[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 #12 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-22 12:08 EST -------
Query Length
============

XML output includes this information once, currently recorded as .query_letters
only.

Plain text output includes this twice, recorded as .query_letters (associated
with the query header) and .query_length (associated with the pairwise
alignments).

e.g.

...
Query= gi|120291|sp|P21297|FLBT_CAUCR FLBT PROTEIN
         (141 letters)
...

>gi|120291|sp|P21297|FLBT_CAUCR FLBT PROTEIN
           Length = 141
...

As far as I know, these are always the same.  An assertion could be added to
the plain text parser to verify this...

For consistency, the XML parser could just populate both .query_length and
.query_letters - a simple change that won't break any old code and makes
migrating from the text parser to the XML parser a little easier.

This does perpetuate the confusion of two names.  We could go further and make
one of these properties officially deprecated (e.g. using a property method to
issue a warning).  But which one should we keep?  Currently the XML parser only
supports .query_letters but .query_length is more natural.


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