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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jan 8 15:24:20 UTC 2007


------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2007-01-08 10:24 -------
Regarding the inconsistent use tuples for _hsp.identities, positives, and gaps
- I would like all the parsers NCBIStandalone and NCBIXML (and ideally the HTML
parser too) to return identical record objects.

To do this, we could either:

(a) change NCBIXML to use tuples instead of integers (as suggested by Jacob)


(b) change NCBIStandalone to use simple integers instead of tuples (is this
what you meant in comment 3 Michiel?)

Choice (b) would seem simpler in the long term - but would probably break more
existing code.  Also, users of NCBIXML are going to have to update their
scripts anyway after bug 2051, so choice (a) would distrupt less people.

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