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

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





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2009-08-05 07:29 EST -------
Thanks for the sample XML file. 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. However, the reason it did this was that
the way the current tag value was built up wasn't context aware. In particular
case, there was white space outside tags like Hsp_midline, which really belong
to the parent tag (Hsp), but was wrongly being combined.

Would you be able to test this please? All you really need to try this is the
new Bio/Blast/NCBIXML.py file (CVS revision 1.23). It might be easiest just to
update to the latest code in CVS (or on github), but I could attach the file
here if you like.

Peter


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