[Biopython] qblast NCBI API broken?

[Peter Cock]

Hi Alex,

The "good" news is your example fails for me right now.

As an aside, I would suggest anything at example.org or similar
versus making up an email address which is potentially real:
https://tools.ietf.org/html/rfc2606

Interestingly test_NCBI_qblast.py seems fine (although much
slower than usual), so I suspect there must be something
breaking on the NCBI side with this specific request?

If I remove the Entrez query it seems to run just fine. I suggest
revisiting this in a few days to see if it has been fixed - or that
you email the NCBI BLAST team directly to enquire.

Regards,

Peter

On Tue, Mar 21, 2017 at 10:33 PM, Alex Lancaster
<alexl at users.sourceforge.net> wrote:
> 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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