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Repository 'seq_filter_by_id'
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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Filter sequences by ID
Divide a FASTA, FASTQ or SFF file in two, those sequences with or without an ID present in the specified column(s) of a tabular file.

Example uses include filtering based on search results from a tool like NCBI BLAST, TMHMM, SignalP, or a read mapper. i.e. Split your sequences according to whether or not they have a BLAST match, transmembrane domain, signal peptide, or map to the reference sequence.

This tool is a short Python script (using Biopython and Galaxy library functions). It requires Biopython to be installed.

Note this tool replaces my three previously separate tools for FASTA, FASTA and SFF filtering by ID.
3:44ab4c0f7683
peterjc
True
263

Repository README files - may contain important installation or license information

Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID

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.

This tool is a short Python script (using both the Galaxy and Biopython library functions) which divides a FASTA, FASTQ, or SFF file in two, those sequences with or without an ID present in the specified column(s) of a tabular file. Example uses include filtering based on search results from a tool like NCBI BLAST before assembly.

This tool is available from the Galaxy Tool Shed at:

See also sister tools:

Automated Installation

This should be straightforward using the Galaxy Tool Shed, which should be able to automatically install the dependency on Biopython, and then install this tool and run its unit tests.

Manual Installation

There are just two files to install to use this tool from within Galaxy:

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

The suggested location is a dedicated tools/seq_filter_by_id folder.

You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. One suggested location is in the filters section. Simply add the line:

<tool file="seq_filter_by_id/seq_filter_by_id.xml" />

If you wish to run the unit tests, also add this to tools_conf.xml.sample and move/copy the test-data files under Galaxy's test-data folder. Then:

$ ./run_functional_tests.sh -id seq_filter_by_id

You will also need to install Biopython 1.54 or later. That's it.

History

Version Changes
v0.0.1
  • Initial version, combining three separate scripts for each file format.
v0.0.4
  • Record script version when run from Galaxy.
  • Faster FASTA code which preserves the original line wrapping.
  • Basic unit test included.
v0.0.5
  • Check for errors using Python script's return code.
  • Cope with malformed FASTA entries without an identifier.
v0.0.6
  • Link to Tool Shed added to help text and this documentation.
  • Automated installation of the Biopython dependency.
  • Use reStructuredText for this README file.
  • Adopt standard MIT License.
  • Updated citation information (Cock et al. 2013).
  • Development moved to GitHub, https://github.com/peterjc/pico_galaxy
  • Renamed folder and adopted README.rst naming.

Developers

This script and related tools were initially developed on the following hg branches: http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter http://bitbucket.org/peterjc/galaxy-central/src/tools

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 seq_filter_by_id.tar.gz tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.* tools/seq_filter_by_id/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular

Check this worked:

$ tar -tzf seq_filter_by_id.tar.gz
tools/seq_filter_by_id/README.rst
tools/seq_filter_by_id/seq_filter_by_id.py
tools/seq_filter_by_id/seq_filter_by_id.xml
tools/seq_filter_by_id/repository_dependencies.xml
test-data/k12_ten_proteins.fasta
test-data/k12_hypothetical.fasta
test-data/k12_hypothetical.tabular

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.

Dependencies of this repository

Repository package_numpy_1_7 revision ef12a3a11d5b owned by iuc (prior install required)

Contents of this repository

Name Description Version
Filter sequences by ID from a tabular file 0.0.6

Automated tool test results

Time tested: 2014-04-17 05:45:47
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: seq_filter_by_id
Tool version: seq_filter_by_id
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.0.6)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
Time tested: 2014-04-16 05:40:09
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: seq_filter_by_id
Tool version: seq_filter_by_id
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.0.6)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
Time tested: 2014-04-15 06:14:46
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: seq_filter_by_id
Tool version: seq_filter_by_id
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.0.6)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
Time tested: 2014-04-14 05:37:11
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: seq_filter_by_id
Tool version: seq_filter_by_id
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.0.6)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886

Categories
Fasta Manipulation
Sequence Analysis
Text Manipulation