[BioPython] NCBIWWW.qblast time outs

[Peter]

On Tue, May 20, 2008 at 5:08 PM, Raul Guerra <colochera at gmail.com> wrote:
> Also,
> I am trying to do a blastp for a fasta file named fastaStr, but I want to
> restrict the sarch to the organim Chlamydomonas. Everytime I run the
> following code
>
> result_handle = NCBIWWW.qblast("blastp", "nr", fastaStr,
> entrez_query='"Chlamydomonas" [ORGN]')
>
> I get
>
>  urllib2.URLError: <urlopen error (110, 'Connection timed out')>
>
> from the Biopresult_handle = NCBIWWW.qblast("blastp", "nr", fastaStr,
> entrez_query='"Chlamydomonas" [ORGN]')
>
> from the Biopython code. Any ideas?

You could try running the same query via your web browser, so get an
idea of if its just a local networking problem or high server load at
the NCBI.

It does seem to be working for me right now, but I am using the latest
CVS version of Biopython where I updated the CGI URL from
http://www.ncbi.nlm.nih.gov/blast/Blast.cgi  to
http://blast.ncbi.nlm.nih.gov/Blast.cgi  - see revision 1.49 for the
change:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIWWW.py?cvsroot=biopython

This might be worth trying... of course, for big tasks you would be
better off installing a local copy of standalone blast, and creating
your own blast database from the genome (i.e. the protein fasta
file(s) for Chlamydomonas in your case).

Peter