Add script to generate HGNC symbol/ID mapping

Author: bgyori

export/hgnc_ids.py

@@ -0,0 +1,47 @@
+"""Several files in this resource use HGNC gene symbols to identify individual
+genes. However, the symbols assigned to HGNC IDs can change over time, and
+therefore previously curated symbols can become invalid. This script
+generates a mapping of current (i.e. at the time of running the script)
+mappings of HGNC IDs to symbols so that the assumptions about the identity
+of the genes in the various tables can be traced."""
+
+import os
+import csv
+from indra.databases import hgnc_client
+
+if __name__ == '__main__':
+    path_this = os.path.dirname(os.path.abspath(__file__))
+    hgnc_symbols = set()
+    # Gather all HGNC symbols from relations.csv
+    relations_file = os.path.join(path_this, os.pardir, 'relations.csv')
+    with open(relations_file, 'r') as f:
+        csvreader = csv.reader(f, delimiter=str(u','), lineterminator='\r\n',
+                               quoting=csv.QUOTE_MINIMAL,
+                               quotechar=str(u'"'))
+        for row in csvreader:
+            ns1, id1, rel, ns2, id2 = row
+            if ns1 == 'HGNC':
+                hgnc_symbols.add(id1)
+            if ns2 == 'HGNC':
+                hgnc_symbols.add(id2)
+
+    # Gather all HGNC symbols from grounding_map.csv
+    gm_file = os.path.join(path_this, os.pardir, 'grounding_map.csv')
+    with open(gm_file, 'r') as f:
+        csvreader = csv.reader(f, delimiter=str(u','), lineterminator='\r\n',
+                               quoting=csv.QUOTE_MINIMAL,
+                               quotechar=str(u'"'))
+        for row in csvreader:
+            namespaces = row[1::2]
+            ids = row[2::2]
+            for ns, id in zip(namespaces, ids):
+                if ns == 'HGNC':
+                    hgnc_symbols.add(id)
+
+    # Create output file
+    out_file = os.path.join(path_this, 'hgnc_symbol_map.csv')
+    with open(out_file, 'w') as fh:
+        for hgnc_symbol in sorted(list(hgnc_symbols)):
+            hgnc_id = hgnc_client.get_hgnc_id(hgnc_symbol)
+            fh.write('%s,%s\r\n' % (hgnc_symbol, hgnc_id))
+