[Biopython-dev] NCBIWWW.qblast: Question about expected run time and time outs

[Lev Tsypin]

Hello everyone,

I have been writing a tool that makes use of Biopython for automatic BLAST
searches--your libraries have made my life so much easier! I really
appreciate your work. I've recently begun to run into some trouble, though,
and I am not quite sure how to explain it, or respond to it, so I wanted to
ask for advice:

The issue is that, of late, when I call the NCBIWWW.qblast function, it
takes forever--literally never finishing. Before, there were sometimes
cases that it would get stuck for a long time (up to an hour or so), but it
would then manage to fight through whatever obstacle and go on. In such
cases, I also found that if I were to artificially restart the request, the
function would rouse itself and go much better. Here's an example of a
function call:

blastp_result = NCBIWWW.qblast('blastp', 'nr',
'MSLSREENIYMGKISEQTERFEDMLEYMKKVVQTGQELSVEERNLLSVAYKNTVGSRRSAWRSISAIQQKEESKGSKHLDLLTNYKKKIETELNLYCEDILRLLNDYLIKNATNAEAQVFFLKMKGDYYRYIAEYAQGDDHKKAADGALDSYNKASEIANSELSTTHPIRLGLALNFSVFHYEVLNDPSKACTLAKTAFDEAIGDIERIQEDQYKDATTIMQLIRDNLTLWTSEFQDDAEEQQE',
entrez_query = 'NOT Ciliata').read()

[In the protein sequence above I have multiple lines so that it fits in the
email, but when I normally run the function I don't have any newline
characters or anything, of course]

My questions are the following: Why does the function sometimes get stuck
for so long, and what should I do now that it never seems to work anymore?
Do you have any suggestions for introducing a 'time out' so that if, for
example, the request takes longer than 10 minutes, it would automatically
retry? I know there is an optional parameter in the urllib2 library for a
time out, but, looking at the source code for NCBIWWW.qblast(), it wasn't
obvious to me whether and how it would work to use it.

Thank you very much for any advice.

Best regards,
Lev
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