[Biopython-dev] fpc and gff

[Jose Blanca]

Sorry for the previous incomplete mail. :(

Hi:
I'm interested in parsing an fpc physical map and writing a gff3 file from it. 
That's done by the fpc people in bioperl and they go from fpc to gff2. I 
would like to do it in python.
I've written the fpc parser looking at the bioperl one. You can take a look 
at:
http://bioinf.comav.upv.es/svn/biolib/biolib/src/biolib/fpc.py

Now I have to create the gff structure and writer. I've been reading Brad's 
code regarding the GFF parser and writer. I would like to integrate my fpc 
work as much as posible with biopython and if you like it we could add the 
fpc to Biopython in the future.
But I have not a clear idea on the relation between GFF and SeqFeature. The 
main problem is the subfeature and the gff feature hierarchy. My take on that 
at the moment is to write a GFFfeature class similar to the gff feature with 
seqid, source, type, start, end, score, etc. and go from the fpc to 
GFFFeature objects. I know that this would not integrate nicely with 
BioPython. Could you give some hint on how to do it in a proper way?
Best regards,

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)