[Biopython-dev] [Bug 3062] GenBank/EMBL parser breaks when features have no qualifiers

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3062





------- Comment #4 from laserson at mit.edu  2010-04-26 19:44 EST -------
I did something stupid, and uploaded the wrong IMGT record.  I will upload the
actual offending record.  However, after stepping through the code with pdb, it
appears that the problem with the offending record is that the feature
qualifiers are indented too far, so that the whitespace is not fully stripped
off.

Has it ever been considered to parse the features by breaking the line with
split(), instead of hardcoding the number of columns?  While the official EMBL
specification may hardcode the size of the fields, the parse may be more robust
to such errors.  (Though I understand the desire to conform exactly to EMBL
standards).  Eitherway, I will notify the curators of the IMGT database.

(And see the attached file with the offending record.)


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