skills/bioskills/bio-database-access-local-blast/scripts/blast_wrapper.py

• require · function · L7-L9 — def require(tool)
• make_blast_db · function · L12-L21 — def make_blast_db(fasta, name, dbtype='nucl', parse_seqids=True, version=5)
• run_blast · function · L24-L38 — def run_blast(query, db, out, program='blastn', task=None, evalue=1e-10, threads=8, hitlist=500, soft_masking=True)
• parse_tabular · function · L41-L53 — def parse_tabular(path)
• top_by_bitscore_per_query · function · L56-L62 — def top_by_bitscore_per_query(rows, n=1)
• filter_hits · function · L65-L69 — def filter_hits(rows, min_pident=30.0, min_qcovs=50.0, max_evalue=1e-5)