[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 #8 from jmjoseph at andrew.cmu.edu  2007-01-10 16:05 -------
> My question to Jacob:
> Why do you need to use the plain-text Blast parser? Is there something it can
> do that the XML parser cannot?

I use only the XML parser.  My greatest concern is not that the plain-text and
XML parsers are different, but rather that the XML parser is not consistent
with Record.py.  An example that I consider completely broken is the definition
of query_length in Record.py, but the use of self._blast.query_letters in
NCBIXML.py.

To avoid breaking the existing plain-text parser code, would it be too
objectionable to use a new class, Record-XML.py, with definitions that exactly
match the usage in NCBIXML.py?  Since few people are likely to use both
parsers, and any using the XML parser have required recent code updates anyway,
perhaps this separation would be easiest.

Thanks. -Jacob


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