[BioPython] GenBank parsing errors

[Michael Maibaum]

On 2 Nov 2004, at 17:56, Michael Maibaum wrote:

>
> Hi,
>
> I'm trying to use biopython to parse genbank files and it is working  
> happily on some genbank files,  but not many others. So far the  
> pattern appears to be
>
> Prokaryotic complete genome => OK
> Eukaryotic complete genome =>failure.
>
> The failures are typically very early in the file and don't have  
> wonderfully useful information in the traceback. It falls over in the  
> Martel Parser giving the error
>
>
> Martel.Parser.ParserPositionException: error parsing at or beyond  
> character 191. As this genome is a bit large to attatch I've just  
> included the +/- 10 lines around 191
>
> The full file, should you want it is at:
> <ftp://ftp.ensembl.org/pub/current_tetraodon/data/flatfiles/genbank/ 
> Tetraodon_nigroviridis.0.dat.gz>
>
> Does anyone have any ideas why this is failing, is it just the joy of  
> tracking NCBI record formats and I need to start looking at the  
> internals for a fix (or use something else) or?
>


hmmph,

forgot some probably pertinent details....

biopython 1.30

python 2.3

Mac OS X 10.3.5