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Convert ENSEMBL stable identifiers to gene symbols
import biomart
def get_ensembl_mappings():
# Set up connection to server
server = biomart.BiomartServer('http://uswest.ensembl.org/biomart')
mart = server.datasets['mmusculus_gene_ensembl']
# List the types of data we want
attributes = ['ensembl_transcript_id', 'mgi_symbol',
'ensembl_gene_id', 'ensembl_peptide_id']
# Get the mapping between the attributes
response = mart.search({'attributes': attributes})
data = response.raw.data.decode('ascii')
ensembl_to_genesymbol = {}
# Store the data in a dict
for line in data.splitlines():
line = line.split('\t')
# The entries are in the same order as in the `attributes` variable
transcript_id = line[0]
gene_symbol = line[1]
ensembl_gene = line[2]
ensembl_peptide = line[3]
# Some of these keys may be an empty string. If you want, you can
# avoid having a '' key in your dict by ensuring the
# transcript/gene/peptide ids have a nonzero length before
# adding them to the dict
ensembl_to_genesymbol[transcript_id] = gene_symbol
ensembl_to_genesymbol[ensembl_gene] = gene_symbol
ensembl_to_genesymbol[ensembl_peptide] = gene_symbol
return ensembl_to_genesymbol
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