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https://github.com/adamtaranto/blast-besties
Rapid discovery of reciprocal best blast pairs.
https://github.com/adamtaranto/blast-besties
Last synced: 3 months ago
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Rapid discovery of reciprocal best blast pairs.
- Host: GitHub
- URL: https://github.com/adamtaranto/blast-besties
- Owner: Adamtaranto
- License: mit
- Created: 2015-05-12T04:47:03.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-01-17T04:07:26.000Z (12 months ago)
- Last Synced: 2024-09-18T12:52:59.662Z (4 months ago)
- Language: Python
- Size: 1.77 MB
- Stars: 10
- Watchers: 4
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Blast-Besties
Rapid discovery of reciprocal best blast pairs from BLAST output files.
## Table of contents
- [Blast-Besties](#blast-besties)
- [Table of contents](#table-of-contents)
- [Install Blast-Besties](#install-blast-besties)
- [Example usage](#example-usage)
- [Input requirements](#input-requirements)
- [Standard options](#standard-options)
- [License](#license)
## Install Blast-Besties
There are 3 options available for installing Blast-Besties locally:
1) Clone from this repository and install as a local Python package.
```bash
git clone https://github.com/Adamtaranto/blast-besties.git && cd blast-besties && pip install -e .
```
1) Pip install directly from this git repository.
```bash
pip install git+https://github.com/Adamtaranto/blast-besties.git
```
3) Install from PyPi.
```bash
pip install blastbesties
```
## 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.
```bash
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.
```bash
blastbesties -e 0.001 -l 40 -s 100 -a AvB.tab -b BvA.tab -o pairs.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: blastbesties [-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.