I am using biopython's NCBIWWW.qblast which sends a request to the ncbi
website and waits for a result. The relevant code can be found at the link
below starting at about 151. Basically it is a while loop waiting for the
blast query.
http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-pysrc.html
My problem; I am submitting about 75 request (one at a time and with
delays) and they can each take minutes to complete. I think sometimes the
request/response/query fails which results in me needing to restart
the process.
I am looking for suggestion on how to monitor and restart the process if I
think it has failed.
I am using the following code to submit the query/
def get_BLAST(taxid, queryseq, args=None):
'''
Input taxid to BLAST queryseq against
'''
e_query = "txid" + taxid + " [ORGN]"
#, other_advanced='-G 4 -E 1'
blast_result = NCBIWWW.qblast("blastn", "nt", queryseq, megablast=True,
entrez_query=e_query, word_size='11', other_advanced='-G 5 -E 2')
return NCBIXML.read(blast_result)
Vincent Davis
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