Mercurial > repos > peterjc > seq_filter_by_id
view tools/filters/seq_filter_by_id.txt @ 2:abdd608c869b draft
Uploaded v0.0.5, checked script return code for errors X copes with a FASTA entry missing an ID.
author | peterjc |
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date | Wed, 24 Apr 2013 11:34:12 -0400 |
parents | 262f08104540 |
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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. Installation ============ There are just two files to install: * seq_filter_by_id.py (the Python script) * seq_filter_by_id.xml (the Galaxy tool definition) The suggested location is in the Galaxy folder tools/filters next to the tool for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. 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="filters/sff_filter_by_id.xml" /> You will also need to install Biopython 1.54 or later. That's it. History ======= 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. Developers ========== This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools This incorporates the previously used hg branch: http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter 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/filters/seq_filter_by_id.* 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 filter/seq_filter_by_id.py filter/seq_filter_by_id.txt filter/seq_filter_by_id.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular Licence (MIT/BSD style) ======================= Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.