Rapid discovery of reciprocal best blast pairs from BLAST output files.
Project description
Blast-Besties
Rapid discovery of reciprocal best blast pairs from BLAST output files.
Table of contents
Install Blast-Besties
There are 3 options available for installing Blast-Besties locally:
- Install from PyPi.
pip install blastbesties
- Pip install latest development version directly from this git repository.
pip install git+https://github.com/Adamtaranto/blast-besties.git
- Clone from this repository and install as a local Python package if you want to edit the code.
git clone https://github.com/Adamtaranto/blast-besties.git && cd blast-besties && pip install -e ".[tests]"
Example usage
Run BLASTp for each protein set AvsB and BvsA. Require vaild alignments to cover 90% of the query sequence and with an e-value of < 0.001.
blastp -qcov_hsp_perc 90 -query A_prot.fa -subject B_prot.fa -out AvB.tab -evalue 0.001 -outfmt 6 -use_sw_tback
blastp -qcov_hsp_perc 90 -query B_prot.fa -subject A_prot.fa -out BvA.tab -evalue 0.001 -outfmt 6 -use_sw_tback
Report reciprocal best match pairs where each hit meets criteria e-value <= 0.001, hit-length >= 40, bitscore >= 100.
blastbesties -e 0.001 -l 40 -s 100 -a AvB.tab -b BvA.tab -o pairs.tab
To run in interactive mode use --tui
to open the terminal user interface.
blastbesties --tui
Input requirements
- Takes two BLAST output files as input. SetA vs SetB, and SetB vs SetA.
- BLAST output format 6 (tabular)
- Hits must be sorted by query name then descending match quality - this is default BLAST behaviour.
Standard options
Usage: blastbesties [-h] [--version] -a BLASTAVB -b BLASTBVA [-l MINLEN] [-e EVAL] [-s BITSCORE] [-o OUTFILE] [-d OUTDIR] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--tui]
Finds reciprocal best BLAST pairs from BLAST output format 6 (tabular). Where hits are sorted by query name then descending match quality.
options:
-h, --help show this help message and exit
--version Show program's version number and exit.
-a BLASTAVB, --blastAvB BLASTAVB
BLAST tab result file for fastaA query against fastaB subject.
-b BLASTBVA, --blastBvA BLASTBVA
BLAST tab result file for fastaB query against fastaA subject.
-l MINLEN, --minLen MINLEN
Minimum length of hit to consider valid. Defaults to 1.
-e EVAL, --eVal EVAL Maximum e-value to consider valid pair. Defaults to 0.001.
-s BITSCORE, --bitScore BITSCORE
Minimum bitscore to consider valid pair. Defaults to 1.0.
-o OUTFILE, --outFile OUTFILE
Write reciprocal BLAST pairs to this file.
-d OUTDIR, --outDir OUTDIR
Directory for new sequence files to be written to.
--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set logging level. Defaults to INFO.
--tui Open Textual UI.
License
Software provided under MIT license.
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