[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 #4 from biopython-bugzilla at maubp.freeserve.co.uk  2009-11-03 08:20 EST -------
(In reply to comment #3)
> (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

There is a <Iteration_message>CONVERGED</Iteration_message> line in the XML we
should be able to use here. I don't recall seeing this in pgpblast output from
older versions of BLAST.

> brecord.query
> brecord.query_letters

Those work (query and query_letters).

> brecord.rounds
> brecord.rounds.alignments
> brecord.rounds.alignments.title
> brecord.rounds.alignments.hsps

Those also work but not via rounds, but as separate BLAST record objects.
See mailing list discussion regarding PSI-BLAST and multiple BLAST queries.

> 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

Again, those are all parsed fine.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.