On Jul 16, 7:21 am, "C. Titus Brown" <[email protected]> wrote: > On Mon, Jul 13, 2009 at 03:36:58PM -0700, David Goodstein wrote: > > -> Thanks Titus. Our group did end up going forward (or at least > -> attempting to go forward) with writing our own classes that consume > ->GFF. Since we've tried to make all our back-end systems capable of > -> emittingGFF, hopefully those classes will be reusable. We started > -> with the C17 cookbook recipe which, sort of, explain how one might go > -> about this. There is still a little bit of mystery (how the various > -> union operations associate exons with genes) but we're making progress. > > Cool, let us know how it goes! > > --titus
I don't know if this is the same idea, but it would be great to mirror some portion of gff files natively in pygr-- gene entries have mRNA children which have exon children. That's a natural graph relationship which would be great to have available in pygr. Is there code already to do this kind of thing? If not, what would be the best approach? I can think of a few... * Read the gff file and store its rows as 'Bags' as Titus did in his gff parser-- have myGene.exons map to the 'exon' entries that are children of myGene. Let pygr pickle this as a dictionary of genes. This would mean having a very large dictionary in-memory whenever you wanted to use the annotations. * Create an sqlite or mysql db from the gff file and make that resource available to pygr. Is there a better way to do this? -- Jake --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
