Hey Jenny, I can see mm5 through mm9 on my end. I believe mm7 maps to NCBI 35.
http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm7 I don't know if there is one place where these mappings are laid out explicitly, but that would be nice. Cheers, Rob On Mon, Oct 13, 2008 at 6:16 PM, Jenny Qing Qian <[EMAIL PROTECTED]>wrote: > Hi Chris, > > I got a request from Peter Saffrey <[EMAIL PROTECTED]>, asking whether the > Python Ensembl API was able to retrieve the NCBI mouse 35 build (the > original e-mail from Peter was attached at the bottom). > > I replied that as long as one provides the species name and version number, > the Python Ensembl API is able to retrieve different genome builds. > > Since internally, the Python Ensembl API retrieves various NCBI genome > builds via pygr.Data, I told Peter that I need to check with you whether > pygr.Data has the NCBI mouse 35 build saved. > > In general, would you let me know the different kinds of NCBI genome builds > currently in pygr.Data? In addition, could we discuss whether it's feasible > to store all the genome builds available from the ensembl database system to > pygr.Data? > > thanks, > > jenny > > P.S. > > The following example shows how to get an ensembl core database object for > the NCBI human 36 build. > > 1 Create a connection to the ensembl MySQL server: > > serverRegistry = get_registry(host='ensembldb.ensembl.org', > user='anonymous') > > *2 Create access to an ensembl core database: * > > *coreDBAdaptor = serverRegistry.get_DBAdaptor('homo_sapiens', 'core', > '47_36i') * > ** > 3 Create access to the gene table in the homo_sapiens_core_47_36i database: > > > e.g. geneAdaptor = coreDBAdaptor.get_adaptor('gene') will return a > geneAdaptor object that can be used to access any record/item in the gene > table. > > 4 Create access to any record in the gene table: > > e.g. gene = geneAdaptor[1] will return a gene item with the unique dbID 1 > > Then you can get all the transcripts for that gene and their exons... > > > Original e-mail from Peter: > > I'm happy to use an existing assembly, but I don't know how to tell the API > that this is the build I want. According to this post: > > > http://listserver.ebi.ac.uk/mailing-lists-archives/ensembl-dev/msg04029.html > > In the Perl API, I need a different API version for a different build. Is > the same thing true of the Python API? > > What I want to do is get the exon and intron coordinates for a list of > genes. > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
