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Repository 'seq_select_by_id'
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/50a8a6917a9c
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Select sequences by ID
Select FASTA, FASTQ, QUAL or SFF sequences using a list of IDs in a tabular file.

A column of a tabular file specifies a list of desired sequences which will be extracted from the given sequence file. The order comes from the tabular file, so in order to do this the sequence file is first indexed.

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

NOTE: I have a similar tool "Filter sequences by ID" which does a similar but less demanding job, but preserves the order of the sequence file.
1:50a8a6917a9c
peterjc
True
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Repository README files - may contain important installation or license information

Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID =============================================================== This tool is copyright 2011 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 Biopython library functions) to extract sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given by a column of a tabular file. The output order follows that of the tabular file, and if there are duplicates in the tabular file, there will be duplicates in the output sequence file. See also the sister tool to filter sequence files according to IDs from column(s) of a tabular file, where the output order follows the sequence file, and any duplicate IDs are ignored. There are just two files to install: * seq_select_by_id.py (the Python script) * seq_select_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. v0.0.3 - Ignore blank lines in input Developers ========== This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools 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_select_by_id.tar.gz tools/filters/seq_select_by_id.* Check this worked: $ tar -tzf seq_select_by_id.tar.gz filter/seq_select_by_id.py filter/seq_select_by_id.txt filter/seq_select_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
Select sequences by ID from a tabular file 0.0.3

Automated tool test results

Time tested: 2014-02-13 12:52:01
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_select_by_id
Tool version: 0.0.3
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/seq_select_by_id/seq_select_by_id/0.0.3
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for seq_select_by_id.

Categories
Fasta Manipulation
Sequence Analysis
Text Manipulation