Forgot to mention that its here: Bio.Seq.Genome.MOUSE.mm5, coming from the default UCLA pygr.Data path...
On Mon, Oct 13, 2008 at 9:28 PM, Rob Kirkpatrick < [EMAIL PROTECTED]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
