Hi David, What sorts of ensembl datasets are you mostly interested in? Which database would you like to interface with first?
Cheers, Jenny On Tue, Jun 2, 2009 at 8:49 PM, David Goodstein <dmgoodst...@lbl.gov> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
