[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 #3 from mdehoon at ims.u-tokyo.ac.jp  2007-01-07 16:25 -------
> In Record.py, HSP.identities, HSP.gaps, and HSP.positives are still
> defined as (None,None) tuples.  However, in NCBIXML.py, these
> variables are set as integers.  I don't see a point of a tuple at all,
> at least for NCBIXML.  (I realize it is used in NCBIStandalone.py).
> Most importantly, the inconsistency makes it difficult to handle cases
> when the parameter is not set.  It seems easiest, though, to just
> retain the tuple format.

I don't see a good reason for a tuple either -- though it may have seemed like
a good idea back in the days that Blast only produced plain-text output.
Instead of making NCBIXML also use a tuple, I'd rather set
HSP.identities|gaps|positives to None instead of (None, None) in Record.py.
This may break some code for people using NCBIStandalone. On the other hand, it
doesn't break Biopython's test suite.


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