Make a FASTA file non-redundant, with a Galaxy wrapper

This tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved. See the licence text below.

This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative.

The script make_nr.py can be used directly (without Galaxy). It requires Biopython.

It comes with an optional Galaxy tool definition file make_nr.xml allowing the Python script to be run from within Galaxy. It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/make_nr

Citation

If you cannot cite the GitHub repository directly, please cite one of the following papers:

Cock et al 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

or (and this would be more appropriate in a Galaxy setting):

NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo GigaScience 2015, 4:39 https://doi.org/10.1186/s13742-015-0080-7

Standalone Installation (outside Galaxy)

Outside of Galaxy, you will need Python and Biopython, the later can usually be installed with pip install biopython or if you are using Conda, try conda install biopython instead. Then to run the script, simply call it using python /full/path/to/make_nr.py -h or similar.

Automated Installation

Installation via the Galaxy Tool Shed should take care of the Galaxy side of things, including the dependency on Biopython.

Manual Installation

There are just two files to install:

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

The suggested location is in a tools/make_nr/ folder. You will then need to modify the tools_conf.xml file to tell Galaxy to offer the tool by adding the line:

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

If you want to run the functional tests, copy the sample test files under sample test files under Galaxy's test-data/ directory. Then:

./run_tests.sh -id make_nr

History

TODO:

• Option to follow BLAST NR style with ctrl+a separator?
• Option to give representative sequences in upper case?

Developers

This tool is developed on the following GitHub repository: https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr

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/make_nr/
...

or:

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

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/make_nr/
...
$ tar -tzf shed_upload.tar.gz
tools/make_nr/README.rst
tools/make_nr/make_nr.py
tools/make_nr/make_nr.xml
tools/make_nr/tool_dependencies.xml
test-data/duplicates.fasta
test-data/duplicates.nr.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.