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

Repository align_back_trans
Owner: peterjc
Synopsis: Thread nucleotides onto a protein alignment (back-translation)
Takes an input file of aligned protein sequences (typically FASTA or Clustal
format), and a matching file of unaligned nucleotide sequences (FASTA format,
using the same identifiers), and threads the nucleotide sequences onto the
protein alignment to produce a codon aware nucleotide alignment - which can
be viewed as a back translation.
Type: unrestricted
Revision: 7:883842b81796
This revision can be installed: True
Times cloned / installed: 664

Repository README files - may contain important installation or license information

Galaxy tool to back-translate a protein alignment to nucleotides

This tool is copyright 2012-2017 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 load a protein alignment, and matching nucleotide FASTA file of unaligned sequences, which are threaded onto the protein alignment in order to produce a codon aware nucleotide alignment - which can be viewed as a back translation.

This tool is available from the Galaxy Tool Shed at:

The underlying Python script can also be used outside of Galaxy, for details run:

$ python align_back_trans.py

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:

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

The suggested location is in a dedicated tools/align_back_trans 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 multiple alignments section. Simply add the line:

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

You will also need to install Biopython 1.62 or later.

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 align_back_trans

That's it.

History

Version Changes
v0.0.1
  • Initial version, based on a previously written Python script
v0.0.2
  • Optionally check the translation is consistent
v0.0.3
  • First official release
v0.0.4
  • Simplified XML to apply input format to output data.
  • Fixed error message when sequence length not a multiple of three.
v0.0.5
  • More explicit error messages when seqences lengths do not match.
  • Tool definition now embeds citation information.
v0.0.6
  • Reorder XML elements (internal change only).
  • Use format_source=... tag.
  • Planemo for Tool Shed upload (.shed.yml, internal change only).
v0.0.7
  • Minor Python code style improvements (internal change only).
v0.0.8
  • Python coding style change to avoid lamba (internal change only).
  • Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
  • Added two recent NCBI genetic code tables,
    • Table 24, Pterobranchia Mitochondrial Code,
    • Table 25, Candidate Division SR1 and Gracilibacteria.
  • Use <command detect_errors="aggressive"> (internal change only).
  • Single quote command line arguments (internal change only).
v0.0.9
  • Python 3 compatible print function.
v0.0.10
  • Remove unused reference to muscle format in wrapper, reported by Björn Grüning (internal change only).

Developers

This script was initially developed on this repository: https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py

With the addition of a Galaxy wrapper, developement moved here: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans

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/align_back_trans/
...

or:

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

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/align_back_trans/
...
$ tar -tzf shed_upload.tar.gz
test-data/demo_nucs.fasta
test-data/demo_nucs_trailing_stop.fasta
test-data/demo_prot_align.fasta
test-data/demo_nuc_align.fasta
tools/align_back_trans/README.rst
tools/align_back_trans/align_back_trans.py
tools/align_back_trans/align_back_trans.xml
tools/align_back_trans/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
Gives a codon aware alignment 0.0.10 16.01

Categories
Fasta Manipulation - Tools for manipulating fasta data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis