[Biopython-dev] [Bug 2929] NCBIXML PSI-Blast parser should gather all information from XML blastgpg output

[bugzilla-daemon at portal.open-bio.org]

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





------- Comment #3 from ibdeno at gmail.com  2009-10-25 10:01 EST -------
(In reply to comment #2)
> What specifically is our parser failing to extract from this example PSI BLAST
> XML file?
> 

(Sorry, I've been away)
Well, currently the code tries to get several pieces of information from the
Blast.Record.PSIBlast (brecord):

brecord.converged
brecord.query
brecord.query_letters
brecord.rounds
brecord.rounds.alignments
brecord.rounds.alignments.title
brecord.rounds.alignments.hsps

then in the hsps:
hsp.identities
hsp.positives
hsp.query
hsp.sbjct
hsp.match
hsp.expect
hsp.query_start
hsp.query_end
hsp.sbjct_start
hsp.sbjct_end

With different XML-tag names I think that all this information is present.
As I said on the mail-list, it would be ideal if the XML parser for PSI-Blast
would work in the same way as the current text-mode PSIBlast parser.

Please, let me know if that was not clear or if you need further information.

Thanks!


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