[Biopython] GFF Parsing

[Peter]

Hello Vipin,

I think your question is probably aimed at Brad, so I will
forward the attachment to him directly as well. Brad's GFF
code isn't in Biopython yet, but we plan to add it later.

Have you signed up to the Biopython mailing list? Once you
have done this you can email biopython at lists.open-bio.org
or biopython at biopython.org with questions like this. I have
copied this reply to the list (without the attachment).

Peter
---------- Forwarded message ----------
From: Vipin TS <vipin.ts at gmail.com>
Date: Fri, Aug 14, 2009 at 1:47 PM
Subject: GFF Parsing
To: biopython-owner at lists.open-bio.org


To whom it may concern,

Thanks for the development of a quick parser for GFF files. It is very
useful.

I have a doubt,
I used the GFFParser.py program to extract the genome annotation from the
file attached with this mail. Please find the attached file. (Because of the
size of file here I included a few lines)
I wrote a python script like this

##################################################
import GFFParser

pgff = GFFParser.GFFMapReduceFeatureAdder(dict(), None)

cds_limit_info = dict(
   gff_type = ["gene","mRNA","CDS","exon"],
   gff_id = ["Chr1"]
   )

pgff.add_features('../PythonGFF/TAIR9_GFF_genes.gff3', cds_limit_info)

pgff.base["Chr1"]

final = pgff.base["Chr1"]

##################################################

By executing this script I am able to extract gene, mRNA and exon annotation
from specified GFF file. But I am unable to extract the CDS related
information from GFF file.
It will be great if you can suggest me an idea to include gene, mRNA, exon
and CDS information in a single strech of parsing of GFF file.

Thanks in advance,

Vipin T S
Scientific programmer
Friedrich Miescher Laboratory of the Max Planck Society
Spemannstrasse 37-39
D-72076 Tuebingen Germany