[BioPython] Problem parsing Blast XML output from different sources

[Michiel Jan Laurens de Hoon]

Which sequence are you running blast on?
I'd like to try this on our local blast installation.

--Michiel.

Steffi Gebauer-Jung wrote:
> Hello,
> 
> because of blastall 2.2.14 output was not parsed from the 
> Bio.Blast.NCBIStandalone parser,
> I tried to switch to the recommended Bio.Blast.NCBIXML parser.
> 
> Thereby I found, that the xml output of the locally installed standalone 
> blastall (2.2.14)
> differs from the web xml output.
> 
> For BlastN hsps on Plus/Minus strands, the xml gives
> query_frame/hit_frame  1 / -1 as usual.
> But query and frame positions and sequences are switched in direction
> (would match frames -1/1).
> 
> As the Bio.Blast.Record returned by the NCBIXML parser only gives 
> frames, sequences
> and start positions it is not possible (without knowing the source of 
> the xml file)
> to be sure to find the right data.
> 
> This is clearly a problem of Blast.
> But because of the missing end positions in the returned record object
> it becomes a problem for users of the parser too.
> 
> Could somebody try to confirm the different behaviour of the xml blast 
> output
> with his/her own examples/installation?
> 
> Thanks, Steffi
> 
> 
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython


-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032