[BioRuby] GFF3

[Tomoaki NISHIYAMA]

Hi,

> A simple implementation would be to store all relations into a
> graph (or graphs) and then extracting information.

I recently wrote a program to extract all the mRNAs, but up to the  
addresses
and not to the sequences.

http://github.com/tomoakin/Bioruby-use/blob/master/src/gff2easytrack.rb

This is not designed to be very general, but might be useful as a  
starting point.
-- 
Tomoaki NISHIYAMA

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


On 2010/08/16, at 21:40, Naohisa GOTO wrote:

> On Mon, 16 Aug 2010 14:05:30 +0200
> Pjotr Prins <pjotr.public14 at thebird.nl> 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?
>
> Currently, the GFF parser in BioRuby is currently based on lines.
> To treat  relations in the lines in a GFF3 file will be needed.
> A simple implementation would be to store all relations into a
> graph (or graphs) and then extracting information.
>
> BTW, for extracting sequence, I prefer GFF3::SequenceCutter or
> ExtractSequence rather than GFF3::Sequence.
>
>
>> Or is that already in there? I must admit I can't find it.
>
> No.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>