On Aug 25, 2009, at 3:21 PM, C. Titus Brown wrote:
> -> 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! I think Titus is referring to me when he says "tutorials-in- progress"... I will be happy to include this, but it would help me a lot to get started on a GFF example if someone could send me their example code for parsing GFF annotations (e.g. exons) from a file (or a database or whatever is a typical place people are already storing their GFF annotations in). I'd prefer to be able to focus my Pygr tutorial effort on illustrating how to use Pygr classes, rather than researching the GFF formats (which I haven't used yet). -- Chris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
