Created
October 1, 2021 19:19
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Convert ENSEMBL stable identifiers to gene symbols
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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 |
Great! I will try.
Best
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I haven't tried it, but it should be possible! The most straightforward way to do so would be to add
'entrezgene_id'
to the end of the attributes list and convert theensembl_to_genesymbol
lines to map entrez to genesymbol e.g.More information on the available attributes can be found here: https://bioconductor.riken.jp/packages/3.4/bioc/vignettes/biomaRt/inst/doc/biomaRt.html