[BioPython] GFF parser

[Sean Davis]

On Dec 9, 2007 10:53 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> 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
>

You might take a look at this project (http://g2.trac.bx.psu.edu/ ).  The
code is available for download.  It might have some GFF parsing abilities
that could be hacked to do what you want.  An alternative is to load the
data using perl and access using Bio.GFF.  If I recall, there is basically a
single perl script for loading GFF data in to a database.

Just some ideas.

Sean