On Tue, Aug 25, 2009 at 01:52:10PM -0700, jbiesinger wrote: -> 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! -> -> 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?
I think the latter approach is the right one, and I'm hoping that one of the tutorials-in-progress will address how to do this. If not I'll lead a counter-charge; this is something I still don't understand how to do in pygr, and I need to do it! cheers, --titus -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
