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.
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