[Biopython] qblast NCBI API broken?

Alex Lancaster alexl at users.sourceforge.net
Tue Mar 21 22:33:55 UTC 2017


Hi there,

I'm trying to use the Biopython qblast interface with Biopython 1.68.  This code was working up until a week or so ago:

from Bio.Blast import NCBIWWW
from Bio import Entrez
Entrez.email = "foobar at foo.com"
result_handle = NCBIWWW.qblast(program="blastn", database="refseq_genomic", sequence="TTTCTTCCAGGA", entrez_query="txid9606[ORGN]")
print result_handle.read()

But now I get the following badly formed XML:

</BlastOutput_iterations>
</BlastOutput>

is this a known issue?  Has NCBI's API changed recently?

Thanks,
Alex


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