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

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





------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2007-01-09 12:29 -------
Tuples/Integers for HSP.identities, HSP.gaps, and HSP.positives
---------------------------------------------------------------
Michiel's option (c) of doing nothing is very pragmatic.

If we go for this, I think we should at least update the record object's
documentation to say it will be a tuple (when used with NCBIStandalone) or an
integer (when used with NCBIXML).  Perhaps we should also change the default in
a new record object too...

query_letters versus query_length
---------------------------------
Another of Jacobs suggestions was to rename the record.query_letters (short for
number of letters in query?) to something like query_length (which is closer to
the actual text of query_len used in the XML file).  I personally am not
inclined to change this even though it would be slightly clearer.

Note that I have corrected the error on line 186 of NCBIXML.py in CVS - well
spotted Jacob.  This mistake was my fault - recently introduced as part of the
changes I made on bug 2051


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