I need your help with something.
I'm trying to making a BLAST search with a nucleotide sequence and print the best matching hit but not sure about which option/command should I use. There are options like ''max_hpsp'' and ''best_hit_overhang''. I don't have an idea about their differences and I want to print just 1 hit. (best matching one) Should i use '' max_hpsp 1'' ?
I wrote this code but it's still not useful. If you could tell me, where i am mistaken and what should to do, I would be very appreciated :) Thank you!
from Bio.Blast import NCBIWWW seq = Seq("GTTGA......CT") def best_matching_hit(seq): try: result_handle = NCBIWWW.qblast("blastn", "nt", seq) except: print('BLAST run failed!') return None blast_record = NCBIXML.read(result_handle) for hit in blast_record.alignments: for hsp in hit.hsps: if hsp.expect == max_hsps 1: print(hit.title) print(hsp.sbjct) best_matching_hit(seq)