blastbesties 1.2.0

Rapid discovery of reciprocal best blast pairs from BLAST output files.

Blast-Besties

Rapid discovery of reciprocal best blast pairs from BLAST output files.

Table of contents

• Blast-Besties
  • Table of contents
  • Install Blast-Besties
  • Example usage
    • Input requirements
    • Standard options
  • License

Install Blast-Besties

There are 3 options available for installing Blast-Besties locally:

1. Install from PyPi.

pip install blastbesties

2. Pip install latest development version directly from this git repository.

pip install git+https://github.com/Adamtaranto/blast-besties.git

3. 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.