Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository 'get_orfs_or_cdss'
http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
unrestricted
Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)
This tool is a short Python script (using Biopython library functions) to search nucleotide sequences for open reading frames (ORFs) or coding sequences (CDSs) where the first potential start codon is used.

It is intended for very simplistic gene finding in Prokaryotes and viruses, or for finding the likely CDS in an EST or mRNA sequence. It is not suitable for Eurakoytic gene prediction since it is not intro aware.

See also the EMBOSS tool 'getorf' which also has a Galaxy wrapper. This offers much of the same functionality, but is likely faster as it is written in C.
6:64e67f172188
peterjc
True
238

Repository README files - may contain important installation or license information

Galaxy tool to find ORFs or simple CDSs

This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence).

This tool is a short Python script (using Biopython library functions) to search nucleotide sequences for open reading frames (ORFs) or coding sequences (CDSs) where the first potential start codon is used. See the help text in the XML file for more information.

This tool is available from the Galaxy Tool Shed at:

See also the EMBOSS tool getorf which offers similar functionality and has also been wrapped for use within Galaxy.

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:

  • get_orfs_or_cdss.py (the Python script)
  • get_orfs_or_cdss.xml (the Galaxy tool definition)

The suggested location is in a dedicated tools/get_orfs_or_cdss 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:

<tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" />

You will also need to install Biopython 1.54 or later. If you want to run the unit tests, include this line in tools_conf.xml.sample and the sample FASTA files under the test-data directory. Then:

./run_functional_tests.sh -id get_orfs_or_cdss

That's it.

History

Version Changes
v0.0.1
  • Initial version.
v0.0.2
  • Correct labelling issue on reverse strand.
  • Use the new <stdio> settings in the XML wrappers to catch errors
v0.0.3
  • Include unit tests.
  • Record Python script version when run from Galaxy.
v0.0.4
  • Link to Tool Shed added to help text and this documentation.
v0.0.5
  • Automated intallation of the Biopython dependency.
  • Use reStructuredText for this README file.
  • Adopt standard MIT License.
  • Updated citation information (Cock et al. 2013).
  • Renamed folder and adopted README.rst naming.
v0.0.6
  • Corrected automated dependency defintion.

Developers

This script and related tools were initially developed on the following hg branch: 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 making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:

$ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/tool_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta

Check this worked:

$ tar -tzf get_orfs_or_cdss.tar.gz
tools/get_orfs_or_cdss/README.rst
tools/get_orfs_or_cdss/get_orfs_or_cdss.py
tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
tools/get_orfs_or_cdss/tool_dependencies.xml
test-data/get_orf_input.fasta
test-data/get_orf_input.Suis_ORF.nuc.fasta
test-data/get_orf_input.Suis_ORF.prot.fasta
test-data/get_orf_input.t11_nuc_out.fasta
test-data/get_orf_input.t11_open_nuc_out.fasta
test-data/get_orf_input.t11_open_prot_out.fasta
test-data/get_orf_input.t11_prot_out.fasta
test-data/get_orf_input.t1_nuc_out.fasta
test-data/get_orf_input.t1_prot_out.fasta
test-data/Ssuis.fasta

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_7 revision ef12a3a11d5b owned by iuc (prior install required)

Name Version Type
biopython 1.62 package

Contents of this repository

Name Description Version
Get open reading frames (ORFs) or coding sequences (CDSs) e.g. to get peptides from ESTs 0.0.5

Automated tool test results

Time tested: 2014-04-17 05:01:09
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
TypeNameVersion
biopython package 1.62
Installation directory
/ToolDepsMain/biopython/1.62/peterjc/get_orfs_or_cdss/64e67f172188
Time tested: 2014-04-16 04:55:19
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
TypeNameVersion
biopython package 1.62
Installation directory
/ToolDepsMain/biopython/1.62/peterjc/get_orfs_or_cdss/64e67f172188
Time tested: 2014-04-15 05:28:33
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
TypeNameVersion
biopython package 1.62
Installation directory
/ToolDepsMain/biopython/1.62/peterjc/get_orfs_or_cdss/64e67f172188
Time tested: 2014-04-14 04:52:26
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu package_biopython_1_62 biopython 3e82cbc44886
TypeNameVersion
biopython package 1.62
Installation directory
/ToolDepsMain/biopython/1.62/peterjc/get_orfs_or_cdss/64e67f172188

Categories
Fasta Manipulation