[BioPython] PSIBlastParser error
Brad Chapman
chapmanb at uga.edu
Sat May 15 07:20:05 EDT 2004
Hi John;
> I am some difficulty with the NCBIStandalone.PSIBlastParser. After
> running blastpgp, I use the parser and get the error message:
>
> $ python psiBlastHomologues.py ./275proteins_allEnteroBact/allEntero
> ./275prote
> ins_allEnteroBact/all275seeds 1 100 1e-3 0 1
[...]
> ValueError: invalid literal for float(): round
>
> I've traced this problem to the following line in the blast output:
> "Sequences not found previously or not previously below threshold:" It
> appears that the parser complains when this line is not followed by any
> sequences AND there is another round afterwards. This is kind of odd,
> since I thought that when there are no sequences following that line,
> psiblast should have converged. However, this is not the case, as I have
> additional rounds (i.e. iterations) afterwards.
Hmmm, that is very strange. But, if blastpgp produces it, we should
be able to parse it.
> I can forward the actual psiblast output file if it helps.
That would be a big help if you could either send me the file
directly, or post it as a bug in the bug database
(http://bugzilla.open-bio.org/) and then attach it there. Either way
we'll have a look and try to get it fixed up.
Thanks for the report.
Brad
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