[Biopython] help with ncbiWWW

[Pejvak Moghimi]

Hi Peter,

That solution, so far, does not seem to have worked nor with 10 neither
with 30 second options.

Cheers,
Pej.

On 26 July 2017 at 13:29, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> I am hoping that putting this near the start of your script will
> apply the default timeout to all your BLAST calls (or other
> network calls, e.g. NCBI Entrez):
>
> import socket
> socket.setdefaulttimeout(30)  # timeout in seconds
>
> Peter
>
> On Wed, Jul 26, 2017 at 1:26 PM, Pejvak Moghimi
> <pejvak.moghimi at york.ac.uk> wrote:
> > 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
> >
> >
>
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