[Biopython] help with ncbiWWW

[Pejvak Moghimi]

Hi Peter,

Thank you. I will give it a go.

Can I use this on my own script to achieve what I want, or is it strictly
useful for altering the qblast script?

Cheers,
Pej.

On 26 July 2017 at 13:06, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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.
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170726/58fc9a3c/attachment.html>