[BioPython] GFF parser

[Peter]

Ernesto wrote:
> Hi all,
>
> can biopython handle GFF files? And GTFs?
>
> Many thanks,
>
> Ernesto

Hi Ernesto,

The short answer is that no, Biopython does not (currently) handle GFF files.

We do have a module, Bio.GFF which is designed to work with an MySQL
database containing GFF data, which you must first setup using
BioPerl.  However, Bio.GFF does not work with the GFF or GTF files
directly.

You are not alone in wanting this sort of functionality - for example
earlier this year Giovanni Marco Dall'Olio asked about GFF files on
this mailing list:

http://lists.open-bio.org/pipermail/biopython/2007-June/003522.html

Peter