Model

Bedding/convert_gene_name_2_ensembl.py

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+import pandas as pd
+from bioservices import *
+
+# Read in the gene mapping file
+gene_mapping = pd.read_csv("gene_mapping.csv")
+
+# Create an instance of the BioMart service
+ensembl = BioMart()
+
+# Connect to the Ensembl database
+ensembl.new_query()
+ensembl.add_dataset_to_xml("hsapiens_gene_ensembl")
+
+# Map the gene names to their Ensembl IDs
+ensembl_ids = []
+for name in gene_mapping['Gene Symbol']:
+    ensembl.add_attribute_to_xml("external_gene_name")
+    ensembl.add_filter_to_xml("external_gene_name", name)
+    result = ensembl.results()
+    if result:
+        ensembl_ids.append(result[0][0])
+    else:
+        ensembl_ids.append(None)
+
+# Add the Ensembl IDs as a new column in the gene mapping file
+gene_mapping['ensembl_id'] = ensembl_ids
+
+# Output the mapped gene mapping file
+gene_mapping.to_csv("mapped_gene_mapping.csv", index=False)