pansapiens / recip-blast

A quick and dirty reciprocal BLAST to find orthologues between two strains

Recip_BLAST

A quick and dirty reciprocal BLAST to find orthologues between two (bacterial?) strains, made by guiding ChatGPT4.

You are probably better off using something like Roary or Panaroo.

NOT WELL TESTED, BUT APPEARS TO WORK ?

Requires: NCBI BLAST+, makeblastdb, blastp and/or blastn

Input: Two FASTA files of protein or nucleotide sequences.

Output:

• A table reciprocal_best_hits.tsv with pairs of orthologues common between the two strains
• a bunch of intermediate file from running BLAST

Quickstart

Example:

# sudo apt install ncbi-blast+

cd example

../recip_blast.py --threads=4 --identity=90 GCF_000827025.1.faa GCF_017821535.1.faa

Output files go to the directory output by default. Look at the file reciprocal_best_hits.tsv for pairs of orthologues common between the two strains.

Tests

You can run some simple unit tests like:

python tests.py

These should be expanded so we can be more confident of the result