Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper

This tool is copyright 2011-2017 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 to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. The script blast_rbh.py can be used directly (without Galaxy) as long as NCBI BLAST+ is installed.

It comes with an optional Galaxy tool definition file blast_rbh.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/blast_rbh

Citation

Please cite the following paper:

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

You should also cite the NCBI BLAST+ tools:

BLAST+: architecture and applications. C. Camacho et al. BMC Bioinformatics 2009, 10:421. https://doi.org/10.1186/1471-2105-10-421

Automated Installation

Installation via the Galaxy Tool Shed should take care of the Galaxy side of things, including the dependency the NCBI BLAST+ binaries.

Manual Installation

There are just three files to install:

• blast_rbh.py (the Python script)
• best_hits.py (helper script, put in same directory)
• blast_rbh.xml (the Galaxy tool definition)

The suggested location is in a tools/blast_rbh/ 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="blast_rbh/blast_rbh.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 blast_reciprocal_best_hits

You will need to have the NCBI BLAST+ binaries installed and on the $PATH.

History

Version	Changes
v0.1.0	Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29
v0.1.1	Supports self-comparison, sometimes useful for spotting duplicates.
v0.1.2	Using optparse for command line API. Tool definition now embeds citation information. Fixed Tool Shed dependency definition.
v0.1.3	Option to make FASTA files non-redundant (via Biopython dependency). Avoid extra database and BLAST search in self-comparison mode.
v0.1.4	Check for duplicate FASTA identifiers (workaround for makeblastdb not treating this as an error, leading to confusing RBH output).
v0.1.5	Clarify documentation for using the Python script outside Galaxy. Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install.
v0.1.6	Offer the new blastp-fast task added in BLAST+ 2.2.30. Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
v0.1.7	Reorder XML elements (internal change only). Planemo for Tool Shed upload (.shed.yml, internal change only). Updated citation information with GigaScience paper.
v0.1.8	Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install.
v0.1.9	Updates to the command line API for the Python script. PEP8 style updates to the Python script (internal change only). Fix parameter help text which was not being displayed.
v0.1.11	Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda. Update Biopython dependency. Tweak Python script to work under Python 2 or Python 3.
v0.1.12	Use <command detect_errors="aggressive"> (internal change only). Single quote command line arguments (internal change only).
v0.2.0	Refactored to use more than one Python file (internal change only).
v0.3.0	Updated to BLAST+ 2.9.0 via conda; removed legacy tool packages.

Developers

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

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/blast_rbh/
...

or:

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

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/blast_rbh/
...
$ tar -tzf shed_upload.tar.gz
test-data/four_human_proteins.fasta
test-data/k12_edited_proteins.fasta
test-data/k12_ten_proteins.fasta
test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
test-data/rbh_blastp_k12.tabular
test-data/rbh_blastp_k12_self.tabular
test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
test-data/rbh_none.tabular
test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
test-data/rhodopsin_nucs.fasta
test-data/rhodopsin_proteins.fasta
test-data/three_human_mRNA.fasta
tools/blast_rbh/README.rst
tools/blast_rbh/blast_rbh.py
tools/blast_rbh/blast_rbh.xml
tools/blast_rbh/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.