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Repository seq_filter_by_id
Owner: peterjc
Synopsis: 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.
Type: unrestricted
Revision: 5:832c1fd57852
This revision can be installed: True
Times cloned / installed: 4607

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 2010-2015 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 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: * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id See also sister tools: * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping 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:: If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: $ ./run_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. v0.0.7 - Correct automated dependency definition. v0.0.8 - Simplified XML to apply input format to output data. v0.2.0 - Can supply ID list as a text parameter (instead of in a file) - Using ``optparse`` for the Python command line API. - Advanced option to ignore paired read suffices. - Updated dependencies to use Biopython 1.64. v0.2.1 - Use Biopython instead of Galaxy for FASTQ handling. - Tool definition now embeds citation information. - Include input dataset name in output dataset names. - If white space is found in the requested tabular field then only the first word is used as the identifier (with a warning to stderr). v0.2.2 - Use the ``format_source=...`` tag. - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== 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 pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ ... or:: $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ ... $ tar -tzf shed_upload.tar.gz test-data/empty_file.dat test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular test-data/k12_hypothetical_alt.tabular test-data/k12_ten_proteins.fasta test-data/sanger-pairs-mixed.fastq test-data/sanger-pairs-names.tabular test-data/sanger-sample.fastq 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/tool_dependencies.xml 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_8 revision 13b249f6ba9a owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)

Name Version Type
biopython 1.64 package

Contents of this repository

Name Description Version Minimum Galaxy Version
from a tabular file 0.2.2 any

Categories
Fasta Manipulation - Tools for manipulating fasta data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Text Manipulation - Tools for manipulating data