[Biopython-dev] [Bug 2176] XML Blast parser: miscellaneous bug fixes and cleanup

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2176





------- Comment #11 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-22 07:42 EST -------
Created an attachment (id=1011)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1011&action=view)
Changes to Bio/Blast/NCBIStandalone.py and Bio/Blast/Record.py

I'd like to make the XML and text parser agree on representing the HSP
identities, positives and gaps as integers.  Currently the text parser (and the
default values in the HSP object) use a tuple of the value and the alignment
length.

The upside is it brings the objects returned by the XML and plain text parsers
into better agreement.  In this case I find storing these properties as simple
integers makes much more sense than as a tuple (a choice probably based on the
layout of the BLAST plain text output itself).

The downside of applying this patch is it could break some existing scripts
parsing the plain text output.


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