> > Hi Chris,
* importing UCSC, Ensembl (much work already done) > * Using SQL db as a backend for the above Last year, as a google summer of code student, I've created an initial API for ensembl homo_sapiens_core_47_36i db using classes from pygr.Data and pygr.sqlgraph. The code is available at git:// github.com/jqian/pyensembl.git into the jenny_pyensembl_new branch. This API provides a 'Perl-like' interface for automatic importing of ensembl data into pygr.Data namespace. Once you have the ensembl data saved in your pygr.Data path of choice, you have the options of retrieving it either via the 'Perl-like' interface (this interface is smart to search the pygr.Data namespace first) or the pygr.Data interface. Right now, I am working on making the API adaptable to the current human core db, so that the annotations retrieved directly from the db are in sync with those from the UCSC browser. If you are interested, we could discuss it. Cheers, Jenny > > > On 25 Mrz., 06:18, "C. Titus Brown" <c...@msu.edu> wrote: > > Hi, Chris & Eden, > > > > look over the projects here, > > > > http://cartwheel.idyll.org/wiki/PygrGsoc2008Projects > > > > and see if there's anything that interests you. A few projects that I > > think are particularly ripe: > > > > -- > > > > pygr.Data server Web interface to list available resources > > > > Fix pickle (in)security. Signed pickles, e.g. with GPG? TrustedPickle? > > prototype? See item #13 on mailing lilst posting, above. > > > > Build tools & libraries to wrap/import a variety of alignment types and > > larger data sets, e.g. CLUSTALW, blastz, LAGAN, ENSEMBL, etc. (#10 & 11 > > on mailing list post, above) > > > > fast NLMSA joins (#4, #6) > > > > Fast result filtering (#5) > > > > -- > > > > Basically, I would suggest picking some things that you vaguely > > understand or find interesting, googling about a bit to see what you can > > figure out, and then posting again to the list, looking for a mentor. > > You can also contact people privately, off-list, but that's riskier -- > > the deadline is soon and people are randomly busy & non-responsive... > > > > 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 -~----------~----~----~----~------~----~------~--~---
