[Biopython-dev] GenBank bug, oriT feature missing

[Iddo Friedberg]

I agree that these things should be handeled better. How about raising 
an UnknownFeature exception, which is not silenced by default. The user 
can then decide whether the parser should trap & silence such an 
exception when it occurs.

./I

Marc Colosimo wrote:
> Hi,
> 
> 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 genbank):
> 
> "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line 38, in 
> fatalError
>     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:
> 
> GenBank.FeatureParser(debug_level=2)
> 
> 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) 
> almost
>                      identical to oriT regions of plasmids from the 
> 'Q-group'"
>                      /evidence=not_experimental
> 
> This really isn't a pretty way of dealing with unknown features. Is 
> there a way to get this to just pass unknown features?
> 
> Thanks,
> 
> Marc
> 
> 
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> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
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http://ffas.ljcrf.edu/~iddo