[Biopython] help with ncbiWWW

[Peter Cock]

Hmm. Do you need this to work on Python 2?

https://docs.python.org/2/library/urllib.html
https://docs.python.org/3/library/urllib.request.html

Python 3 added a timeout argument to the urlopen function,
which it says defaults to the "global default timeout".

Does this help:

import socket
socket.setdefaulttimeout(30)  # timeout in seconds

I'm guessing at a sensible limit here - you will
probably need to experiment.

Regards,

Peter

On Wed, Jul 26, 2017 at 12:26 PM, Pejvak Moghimi
<pejvak.moghimi at york.ac.uk> wrote:
> Hi all,
>
> I'm working on a script to to do blast using the ncbiWWW module, but very
> often one query sequence takes way too long, if at all, to return with
> results. This is always, in my experience, immediately solved if I just stop
> the script and re-run it (for the same query sequence); I get the results as
> quickly as I did for the other query sequences.
>
> I think this hints that this is something to do with ncbi servers. So, in
> order to tackle it, I need to simply modify my while loop to stop and re-run
> the "ncbiwww.qblast(..." line, if it takes longer than a reasonable length
> of time (I do understand shorter than a certain waiting-time would not be
> allowed by ncbi).
>
> I have no idea how to tackle this, except by either multithreading (not so
> sure how to go on about this though) or changing the qblast script (locally
> of course).
>
> I would really appreciate any help. Please do let me know if you would like
> to have a look at the script.
>
> Cheers,
> Pej.
>
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