage information.\n"); exit(1); break; } } return 1; } fastx_toolkit-0.0.14/src/libfastx/fastx_args.h000066400000000000000000000024761226234573700214270ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #ifndef __FASTX_ARGS__ #define __FASTX_ARGS__ #ifdef __cplusplus extern "C" { #endif //One day this would all be OO :-) const char* get_input_filename(); const char* get_output_filename(); int verbose_flag(); int compress_output_flag(); int get_fastq_ascii_quality_offset(); FILE* get_report_file(); typedef int (*parse_argument_func)(int optind, int optc, char* optarg) ; int fastx_parse_cmdline( int argc, char* argv[], const char* program_options, parse_argument_func program_parse_arg ) ; #ifdef __cplusplus } #endif #endif fastx_toolkit-0.0.14/src/libfastx/sequence_alignment.cpp000066400000000000000000000504741226234573700234700ustar00rootroot00000000000000#include #include #include #include #include #include #include #include #include #include "sequence_alignment.h" using namespace std; void SequenceAlignmentResults::print(std::ostream& strm) const { size_t delta; size_t index; strm << "Query-Alingment = " << query_alignment << endl ; strm << "target-Alingment= " << target_alignment << endl ; strm << (alignment_found ? "Alignment Found" : "Alignment NOT found") << endl; strm << "Score = " << score << " (" << matches << " matches, " << neutral_matches << " neutral-matches, " << mismatches << " mismatches, " << gaps << " gaps) " << std::endl ; strm << "Query = " << query_sequence << "(qsize " << query_size << " qstart " << query_start << " qend " << query_end << std::endl ; strm << "Target= " << target_sequence << "(tsize " << target_size << " tstart " << target_start << " tend " << target_end << std::endl ; strm << endl; delta = max(target_start, query_start); //Spaces before the query string if ( delta - query_start > 0 ) strm << std::string( delta - query_start-1, ' ') ; //Un-Aligned query part (prefix) if ( query_start > 0 ) strm << query_sequence.substr(0, query_start-1) ; //Aligned query part strm << "(" << query_alignment << ")"; //Un-Aligned query part (suffix) if ( query_end < query_sequence.length() ) strm << query_sequence.substr( query_end+1 ) ; strm << std::endl ; //Alignment bars if ( delta > 0 ) strm << std::string( delta-1, ' ') ; strm << "(" ; for (index=0; index 0 ) strm << std::string( delta - target_start, ' ') ; //Un-Aligned target part (prefix) if ( target_start > 0 ) strm << target_sequence.substr(0, target_start-1); //Aligned target part strm << "(" << target_alignment << ")"; //Un-Aligned target part (suffix) if ( target_end < target_sequence.length() ) strm << target_sequence.substr( target_end+1 ); strm << std::endl; } SequenceAlignment::SequenceAlignment ( ) : _gap_panelty(-5), _match_panelty(1), _mismatch_panelty(-1), _neutral_panelty(0.1) { } void SequenceAlignment::set_sequences(const std::string& _query, const std::string& _target) { _query_sequence = _query ; _target_sequence = _target ; } void SequenceAlignment::reset_alignment_results() { _alignment_results = SequenceAlignmentResults() ; // //Reset the results _alignment_results.query_sequence = query_sequence() ; _alignment_results.target_sequence = target_sequence() ; } const SequenceAlignmentResults& SequenceAlignment::align ( const std::string& query, const std::string& target ) { set_sequences ( query, target ) ; reset_alignment_results(); resize_matrix ( query_sequence().length(), target_sequence().length() ) ; populate_match_matrix(); reset_matrix( matrix_width(), matrix_height() ); populate_matrix(); find_optimal_alignment(); post_process(); return _alignment_results; } void SequenceAlignment::resize_matrix(size_t width, size_t height) { size_t i; if ( matrix_width() >= width && matrix_height() >= height ) return ; query_border.resize ( width ) ; target_border.resize ( height ) ; score_matrix.resize ( width ); for (i=0;i0) ? score : 0 ; //NOTE // not sure ">=" is strictly correct SW (might be just ">") if ( score > highest_score ) { highest_scored_query_index = query_index ; highest_scored_target_index = target_index ; highest_score = score ; } } } } void LocalSequenceAlignment::find_optimal_alignment ( ) { size_t query_index = highest_scored_query_index ; size_t target_index = highest_scored_target_index; _alignment_results.query_end = query_index-1 ; _alignment_results.target_end= target_index-1 ; _alignment_results.score = score_matrix[query_index][target_index]; _alignment_results.matches = 0 ; _alignment_results.mismatches = 0 ; while ( query_index > 0 || target_index > 0 ) { if ( score_matrix[query_index][target_index]==0) break ; //go "left" in the matrix if ( query_index>0 && score_matrix[query_index][target_index] == score_matrix[query_index-1][target_index] + gap_panelty() ) { _alignment_results.target_alignment += "-" ; _alignment_results.query_alignment += query_sequence()[query_index-1] ; query_index--; } else //go "up-left" in the matrix if ( query_index>0 && target_index>0 && score_matrix[query_index][target_index] == score_matrix[query_index-1][target_index-1] + match_score(query_index, target_index) ) { _alignment_results.target_alignment += target_sequence()[target_index-1]; _alignment_results.query_alignment += query_sequence()[query_index-1] ; (query_sequence()[query_index-1] == target_sequence()[target_index-1]) ? (++_alignment_results.matches) : (++_alignment_results.mismatches) ; query_index--; target_index--; } else //go "up" in the matrix { _alignment_results.target_alignment += target_sequence()[target_index-1]; _alignment_results.query_alignment += "-" ; target_index--; } } _alignment_results.query_start = query_index ; _alignment_results.target_start= target_index ; _alignment_results.query_size = query_sequence().length(); _alignment_results.target_size= target_sequence().length(); std::reverse(_alignment_results.target_alignment.begin(), _alignment_results.target_alignment.end()); std::reverse(_alignment_results.query_alignment.begin(), _alignment_results.query_alignment.end()); } #endif void HalfLocalSequenceAlignment::set_sequences(const std::string& _query, const std::string& _target) { //_query_sequence = _query + std::string( _target.length(), 'N' ); //_target_sequence = std::string( _query.length(), 'N' ) + _target; _query_sequence = _query ; _target_sequence = _target ; } void HalfLocalSequenceAlignment::reset_matrix( size_t width, size_t height ) { size_t x,y ; highest_scored_query_index = 0 ; highest_scored_target_index = 0 ; for (x=0; x3 && target_index-3 > query_index ) { left_score = -100000 ; } //printf("query_index=%d, target_index=%d, upscore=%f, left_score=%f, upleft_score=%f\n", // query_index, target_index, up_score,left_score,upleft_score ); score_type score = -100000000 ; if ( upleft_score > score ) { score = upleft_score ; origin = FROM_UPPER_LEFT; } if ( up_score > score ) { score = up_score ; origin = FROM_UPPER ; } if ( left_score > score ) { score = left_score ; origin = FROM_LEFT ; } //printf("query_index=%d, target_index=%d, score=%f origin=%d\n", // query_index, target_index, score, origin ); /*if (score<0) { score = 0 ; origin = FROM_NOWHERE ; }*/ score_matrix[query_index][target_index] = score ; origin_matrix[query_index][target_index] = origin ; //NOTE // not sure ">=" is strictly correct SW (might be just ">") if ( score > highest_score ) { highest_scored_query_index = query_index ; highest_scored_target_index = target_index ; highest_score = score ; } } } } bool HalfLocalSequenceAlignment::starting_point_close_to_end_of_sequences(const size_t query_index, const size_t target_index) const { if ( (size_t)query_index >= query_sequence().length() - 2 || (size_t)target_index >= target_sequence().length() - 2 ) { /* We've reach either the end of the Adapter * (and the adapter is shorter than the query) * Or the end of the query * (and the adapter covers up to the end of the query, and then continues on) * * So we can safely start the alignment from this point */ return true; } else { /* The adapter is not covering the query until the end. */ return false; } } #undef DEBUG_STARTING_POINT void HalfLocalSequenceAlignment::find_alignment_starting_point(ssize_t &new_query_index, ssize_t &new_target_index) const { /* * Force the alignment to start from the end of the query, * find the best score at the end of the query * * Try (desperately) to find a match that starts at the end of the query or the end of the target/adapter) */ score_type max_score = score( matrix_width()-1, matrix_height()-1 ) ; for ( size_t q_index = 0 ; q_index < matrix_width(); q_index++ ) { for ( size_t t_index = matrix_height()-2 ; t_index < matrix_height(); t_index++ ) { if ( origin ( q_index, t_index ) > 0 && safe_score ( q_index, t_index ) > max_score ) { max_score = safe_score ( q_index, t_index ) ; #ifdef DEBUG_STARTING_POINT printf("Found new max score = %f at %d,%d\n", max_score, q_index, t_index ) ; #endif new_target_index = t_index ; new_query_index = q_index ; } } } for ( size_t q_index = matrix_width()-2 ; q_index < matrix_width(); q_index++ ) { for ( size_t t_index = 0 ; t_index < matrix_height(); t_index++ ) { if ( origin ( q_index, t_index ) > 0 && safe_score ( q_index, t_index ) > max_score ) { max_score = safe_score ( q_index, t_index ) ; #ifdef DEBUG_STARTING_POINT printf("Found new max score = %f at %d,%d\n", max_score, q_index, t_index ) ; #endif new_target_index = t_index ; new_query_index = q_index ; } } } #ifdef DEBUG_STARTING_POINT printf("Forcing alignment from query_index=%d, target_index=%d, score=%f, origin=%d\n", new_query_index, new_target_index, score ( new_query_index, new_target_index ), origin ( new_query_index, new_target_index ) ); #endif } #undef DEBUG_FIND_OPTIMAL_ALIGNMENT SequenceAlignmentResults HalfLocalSequenceAlignment::find_optimal_alignment_from_point ( const size_t query_start, const size_t target_start ) const { SequenceAlignmentResults results; results.query_sequence = query_sequence(); results.target_sequence= target_sequence(); ssize_t query_index = query_start; ssize_t target_index = target_start ; results.query_end = query_index ; results.target_end= target_index ; #ifdef DEBUG_FIND_OPTIMAL_ALIGNMENT printf ( "backtrace starting from (qindex=%d, tindex=%d, score=%f)\n", query_index, target_index, score_matrix[query_index][target_index]) ; #endif while ( query_index >= 0 && target_index >= 0 ) { const char q_nuc = query_nucleotide(query_index); const char t_nuc = target_nucleotide(target_index); const DIRECTION current_origin = origin(query_index, target_index); const char current_match = match ( query_index, target_index ) ; #ifdef DEBUG_FIND_OPTIMAL_ALIGNMENT const score_type current_score = score(query_index, target_index); printf("query_index=%d target_index=%d query=%c target=%c score_matrix=%3.1f origin=%d accumulated_score = %3.2f\n", query_index, target_index, q_nuc, t_nuc, current_score, current_origin, results.score) ; #endif results.query_start = query_index ; results.target_start= target_index ; switch ( current_origin ) { case FROM_LEFT: results.target_alignment += "-" ; results.query_alignment += q_nuc ; results.gaps++; results.score += gap_panelty(); query_index--; break ; case FROM_UPPER_LEFT: results.target_alignment += t_nuc; results.query_alignment += q_nuc ; switch ( current_match ) { case 'N': results.neutral_matches++ ; results.score += neutral_panelty(); break ; case 'M': results.matches++; results.score += match_panelty(); break; case 'x': results.mismatches++; results.score += mismatch_panelty(); break ; default: errx(1,"Internal error: unknown match type (%c) at query_index=%zu, target_index=%zu\n", current_match, query_index, target_index ) ; } query_index--; target_index--; break ; case FROM_UPPER: results.target_alignment += t_nuc ; results.query_alignment += "-" ; results.gaps++; results.score += gap_panelty(); target_index--; break; case FROM_NOWHERE: default: print_matrix(); printf("Invalid origin (%d) at query_index=%zu, target_index=%zu\n", current_origin, query_index, target_index ) ; printf("Query = %s\n", query_sequence().c_str()); printf("Target= %s\n", target_sequence().c_str()); exit(1); } } results.query_size = query_sequence().length(); results.target_size= target_sequence().length(); std::reverse(results.target_alignment.begin(),results.target_alignment.end()); std::reverse(results.query_alignment.begin(), results.query_alignment.end()); return results; } void HalfLocalSequenceAlignment::find_optimal_alignment ( ) { SequenceAlignmentResults results ; //Try to find a good alignment, //starting from the highest score cell. results = find_optimal_alignment_from_point ( highest_scored_query_index, highest_scored_target_index ) ; //Some heuristics: //If the adapter matched 7 nucleotides anywhere in the query //without mismatches/gaps, accept it. if ( results.matches >= 7 && results.mismatches == 0 && results.gaps == 0 ) { _alignment_results = results ; return ; } if ( starting_point_close_to_end_of_sequences ( highest_scored_query_index, highest_scored_target_index ) ) { //We're already very close to the end of the target or query, //can't improve much else, so return what we've got. _alignment_results = results ; return ; } //More heuristics: /* The adapter is not covering the query until the end. * Force the alignment to start from the end of the query, * find the best score at the end of the query * * Try (desperately) to find a match that starts at the end of the query or the end of the target/adapter) */ ssize_t query_index = highest_scored_query_index ; ssize_t target_index = highest_scored_target_index; find_alignment_starting_point ( query_index, target_index ) ; _alignment_results = results ; } void HalfLocalSequenceAlignment::post_process() { #if 0 //Removes the Ns which were added in 'set_sequences' //And adjust the results values accordingly //return ; //_query_sequence.erase ( _query_sequence.find_last_not_of('N') + 1) ; //_target_sequence.erase ( 0, _target_sequence.find_first_not_of('N') ) ; _alignment_results.query_sequence.erase ( _query_sequence.find_last_not_of('N') + 1) ; _alignment_results.target_sequence.erase ( 0, _target_sequence.find_first_not_of('N') ) ; _alignment_results.query_size = _alignment_results.query_sequence.length(); _alignment_results.target_size = _alignment_results.target_sequence.length(); size_t query_n_position = _alignment_results.query_alignment.find_last_not_of('N') ; int query_n_count; if ( query_n_position != string::npos ) query_n_count = _alignment_results.query_alignment.length() - query_n_position ; else query_n_count = 0 ; int target_n_count = _alignment_results.target_alignment.find_first_not_of('N') ; if (query_n_position != string::npos ) _alignment_results.query_alignment.erase( query_n_position ) ; _alignment_results.target_alignment.erase( 0,target_n_count ) ; //Update Results strucure _alignment_results.query_start+= target_n_count ; _alignment_results.query_end -= query_n_count ; _alignment_results.target_start = 0; _alignment_results.target_end = _alignment_results.query_end - _alignment_results.query_start ; _alignment_results.query_alignment.erase ( 0, _alignment_results.query_start ) ; _alignment_results.target_alignment.erase ( _alignment_results.target_end+1 ) ; //Update match/mismatch/gap counts _alignment_results.matches = 0 ; _alignment_results.mismatches = 0 ; _alignment_results.gaps = 0 ; for (size_t index=0; index<_alignment_results.query_alignment.length(); index++) { char q = _alignment_results.query_alignment[index]; char t = _alignment_results.target_alignment[index]; if ( q == '-' || t=='-' ) { _alignment_results.gaps ++ ; } else { if ( q== t ) _alignment_results.matches++; else _alignment_results.mismatches++; } } #endif } fastx_toolkit-0.0.14/src/libfastx/sequence_alignment.h000066400000000000000000000153251226234573700231310ustar00rootroot00000000000000/* FASTX-toolkit - FASTA/FASTQ preprocessing tools. Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see . */ #ifndef __SEQUENCE_ALIGNMENT_HEADER__ #define __SEQUENCE_ALIGNMENT_HEADER__ #include struct SequenceAlignmentResults { int alignment_found ; size_t query_size ; size_t query_start ; size_t query_end ; size_t target_size ; size_t target_start ; size_t target_end ; size_t gaps; size_t neutral_matches ; size_t matches ; size_t mismatches ; float score ; std::string query_alignment ; std::string target_alignment ; std::string query_sequence ; std::string target_sequence ; SequenceAlignmentResults() : alignment_found(false), query_size(0), query_start(0), query_end(0), target_size(0), target_start(0), target_end(0), gaps(0), neutral_matches(0), matches(0), mismatches(0), score(0) { } void print( std::ostream& ostrm = std::cout ) const; virtual ~SequenceAlignmentResults() {} } ; class SequenceAlignment { protected: typedef float score_type; typedef enum { FROM_UPPER = 1, FROM_LEFT = 2, FROM_UPPER_LEFT = 3, FROM_NOWHERE = 4 //STOP_MARKER = 5 } DIRECTION ; std::vector < score_type > query_border ; std::vector < score_type > target_border ; std::vector< std::vector< score_type > > score_matrix ; std::vector< std::vector< DIRECTION > > origin_matrix ; std::vector< std::vector< char > > match_matrix ; score_type _gap_panelty ; score_type _match_panelty ; score_type _mismatch_panelty ; score_type _neutral_panelty ; SequenceAlignmentResults _alignment_results ; std::string _query_sequence; std::string _target_sequence; public: SequenceAlignment ( ) ; virtual ~SequenceAlignment() {} size_t matrix_width() const { return score_matrix.size(); } size_t matrix_height() const { return score_matrix[0].size(); } score_type gap_panelty() const { return _gap_panelty ; } score_type match_panelty() const { return _match_panelty ; } score_type mismatch_panelty() const { return _mismatch_panelty ; } score_type neutral_panelty() const { return _neutral_panelty ; } const std::string& query_sequence() const { return _query_sequence; } const std::string& target_sequence() const { return _target_sequence; } char query_nucleotide(size_t query_index) const { return _query_sequence[query_index] ; } char target_nucleotide(size_t target_index) const { return _target_sequence[target_index] ; } const SequenceAlignmentResults& results() const { return _alignment_results; } char match_value ( const char q, const char t ) const { if ( q=='N' || t=='N' ) return 'N' ; return ( q==t ) ? 'M' : 'x' ; } char match ( const size_t query_index, const size_t target_index) const { return match_matrix[query_index][target_index]; } DIRECTION origin ( const size_t query_index, const size_t target_index) const { return origin_matrix[query_index][target_index]; } score_type score ( const size_t query_index, const size_t target_index) const { return score_matrix[query_index][target_index]; } score_type safe_score ( const ssize_t query_index, const ssize_t target_index) const { if (query_index==-1) return target_border[target_index]; if (target_index==-1) return query_border[query_index]; return score_matrix[query_index][target_index]; } score_type nucleotide_match_score(const size_t query_index, const size_t target_index) const { char q = query_nucleotide(query_index); char t = target_nucleotide(target_index); if ( q=='N' && t=='N' ) return 0.0 ; if ( q=='N' || t=='N' ) return neutral_panelty() ; return ( q==t ) ? match_panelty() : mismatch_panelty() ; } void print_matrix(std::ostream& strm = std::cout) const; #if 0 score_type calculate_alignment_score(const size_t query_index, const size_t target_index) const { score_type score = -100000000; /* score_type //Score from the left-cell if ( query_index > 0 ) if ( (score(query_index-1,target_index) + gap_panelty()) > score) score = score_matrix[query_index-1][target_index] + gap_panelty(); //Score from the upper-cell if ( target_index > 0 ) if ((score_matrix[query_index][target_index-1] + gap_panelty()) > score) score = score_matrix[query_index][target_index-1] + gap_panelty(); //Score from the upper-left-cell if ( target_index>0 && query_index> 0) { if (score_matrix[query_index-1][target_index-1] + match_score(query_index,target_index) > score) score = score_matrix[query_index-1][target_index-1] + match_score(query_index,target_index) ; }*/ return score; } #endif const SequenceAlignmentResults& align ( const std::string& query, const std::string& target ) ; protected: void resize_matrix(size_t width, size_t height); void populate_match_matrix(); virtual void reset_alignment_results() ; virtual void set_sequences ( const std::string& _query, const std::string &target ) ; virtual void reset_matrix( size_t width, size_t height ) = 0 ; virtual void populate_matrix ( ) = 0; virtual void find_optimal_alignment ( ) = 0 ; virtual void post_process() ; } ; #if 0 class LocalSequenceAlignment : public SequenceAlignment { protected: size_t highest_scored_query_index ; size_t highest_scored_target_index ; public: virtual void reset_matrix( size_t width, size_t height ) ; virtual void populate_matrix ( ) ; virtual void find_optimal_alignment ( ) ; }; #endif class HalfLocalSequenceAlignment : public SequenceAlignment { protected: size_t highest_scored_query_index ; size_t highest_scored_target_index ; public: virtual void set_sequences ( const std::string& _query, const std::string &target ) ; virtual void reset_matrix( size_t width, size_t height ) ; virtual void populate_matrix ( ) ; virtual void find_optimal_alignment ( ) ; virtual void post_process() ; bool starting_point_close_to_end_of_sequences(const size_t query_index, const size_t target_index) const; void find_alignment_starting_point(ssize_t &new_query_index, ssize_t &new_target_index) const; SequenceAlignmentResults find_optimal_alignment_from_point ( const size_t query_start, const size_t target_start ) const ; }; #endif fastx_toolkit-0.0.14/src/seqalign_test/000077500000000000000000000000001226234573700201325ustar00rootroot00000000000000fastx_toolkit-0.0.14/src/seqalign_test/Makefile.am000066400000000000000000000012401226234573700221630ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. noinst_PROGRAMS = seqalign_test AM_CPPFLAGS = \ $(CC_WARNINGS) \ -I$(top_srcdir)/src/libfastx seqalign_test_SOURCES = seqalign_test.cpp seqalign_test_LDADD = ../libfastx/libfastx.a fastx_toolkit-0.0.14/src/seqalign_test/seqalign_test.cpp000066400000000000000000000005221226234573700234770ustar00rootroot00000000000000#include #include #include #include #include #include "sequence_alignment.h" int main( /*int argc, char* argv[] */) { HalfLocalSequenceAlignment lsa ; const SequenceAlignmentResults& results = lsa.align("AAAGGTTTCCC","AGGCTT" ); lsa.print_matrix(); results.print(); return 0; }