[Biopython] help with ncbiWWW

[Pejvak Moghimi]

Hi Peter,

Here it is:

Traceback (most recent call last):

  File "<ipython-input-107-561cd74d2097>", line 1, in <module>
    runfile('D:/Dropbox/Pejvak
Moghimi/DMT_project/blast_for_clav_seqs/blastScript(altered).py',
wdir='D:/Dropbox/Pejvak Moghimi/DMT_project/blast_for_clav_seqs')

  File
"C:\Users\pezhv\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py",
line 880, in runfile
    execfile(filename, namespace)

  File
"C:\Users\pezhv\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py",
line 102, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "D:/Dropbox/Pejvak
Moghimi/DMT_project/blast_for_clav_seqs/blastScript(altered).py", line 116,
in <module>
    result_handle = NCBIWWW.qblast("blastp", "nr", sequence,
hitlist_size=500, entrez_query = orgn_specified)

  File "C:\Users\pezhv\Anaconda3\lib\site-packages\Bio\Blast\NCBIWWW.py",
line 164, in qblast
    *time.sleep(wait)*


Cheers,
Pej.


On 26 July 2017 at 14:57, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Hi Pej.
>
> Hmm. Maybe setting the timeout is not going to solve your
> problem. I was hoping that would be a neat solution.
>
> Can you show us the stack trace when you had to stop a job
> please?
>
> I assume you are using control+c to do this, in which case
> Python ought to stop with the exception KeyboardInterrupt.
> What I am interested in here is where in the code Python
> is getting stuck. That would be a good clue.
>
> Peter
>
> On Wed, Jul 26, 2017 at 2:47 PM, Pejvak Moghimi
> <pejvak.moghimi at york.ac.uk> wrote:
> > 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
>
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