[Biopython] Problems parsing with PSIBlastParser

[Peter]

On Thu, Oct 15, 2009 at 5:24 PM, Miguel Ortiz Lombardia
<ibdeno at gmail.com> wrote:
>
> 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.

They were on the dev list, so that makes sense.

> 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 idea of the NCBIStandalone.PSIBlastparser plain text parser, and
its object structure makes sense.

> 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.

Lovely - thank you. So that is a single query, with 3 iterations.
What would be *really* nice, is a multiple query file (say three
queries, each needing just a few iterations to keep the file small).

Peter