[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 #7 from mdehoon at ims.u-tokyo.ac.jp  2007-01-10 15:47 -------
> 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.

In principle I agree with Jacob on this one. But as Jacob also indicates, there
are probably more variable names that are less than ideal. So if we change
these variable names, it's better to change all of them at the same time. This,
however, will break a lot of existing code. With all the other changes to the
Blast parsers, now doesn't seem to be the best time for such a change. However,
let's get back to this point once the dust settles with the Blast parsers.

With hit_id, hit_def, and hsp.align_length, I see no problems with Jacob's
suggestion. Objections, anybody?


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