blastbesties 1.1.1

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

* [Example usage](#example-usage)
* [Input requirements](#input-requirements)
* [Standard options](#standard-options)
* [License](#license)

# Example usage

Run BLASTp for each protein set AvsB and BvsA.
Require vaild alignments to cover 95% of the query sequence and with an e-value of < 0.001.

```bash
blastp -qcov_hsp_perc 95 -query A_prot.fa -subject B_prot.fa -out AvB.tab -evalue 0.001 -outfmt 6 -use_sw_tback
blastp -qcov_hsp_perc 95 -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 >= 100, bitscore >= 100.

```bash
./blastBesties.py -e 0.001 -l 100 -s 100 -a *blastAvB.tab* -b *blastBvA.tab
```

## 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: BLAST-Besties [-h] [-v] -a BLASTAVB -b BLASTBVA [-l MINLEN] [-e EVAL]
[-s BITSCORE] [-o OUTFILE] [-d OUTDIR]

Options:

# Info
-h, --help Show this help message and exit.
-v, --version Show program's version number and exit.

# Input
-a, --blastAvB Blast tab result file for fastaA query against fastaB
subject.
-b, --blastBvA Blast tab result file for fastaB query against fastaA
subject.

# Settings
-l, --minLen Minimum length of hit to consider valid.
-e, --eVal Maximum e-value to consider valid pair.
-s, --bitScore Minimum bitscore to consider valid pair.

# Output
-o, --outFile Write reciprocal blast pairs to this file.
-d, --outDir Directory for new sequence files to be written to.
```

# License

Software provided under MIT license.