schemarecomb.parent_alignment.query_blast¶

schemarecomb.parent_alignment.query_blast(query_seq, database='refseq_protein', maximum_hits=10000)¶

Gets sequences from query_seq BLAST hits.

Direct copy of Peter Cock’s Bio.Blast.NCBIWWW.qblast, with simplifications and added progress print-outs.

Parameters

query_seq (str) – Query sequence for BLAST search.
database (str) – BLAST database to search. Must be either ‘refseq_protein’ or ‘pdbaa’
maximum_hits (int) – Maximum number of hits allowed to be returned. Affects runtime: reducing this number is faster but you risk missing good candidate sequences.

Return type

FastaIterator

Returns

FASTA generator for sequence hits.

Raises

ValueError – If database is not “refseq_protein” or “pdbaa”.

schemarecomb