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Repository 'seq_filter_by_id'
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/5844f6a450ed
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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.
0:5844f6a450ed
peterjc
True
267

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 by Peter Cock, SCRI, 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. 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: 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. 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://community.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.* 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 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.

Contents of this repository

Name Description Version
Filter sequences by ID from a tabular file 0.0.1

Automated tool test results

Time tested: 2014-02-13 12:59:57
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12484:b463c73f3348
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: seq_filter_by_id
Tool version: 0.0.1
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.0.1
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for seq_filter_by_id.

Categories
Fasta Manipulation
Sequence Analysis
Text Manipulation