[Biopython-dev] [Bug 2896] BLAST XML parser: stripped leading/trailing spaces in Hsp_midline

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2896





------- Comment #6 from volkmer at mpi-cbg.de  2009-08-06 03:56 EST -------
(In reply to comment #3)
> I could reproduce this, I think I have fixed
> it. 
> hsp.query, hsp.match and hsp.sbjct should all be the same length.
> 
> Previously, at the end of each tag our XML parser strips the leading/trailing
> white space from the tag's value before processing it. In the case of
> Hsp_midline this is a very bad idea. 

Ok, the fix seems to solve the problem.
Well I guess the only time when this problem appears is when you have
filtered/masked residues at the beginning/end of the query hsp. Otherwise the
hsp would just start with the first match and end with the last one.

Thanks,
Michael


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