4389d5f48220ed09aff243f8ff13b064e7dc7e0b
braney
  Wed Feb 22 17:32:10 2012 -0800
moving various pieces of code to build the omim table into one place #6943
diff --git src/utils/omim/buildOmimTracks.csh src/utils/omim/buildOmimTracks.csh
index 6142f69..5c4a34c 100755
--- src/utils/omim/buildOmimTracks.csh
+++ src/utils/omim/buildOmimTracks.csh
@@ -39,31 +39,31 @@
 hgsql $1 -e 'load data local infile "mim2gene.tab" into table mim2gene ignore 1 lines'
 
 
 hgsql $1 -e 'drop table omim2gene'
 hgsql $1 < ~/kent/src/hg/lib/omim2gene.sql
 
 hgsql $1 -e 'load data local infile "mim2gene.updated.txt" into table omim2gene ignore 1 lines'
 
 # build omimGeneSymbol table
 
 doOmimGeneSymbols $1 j.out
 cat j.out |sort -u >omimGeneSymbol.tab
 
 hgLoadSqlTab -warn $1 omimGeneSymbol ~/kent/src/hg/lib/omimGeneSymbol.sql omimGeneSymbol.tab 
 
-perl ./script1.pl --gene-map-file=genemap >omimPhenotype.tab
+perl ./parseGeneMap.pl --gene-map-file=genemap >omimPhenotype.tab
 
 hgLoadSqlTab -warn $1 omimPhenotype ~/kent/src/hg/lib/omimPhenotype.sql omimPhenotype.tab 
 
 hgsql $1 -e 'update omimPhenotype set omimPhenoMapKey = -1 where omimPhenoMapKey=0'
 hgsql $1 -e 'update omimPhenotype set phenotypeId = -1 where phenotypeId=0'
 
 doOmimGene2 $1 j.tmp
 cat j.tmp |sort -u > omimGene2.tab
 
 hgLoadBed $1 omimGene2 omimGene2.tab
 
 rm j.tmp
 ##############################################################
 # build the omimAvSnp track
 
