[BioRuby] GFF3

[Pjotr Prins]

Hi,

I am in the process of providing GFF3 support for extracting mRNA,
exons and CDSs from a GFF file. The BioRuby plugin is at:

  http://github.com/pjotrp/bioruby-gff3-plugin

and the writeup is at:

  http://thebird.nl/bioruby/BioRuby_GFF3.html

You are invited to comment on its contents.

The first genome I am trying has over 600Mb of data, which, sadly,
won't fit in a 2Gb RAM Thinkpad. I could use a large memory server or
database, but that I consider cheating ;).

BTW I am not suprised GFF3 support in, for example, BioSQL is patchy.
The GFF3 standard is somewhat loosely defined, and open to
interpretation. Not that it necessarily is a bad thing, though it is
probably impossible to write the all encompassing parser. See the
writeup. 

Pj.