[Bioperl-guts-l] Bug in genbank.pm?

Chris Fields cjfields at illinois.edu
Thu Jun 4 21:05:38 EDT 2009


Marcos,

We need the GenBank file (or the accession) you are attempting to  
parse.  Also, what version are you using?  We have released v. 1.6 on  
CPAN, and I intend on releasing 1.6.1 soon.

chris

On Jun 4, 2009, at 5:57 PM, Marcos S. Barbeitos wrote:

> Hello.  I am trying to parse the Info from GeneBank flat files using
> Bio::SeqIO.  I got two file which are virtually identical and one of  
> them
> gets parsed just fine.  However, in the case of the other, the program
> croaks when trying to parse the features and gives me:
>
>
>
> -------------------- WARNING ---------------------
>
> MSG: Unexpected error in feature table for  Skipping feature,  
> attempting to
> recover
>
> ---------------------------------------------------
>
>
>
> I noticed that it does that after it reads the entry '/organism' in
> Features.  The only difference I can see between the two files is the
> presence of the feature ' /organelle' and of the line BASE COUNT in  
> one of
> them, but the error persists even after I remove these lines.  Apart  
> from
> that, there are the number of white spaces that precede the  
> beginning of
> each line.   Any ideas?
>
>
>
> Thanks!
>
>
>
> Marcos S. Barbeitos
>
> Post-Doc Fellow
>
> The University of Kansas
> Department of Ecology and Evolutionary Biology
> 2041 Haworth Hall
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045
> p: 785.864.5887
> f: 785.864.5860
>
>
>
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