[Biopython] Problems parsing with PSIBlastParser

[Miguel Ortiz Lombardia]

Le 15 oct. 09 à 18:09, Peter a écrit :
>>
>> IMHO, the NCBIXML parser should behave (concerning PSI-BLAST) just  
>> like
>> NCBIStandalone.PSIBlastparser. Perhaps a NCBIXML.PSIBlasparser  
>> should be
>> created ? Just an idea...
>
> Michiel also thinks the PSI BLAST XML parser could be better, see:
>
> http://lists.open-bio.org/pipermail/biopython-dev/2009-September/006780.html
> ...
> http://lists.open-bio.org/pipermail/biopython-dev/2009-September/006791.html
> http://lists.open-bio.org/pipermail/biopython-dev/2009-September/006802.html
>

Sorry to have missed them.
I still believe that the logic behind the  
NCBIStandalone.PSIBlastparser is correct or, at least, useful. But I  
could change my mind if you think otherwise.

The XML file that I sent to Peter came from blastpgp 2.2.22. It seems  
to me that it is a proper XML file, not a concatenation.

> Can you file a new bug about PSI-BLAST XML parsing (and attach that  
> example)
> please? I'd have to look over the new PSI-BLAST XML files before  
> having an
> informed opinion.


I have filed the bug:

http://bugzilla.open-bio.org/show_bug.cgi?id=2929

and have upload the XML from blastpgp v. 2.2.22 mentioned above.

Best,


-- Miguel