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Repository get_orfs_or_cdss
Owner: peterjc
Synopsis: 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.
Type: unrestricted
Revision: 12:71905a6d52a7
This revision can be installed: True
Times cloned / installed: 2728

Repository README files - may contain important installation or license information

Galaxy tool to find ORFs or simple CDSs

This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. Additions copyright 2015-2016 by Eric Rasche. 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 1.65 or later (slightly older versions should be fine, but will not have the latest NCBI genetic code tables).

If you wish to run the unit tests, also move/copy the test-data/ files under Galaxy's test-data/ folder. Then:

./run_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.
v0.0.7
  • Tool definition now embeds citation information.
v0.1.0
  • Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
  • Using optparse for the Python command line API (Eric Rasche).
  • Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
v0.1.1
  • Reorder XML elements (internal change only).
v0.2.0
  • Tool now also outputs GFF3 formatted calls (Eric Rasche).
v0.2.1
  • Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
  • Added NCBI genetic code table 24, Candidate Division SR1 and Gracilibacteria.
v0.2.2
  • Use <command detect_errors="aggressive"> (internal change only).
  • Single quote command line arguments (internal change only).
v0.2.3
  • Python 3 compatible print function.

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 pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ~/.planemo.yml and that you have access rights on the Tool Shed):

$ planemo shed_update -t testtoolshed --check_diff tools/get_orfs_or_cdss/
...

or:

$ planemo shed_update -t toolshed --check_diff tools/get_orfs_or_cdss/
...

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/get_orfs_or_cdss/
...
$ tar -tzf shed_upload.tar.gz
test-data/Ssuis.fasta
test-data/get_orf_input.Suis_ORF.bed
test-data/get_orf_input.Suis_ORF.nuc.fasta
test-data/get_orf_input.Suis_ORF.prot.fasta
test-data/get_orf_input.fasta
test-data/get_orf_input.t11_bed_out.bed
test-data/get_orf_input.t11_nuc_out.fasta
test-data/get_orf_input.t11_open_bed_out.bed
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_bed_out.bed
test-data/get_orf_input.t1_nuc_out.fasta
test-data/get_orf_input.t1_prot_out.fasta
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/README.rst
tools/get_orfs_or_cdss/tool_dependencies.xml

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_9 revision 83d12e13dbbd owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)
Repository package_python_2_7 revision f761bd14343e owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision 944f93d45594 owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision c8a5c11cc921 owned by iuc (prior install required)
Repository package_gdbm_1_11 revision ed2537bccffc owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_libtool_2_4 revision 7f67694b167c owned by iuc (prior install required)

Name Version Type
biopython 1.67 package

Contents of this repository

Name Description Version Minimum Galaxy Version
e.g. to get peptides from ESTs 0.2.3 16.01

Categories
Fasta Manipulation - Tools for manipulating fasta data