> > > I think we could divide this into two types, MySQL version using public > mysql database and Collection version downloaded from UCSC website (.sql and > .txt.gz files). For MySQL version, we could identify "type" of table by > "desc" SQL syntax and supply convenient method to query/retrieve annotations > from public mysql server, just like ensembl module by Jenny. >
I could try the mysql version. Could you clarify the point of doing both? thanks, Jenny > For Collection version, we could download .sql file from web and > parse/identify table types, then add AnnotationDB by reading .txt.gz files. > > I think I could do the Collection version and add to the biodb2 XMLRPC > server. Proposed table will be Gene prediction, Repeats, SNP tables. > > > -- > Namshin Kim > > > > > > On Tue, Sep 1, 2009 at 4:01 PM, Christopher Lee <[email protected]>wrote: > >> >> >> On Aug 31, 2009, at 7:03 PM, Jenny Qing Qian wrote: >> >> > As the ensembl database, the ucsc database has various kinds of >> > annotation feature tables like exons and genes. I am not sure >> > whether they also have a seq_region table. I assume they directly >> > map their annotations to their reference genomes, not via >> > contigs... If this is the case, then we could just simplify the >> > seqregion.py and work out the mapping. Agree? >> > >> > There is no seqregion table. >> > >> > Thanks. That helps to simplify the case. If they don't store the >> > sequences at contig-level in a separate table, they probably don't >> > need a seqregion table for coordinates transformation. >> >> I'd expect that UCSC would map the Ensembl annotations directly onto >> their own assembly (i.e. no more seq_region; "stop the madness!"), and >> it sounds like that's what they've actually done. If you can identify >> a few candidate tables in their MySQL server that store gene and exon >> annotations, we can quickly do an experiment to see how hard it would >> be to plug these annotations into Pygr. I bet it'll be >> straightforward, and could be good to include in the tutorial. >> >> -- 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 -~----------~----~----~----~------~----~------~--~---
