We have a local EnsEMBL MySQL database containing annotated mosquito genomes.
The PyCogent cookbook states **Here** that you can access/query data from a local MySQL EnsEMBL database via the
cogent.db.ensembl.HostAccount module. **Here** is the source code for PyCogent's ensembl-api.
But I cannot access the data as the functions assume a priori that I know the exact names of species (string) whose genomes I am trying to query... After hours of searching online, I would greatly appreciate if somebody could tell me how I can list the names of species (that PyCogent would understand) so that I can finally query the local database for the genome data.
This code shows my problem, note the commenting:
Release = 73 from cogent.db.ensembl import HostAccount, Genome acc = HostAccount('localhost', 'username1', 'password1') # login details to MySQL server genome = Genome(Species='?????',Release=73,account=acc) # Where can I find the available Species list so I can replace the '?????'