[Biopython-dev] [Bug 3069] Support for EMBL-like files from IMGT

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3069





------- Comment #23 from laserson at mit.edu  2010-05-18 20:30 EST -------
(In reply to comment #22)

So I tried parsing the whole imgt.dat file, and we do pretty well.  The only
two problems I see are the broken location qualifiers, and a few records where
the lengths annotated in their ID strings don't match the actual lengths of the
sequences.

> In this case (and the other locations with missing text) there is no good work
> around so I would agree - get the IMGT to fix them.

So let's go ahead and change the warnings back to errors.  In the meanwhile, we
can parse properly using the SeqIO.index function and just catch and ignore all
the bad records.  And I will compile a list of bad records and give them to the
curators at IMGT.


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