[BioPython] Parsing BLAST results
Atkinson, GC
gca500 at york.ac.uk
Thu Nov 4 07:04:06 EST 2004
Hi Everyone,
You've probably had this same query hundreds of times before and are
sick of answering it, but I'm stuck and need your help!
I'm new to Biopython, and I'm trying to run BLAST from a script like the
example in the Cookbook:
from Bio import Fasta
from Bio.Blast import NCBIWWW
fasta= open('m_cold.fasta','r')
f_iterator=Fasta.Iterator(fasta)
record=f_iterator.next()
b_results=NCBIWWW.blast('blastn','nr',record)
save_file=open('cold.out','w')
results=b_results.read()
save_file.write(results)
save_file.close()
All I get in the results file is the HTML page that comes up when
waiting for results ("....<p><hr>This page will be automatically updated
in <b>14</b> seconds until search is done<BR>")
I realise Blast output keeps changing, so the code needs to be updated
but I just don't know how!
Gemma
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