Thanks Jenny. It will be worthwhile taking a look at the steps you followed to interface with Ensembl.
--David David M. Goodstein Computational Genomics and Plant Genomics Program Joint Genome Institute USDOE - Lawrence Berkeley National Lab http://www.phytozome.net On Jun 2, 2009, at 6:58 PM, Jenny Qing Qian wrote: > Hi Titus and David, > > My ENSEMBL interface relies on Pygr code added after the latest > public Pygr release pygr-0.7.1.tar.gz. To get a working copy, you > could pull from git://github.com/jqian/pyensembl.git. This > interface is handy in importing Ensembl annotation datasets into > Pygr worldbase. > > Cheers, > Jenny > > On Tue, Jun 2, 2009 at 6:05 PM, C. Titus Brown <c...@msu.edu> wrote: > > On Tue, Jun 02, 2009 at 05:23:36PM -0700, dmgood11 wrote: > -> I was wondering if there had been any work on supporting fetches > from > -> BioMart or GBrowse/GFF databases (for those of us whose genomic > data > -> are not stored in Santa Cruz format)? > > Hi David, > > none that I know of, although Jenny Qian worked on an ENSEMBL > interface > -- you can take a look at it here, > > http://pygr.googlecode.com/files/pyensembl-0.1.0.tar.gz > > although I think it is not yet mature. Jenny, any comments? > > I expect to write some wrappers to load in GFF3 later this summer. > I'll > post them here as I work on it. > > cheers, > --titus > -- > C. Titus Brown, c...@msu.edu > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
