Python3 module to run blast+ or blastall in parallel on an LSF compute farm
Prerequisites:
- NCBI BLAST NCBI BLAST blast+, and optionally blastall, installed and their commands in your path
- Fastaq Fastaq >= v0.1
- Farmpy Farmpy >= v0.2
Once the prerequisites are installed, run the tests:
python3 setup.py test
Note that the tests check that blast+ is installed, but not blastall because it is optional. If all was OK, then install:
python3 setup.py install
Compare a query and a reference using blast+ blastn:
farm_blast reference.fasta query.fasta
Compare a query and a reference using blastall blastn:
farm_blast --blastall reference.fasta query.fasta
Run blast+ megablast:
farm_blast --blast_type megablast reference.fasta query.fasta
Run blastall tblastx:
farm_blast --blast_type tblastx --blastall reference.fasta query.fasta
Set the e-value and word length and do not filter the query sequence:
farm_blast --no_filter -e 0.1 -W 30 reference.fasta query.fasta
To get all the options, use --help:
farm_blast --help