[Biopython] qblast error, probably due to BLAST server overload: any way to handle this error better?
Dan
dan837446 at gmail.com
Wed Mar 27 03:04:09 UTC 2013
Hi, I have a script that runs Qblast over a multiline fasta file
(protein).. the relevant code is:
for seq_record in SeqIO.parse(args.infile,"fasta"):
blast_result_handle = NCBIWWW.qblast(args.program, args.database, \
seq_record.format("fasta"),expect=args.expect, hitlist_size=args.num_hits, \
service=args.service)
time.sleep(5)
for a generalised case and in the particular case I am looking at it's:
for seq_record in SeqIO.parse(args.infile,"fasta"):
blast_result_handle = NCBIWWW.qblast(blastp, nr, \
seq_record.format("fasta"),expect=args.expect, hitlist_size=args.num_hits, \
service=args.service)
time.sleep(5)
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