[BioPython] NCBIWWW.qblast time outs
Peter
biopython at maubp.freeserve.co.uk
Tue May 20 16:21:12 UTC 2008
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
More information about the Biopython
mailing list