[BioPython] PSIBlastParser error

[Brad Chapman]

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