view tools/filters/seq_select_by_id.txt @ 2:28d52478ace9 draft

Uploaded v0.0.4 which adds a unit test.

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:

<tool file="filters/seq_select_by_id.xml" />

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.
v0.0.4 - Record script version when run from Galaxy.
       - Basic unit test included.


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://toolshed.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.* test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular

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
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.