[Biopython-dev] [Bug 2927] Problem parsing PSI-BLAST plain text output with NCBStandalone.PSIBlastParser

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http://bugzilla.open-bio.org/show_bug.cgi?id=2927





------- Comment #10 from ibdeno at gmail.com  2009-12-24 07:00 EST -------
(In reply to comment #9)
> (In reply to comment #8)
> > (In reply to comment #7)
> I was also able to confirmed the problem is present in blastpgp 2.2.22,
> however it seems to have been fixed in the "new" BLAST+ suite, psiblast
> 2.2.22+ as described here:
> http://lists.open-bio.org/pipermail/bioperl-l/2009-December/031811.html
> 
> Given this new information, this does look like an NCBI BLAST bug, and not
> a problem in Biopython itself. We *might* be able to get our parser to cope
> with the funny BLAST output, but it does look difficult and risky to me.
> 

I think the best strategy will be to use the BLAST+ suite, since the "old"
programs will be abandoned, as I learnt from NCBI. Also, I think we should use
XML output.  I know I promised to work on testing that, but I don't think I
will able to do the test before Februare...

> Miguel - Is it possible the BLAST bug is relatively recent and first showed
> up when you updated blastpgp to 2.2.18?
> 

I had been using 2.2.18 for quite a while (months) and never had a problem. I
think I initially thought it might be a problem with the actual databases, more
than with the program...

Best regards,


Miguel


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