[Biopython] getting multiple BLAST (NCBIWWW) queries to work

[James Wagner]

Hello:

I was trying just as a proof of concept to do an NCBI WWW BLAST query
with a FASTA file containing more than one sequence (but still a small
number of sequences).

I tried with the opuntia.fasta file from the website, and set it up as follows:

result_handle = NCBIWWW.qblast("blastn", "nr", open("opuntia.fasta","r"))
blast_records = NCBIXML.parse(result_handle)

then I try:

for record in blast_records:
      print record.alignments

and I obtain:
[]


Surely at the very least since there were 7 sequences in this file, I
should get 7 empty lists, assuming of course none of the sequences
gives a hit in nr, which I am sure is not the case either?

What is still missing? I realize I could use SeqIO.parse to obtain
each sequence from the FASTA file and do a separate qblast, but surely
doing this separately for each protein would create unnecessary
overhead with the network traffic compared to somehow sending off all
the protein queries at once?