60ff056e1f85059922a4cb8532a9c8d1a7a7218d
braney
  Wed Aug 31 11:47:17 2022 -0700
update OMiM otto process to use ncbiRefSeq

diff --git src/hg/utils/otto/omim/buildOmimTracks.sh src/hg/utils/otto/omim/buildOmimTracks.sh
index a6a952e..d1abc0e 100755
--- src/hg/utils/otto/omim/buildOmimTracks.sh
+++ src/hg/utils/otto/omim/buildOmimTracks.sh
@@ -43,31 +43,36 @@
 ############################################################
 # Load mim2gene table and omimGene2
 # note: doOmimGene2 depends on omim2gene
 
 # split gene/phenotype entries, omit Ensembl gene IDs
 grep -v '^#' mim2gene.txt | tawk '$2 ~ "gene/phenotype" \
   {$2 = "gene"; print $1,$2,$3,$4; $2 = "phenotype"}; {print $1,$2,$3,$4}' > mim2gene.updated.txt
 
 # quick hack - frequently there's no gene ID and mysql complains
 tawk '$3 == "" {$3 = 0}; {print $0}' mim2gene.updated.txt |
 hgLoadSqlTab -verbose=0 -warn $db omim2geneNew $SQLDIR/omim2gene.sql stdin
 
 # Not sure what this file is created for.  Can probably remove this?
 tawk '{print $1, $3, $2}' mim2gene.updated.txt > mim2gene.tab
 
+if [ $db != "hg18" ]
+then
+    ../../doOmimGene2.sh $db omimGene2.tab
+else
     ../../doOmimGene2 $db stdout | sort -u > omimGene2.tab
+fi
 
 hgLoadBed -verbose=0 $db omimGene2New omimGene2.tab
 
 ############################################################
 # build omimGeneSymbol and omimPhenotype tables
 # note: doOmimGeneSymbol depends on omimGeneMap2 table
 
 ../../doOmimGeneSymbols $db stdout | sort -u > omimGeneSymbol.tab
 
 hgLoadSqlTab -verbose=0 -warn $db omimGeneSymbolNew $SQLDIR/omimGeneSymbol.sql omimGeneSymbol.tab
 
 ./doOmimPhenotypeNew genemap2.txt omimPhenotypeNew.tab
 
 hgLoadSqlTab -verbose=0 -warn $db omimPhenotypeNew $SQLDIR/omimPhenotype.sql omimPhenotypeNew.tab