On Tue, 15 Dec 2009 06:37:44 -0800 "C. Titus Brown" <c...@msu.edu> wrote:
> could you post a script or two showing how you might work with this > schema in practice? Thanks! Uncommented test scripts are just > fine :) I suggest you have a look at pygr/apps/ucsc_ensembl_annot.py in my 'ucsc_ensembl' GitHub branch. Note that I keep changing this script on a regular basis; that said, in this post I shall use http://github.com/mkszuba/pygr/commit/b50f1b8b792c58180cac10d778ba22ab263272d0 as reference. Don't mind the ugly code, it is as I mentioned earlier a prototype and will be reorganised before the release. > > One question: shall we hide from the user that protein data (s)he > > gets is actually transcript data (i.e come up with some sort of a > > wrapper) or just let him/her have it as it is? > I don't understand this question... is the problem that the > "transcript IDs" would actually be protein IDs? If only for > traceability, I would suggest a wrapper. See lines 137-140 in my script, which produce the following output: ENSP00000372525 annotENST00000383052[0:47226] chrY[2863321:2910547] What I meant by hiding from the user was creating a wrapper that would use data from the transcript database but with protein identifiers; right now protein-to-transcript-ID mapping is done explicitly and the database is still just a transcript database. -- MS -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@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.
