[Biopython-dev] GenBank bug, oriT feature missing

Marc Colosimo mcolosimo at mitre.org
Fri Feb 27 16:25:20 EST 2004


I've just spent a good part of a day trying to understand what was 
going wrong and I think I finally know. Here is the problem:

I was getting this exception for reading in a GenBank file (from 

"/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line 38, in 
     raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond 
character 1981

After digging into the GenBank code (__init.py__) and then into 
Martel's code. I found I could turn on debugging:


I finally see where things die (and what character 1981 means).

for AE000070 there is a  feature tag "oriT", which seems to be missing 
from genbank_record.py and __init__.py

      oriT            81..92
                      /note="region including origin of transfer (oriT) 
                      identical to oriT regions of plasmids from the 

This really isn't a pretty way of dealing with unknown features. Is 
there a way to get this to just pass unknown features?



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