Hey Rob, Thank you! I'll need to change the Python Ensembl API a bit, so that it will be able to retrieve sequence slices from Bio.Seq.Genome.MOUSE.mm5 via the UCLA pygr.Data server. Shouldn't be hard. Do you know which core database in the ensembl database system corresponds to this genome assembly?
Cheers, Jenny On Tue, Oct 14, 2008 at 1:38 PM, Rob Kirkpatrick < [EMAIL PROTECTED]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
