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Repository 'fastq_paired_unpaired'
http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
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Divide FASTQ file into paired and unpaired reads
Using the common read name suffix conventions, it divides a FASTQ file into paired reads, and orphan or single reads.

The input file should be a valid FASTQ file which has been sorted so that any partner forward+reverse reads are consecutive. The output files all preserve this sort order. Pairings are recognised based on standard name suffices.

Any reads where the forward/reverse naming suffix used is not recognised are treated as orphan reads. The tool supports the old /1 and /2 convention used by Illumina, the new Illumina convention, the .f and .r convention, and the Sanger convention (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details).
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peterjc
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Repository README files - may contain important installation or license information

Galaxy tool to divide FASTQ files into paired and unpaired reads

This tool is copyright 2010-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence).

This tool is a short Python script which divides a FASTQ file into paired reads, and single or orphan reads. You can have separate files for the forward/reverse reads, or have them interleaved in a single file.

Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even Color Space should all work equally well).

This tool is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired

Automated Installation

This should be straightforward, Galaxy should automatically download and install the tool from the Galaxy Tool Shed, and run the unit tests

Manual Installation

There are just two files to install:

  • fastq_paired_unpaired.py (the Python script)
  • fastq_paired_unpaired.xml (the Galaxy tool definition)

The suggested location is in the Galaxy folder tools/fastq next to other FASTQ tools provided with Galaxy.

You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. One suggested location is next to the fastq_filter.xml entry. Simply add the line:

<tool file="fastq/fastq_paired_unpaired.xml" />

That's it.

History

Version Changes
v0.0.1
  • Initial version, using Biopython
v0.0.2
  • Help text; cope with multiple pairs per template
v0.0.3
  • Galaxy XML wrappers added
v0.0.4
  • Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
v0.0.5
  • Handle Illumina 1.8 style pair names
v0.0.6
  • Record script version when run from Galaxy
  • Added unit test (FASTQ file using Sanger naming)
v0.0.7
  • Link to Tool Shed added to help text and this documentation.
v0.0.8
  • Use reStructuredText for this README file.
  • Adopt standard MIT License.
  • Updated citation information (Cock et al. 2013).

Developers

This script and other tools for filtering FASTA, FASTQ and SFF files were initially developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter

Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:

$ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq

Check this worked:

$ tar -tzf fastq_paired_unpaired.tar.gz
tools/fastq/fastq_paired_unpaired.py
tools/fastq/fastq_paired_unpaired.rst
tools/fastq/fastq_paired_unpaired.xml
test-data/sanger-pairs-forward.fastq
test-data/sanger-pairs-interleaved.fastq
test-data/sanger-pairs-mixed.fastq
test-data/sanger-pairs-reverse.fastq
test-data/sanger-pairs-singles.fastq

Licence (MIT)

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.

Contents of this repository

Name Description Version
Divide FASTQ file into paired and unpaired reads using the read name suffices 0.0.7

Automated tool test results

Time tested: 2014-04-16 05:42:50
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Time tested: 2014-04-15 06:17:30
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Time tested: 2014-04-14 05:39:53
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Time tested: 2014-04-13 05:56:14
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)
Tool id: fastq_paired_unpaired
Tool version: fastq_paired_unpaired
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/fastq_paired_unpaired/fastq_paired_unpaired/0.0.7)

Categories
Text Manipulation
Sequence Analysis