Entering edit mode
3.4 years ago
Filippo Grazioli
•
0
I'd like to convert the genes identifiers from the following format to ensembl with mygene:
'RP11.27G24.3', 'CTD.2035E11.4', 'CTD.2515C13.2', 'RP11.366M4.18'
This is the function:
import mygene
def get_ensembl_gene_mapping(ensembl_gene_ids):
mg = mygene.MyGeneInfo()
records = mg.querymany(
ensembl_gene_ids,
scopes='symbol',
fields='ensembl.gene',
species='human'
)
symbol_to_ensembl = dict()
ensembl_to_symbol = dict()
for record in records:
if 'ensembl' in record:
if 'gene' in record['ensembl']:
symbol_to_ensembl[record['query']] = record['ensembl']['gene']
ensembl_to_symbol[record['ensembl']['gene']] = record['query']
return symbol_to_ensembl, ensembl_to_symbol
With scopes='symbol'
, the gene symbols above cannot be found. Does anybody know what the correct scope is?