e4g-123/Translation of raw Function Class terms to MGI Function Class…

… Values

HISTORY

@@ -1,5 +1,5 @@
 TAG: mgidbmigration-6-0-25-?
-DATE: 01/22/2025
+DATE: 01/27/2025
 STAFF: lec
 CHANGES:
 e4g-123/Translation of raw Function Class terms to MGI Function Class Values

snpfunctionclass/snpfunc.csh

@@ -99,5 +99,7 @@ and t._term_key = a._object_key
 and a._mgitype_key = 13
 ;
 
+drop index if exists snp.SNP_ConsensusSnp_Marker_idx_consensussnp_key;
+
 EOSQL
 

snpfunctionclass/snpfunc.py

@@ -5,6 +5,24 @@
 import sys 
 import os
 import gzip
+import db
+
+fxLookup = {}
+results = db.sql('''
+select t._term_key, t.term, s.badname, a.accid
+from voc_term t, mgi_translation s, acc_accession a
+where t._vocab_key = 49
+and s._translationtype_key = 1014
+and s._object_key = t._term_key
+and t._term_key = a._object_key
+and a._mgitype_key = 13
+''', 'auto')
+for r in results:
+    key = r['badname']
+    value = r['term']
+    fxLookup[key] = []
+    fxLookup[key].append(value)
+#print(fxLookup)
 
 inFile = gzip.open('/data/downloads/download.alliancegenome.org/variants/7.4.0/MGI/MGI.vep.vcf.gz', 'rt')
 for line in inFile:
@@ -38,6 +56,8 @@
                 symbol = fields[3]
                 mgiid = fields[4]
                 for term in cterms:
-                    print(symbol + "|" + mgiid + "|" + rsid + "|" + term)
+                    if term in fxLookup:
+                        for t in fxLookup[term]:
+                            print(rsid + "|" + mgiid + "|" + symbol + "|" + term + "|" + t)
 
 inFile.close()