[BioRuby] GFF3

[Tomoaki NISHIYAMA]

Hi,

It sounds me nice to have such feature.
Maybe first thing to do for the implementation is to make a function
to collect exons of a mRNA, sort and write join addresses,
and finally pass to Sequence::NA.splicing.

One thing needed before implementation is how to specify the sequene.
GFF files sometimes comes without the sequence part and sometimes  
with the
sequence.  When the sequence is accompanied within the file its  
simple: just use it.
If the sequence is not accompanied, may be we should pass a Hash of  
Bio::Sequence::NA?
When a hash is supplied for a GFF with Sequence should the hash  
override the accompanied
sequence?

Some more exceptional thing would be handling circular genomes with some
annotation spanning over the cut site of the genome.

-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan


On 2010/08/16, at 21:05, Pjotr Prins wrote:

> The GFF3 module parses GFF3 files and stores them in memory. We could
> do something with that data. Most people will want to fetch mRNA and
> CDS's. BioPerl has some similar facility.
>
> How about adding a module GFF3::Sequence with methods that fetch the
> mRNA (splicing) variants and CDS's that belong to an ID? Or do you
> think an implementation would be ambiguous?
>
> Or is that already in there? I must admit I can't find it.
>
> Pj.
>
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