[Biopython-dev] "Your XML file did not start with <?xml"
Peter
biopython at maubp.freeserve.co.uk
Sun Jun 14 18:16:08 UTC 2009
On 6/14/09, Cymon Cox <cy at cymon.org> wrote:
> Folks,
>
> I've been using qblast recently, and got a lot of invalid replies from NCBI
> of this sort:
>
> Traceback (most recent call last):
> ...
> ValueError: Your XML file did not start with <?xml...
I've seen message that from the unit test sometimes, and assumed the
NCBI was returning a temporary HTML error page of some kind -
rerunning our test would normally work. Without checking the
traceback, I would guess this is the same issue you have found.
> Which is true: NCBI is returning "\n\n". If you code around this and just
> keep going the results eventually arrive:
> ...
At first glance, something based on your change looks sensible. Next
time I spot the unit test failing I'll try and reproduce this.
Peter
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