[Biopython-dev] NCBIWWW.qblast: Question about expected run time and time outs

[Peter Cock]

On Wed, Jun 24, 2015 at 5:08 AM, Lev Tsypin <ltsypin at uchicago.edu> wrote:
> Hi Peter,
>
> It seems that I may have been black-listed, unfortunately. I didn't think it
> was the case because I've been traveling (and so my IP address has been
> changing), but when I tried running my program with a VPN, it worked fine
> again. I'll be more careful.

That's unlucky. Hopefully this was a temporary ban, and with moderate
usage in future you will be fine.

>
> I am getting an error with the test_NCBI_qblast.py, though:
>
> FAIL: test_orchid_est (__main__.TestQblast)
> ------------------------------------------------------------
> Traceback (most recent call last):
>   File "test_NCBI_qblast.py', line 69, in test_orchid_est
>     0.0000001, None, ["21554275", "18409071", "296087288"])
>   File "test_NCBI_qblast.py', line 124, in run_qblast
>     % ", ".join(expected_hits)
> AssertionError: Missing all of 21554275, 18409071, 296087288 in alignments
> ------------------------------------------------------------
>
> Thank you for your help!

Thanks. The EST database has changed enough that our test
failed - probably someone sequenced lots more orchids.
The test has been updated ready for the next Biopython release:

https://github.com/biopython/biopython/commit/08c72f8778a87701586a03dffcce33c7589bc6d7

Peter