[BioPython] Problem parsing genbank file

[Brad Chapman]

Hi Andy;

> I just updated from cvs and got this error when trying to parse a genbank
> file that had mutliple genbank files in it, I got this error :
> Traceback (most recent call last):
[...]
> Martel.Parser.ParserPositionException: error parsing at or beyond character
> 20805

Thanks for sending me the file separately. It actually looks like
one of the records in the file: AF124045, was somehow corrupted. The
region where the parser fails looks like:

     misc_feature    <38880..>39000
                     /note="putative breakpoint of recombination in orthologous
                     maize region, 
                     38875 bp is the end of homology, >38875-50877repeat_region   join(<38904..38924,38960..>39022)
                     /note="CT-rich stretches"
                     /evidence=not_experimental

where in the original file (from NCBI), it looks like:

     misc_feature    <38880..>39000
                     /note="putative breakpoint of recombination in orthologous
                     maize region,
                     38875 bp is the end of homology, >38875-50877< region
                     missing in maize; Region: Breakpoint"
                     /evidence=not_experimental
     repeat_region   join(<38904..38924,38960..>39022)
                     /note="CT-rich stretches"
                     /evidence=not_experimental

So somehow it looks like the text from "< region missing in" to the
next feature key (repeat_region) was deleted.

I've not seen something like this before, but the best solution
seems to be to re-download this record and try parsing it all again.
All of the other records in your file seem to parse fine.

Hope this helps.
Brad