4832738cf85ebd564d9e4303073f0c9fd150b441
fanhsu
  Thu Aug 18 11:14:52 2011 -0700
Created buildOmimTracks.csh
diff --git src/utils/omim/buildOmimTracks.csh src/utils/omim/buildOmimTracks.csh
new file mode 100755
index 0000000..6142f69
--- /dev/null
+++ src/utils/omim/buildOmimTracks.csh
@@ -0,0 +1,167 @@
+#!/bin/tcsh
+# BUILD $1 OMIM RELATED TRACKS
+
+cat genemap|sed -e 's/|/\t/g' > genemap.tab
+
+hgLoadSqlTab -warn $1 omimGeneMap ~/kent/src/hg/lib/omimGeneMap.sql genemap.tab
+
+# Load mim2gene table
+
+fgrep -v "gene/phenotype" mim2gene.txt > j.tmp.1
+fgrep  "gene/phenotype" mim2gene.txt > j.tmp.2
+
+cut -f 2 j.tmp.2|sed -e 's/\//\t/' >j.tmp
+
+cut -f 1 j.tmp.2 >j.1
+
+cut -f 1 j.tmp >j.g
+cut -f 2 j.tmp >j.p
+
+cut -f 3-5 j.tmp.2 >j.345
+
+paste j.1 j.g j.345 >jj.g
+paste j.1 j.p j.345 >jj.p
+
+cat j.tmp.1 jj.g jj.p >mim2gene.updated.txt 
+
+rm j.* jj.*
+
+
+cut -f 1 mim2gene.updated.txt >j1
+cut -f 2 mim2gene.updated.txt >j2
+cut -f 3 mim2gene.updated.txt >j3
+
+paste j1 j3 j2 >mim2gene.tab
+
+hgsql $1 -e 'drop table mim2gene'
+hgsql $1 < ~/kent/src/hg/lib/mim2gene.sql
+
+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
+
+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
+
+mkdir -p av
+cd av
+
+# get the mimAV.txt data file from OMIM
+
+cp ../mimAV.txt . -p
+
+cut -f 1 mimAV.txt >j1
+cut -f 2 mimAV.txt >j2
+cut -f 3  mimAV.txt >j3
+cut -f 4  mimAV.txt >j4
+cut -f 5  mimAV.txt >j5
+
+cat j1 |sed -e 's/\./\t/' >j1.2
+
+cat j4 |sed -e 's/,/\t/' >j4-2
+cut -f 1 j4-2 >j4.1
+cut -f 2 j4-2 >j4.2
+
+paste j1 j1.2 j3 j4 j4.1 j4.2 j5 j2 >omimAv.tab
+
+hgsql $1 -e 'drop table omimAv'
+hgsql $1 < ~/src/hg/lib/omimAv.sql
+hgsql $1 -e 'load data local infile "omimAv.tab" into table omimAv ignore 1 lines'
+hgsql $1 -e 'update omimAv set repl2 = rtrim(ltrim(repl2))'
+
+doOmimAv $1 omimAvRepl.tab j.err
+
+hgsql $1 -e "drop table omimAvRepl"
+hgsql $1 < ~/kent/src/hg/lib/omimAvRepl.sql
+hgsql $1 -e 'load data local infile "omimAvRepl.tab" into table omimAvRepl'
+
+rm j1.2  j1 j2 j3  j4  j4-2  j4.1  j4.2  j5
+
+if ($1 == "hg18") then
+   hgsql $1 -N -e 'select chrom, chromStart, chromEnd, avId from omimAvRepl r, snp130 s where s.name = dbSnpId order by avId' |sort -u > omimAvSnp.tab
+else
+   hgsql $1 -N -e 'select chrom, chromStart, chromEnd, avId from omimAvRepl r, snp132 s where s.name = dbSnpId order by avId' |sort -u > omimAvSnp.tab
+endif
+
+hgLoadBed -allowStartEqualEnd  $1 omimAvSnp omimAvSnp.tab
+cd ..
+
+##############################################################
+echo build omimLocation ...
+
+mkdir -p location
+cd location
+
+doOmimLocation $1 omimLocation.bed j.err
+
+hgLoadBed $1 omimLocation omimLocation.bed
+
+# Remove all gene entries in omimGene2 from omimLocation table
+
+hgsql $1 -N -e \
+'delete from omimLocation where name  in (select name from omimGene2) '
+
+# Per OMIM request, delete all the gray entries in omimLocation table.
+
+mkdir -p cleanUpOmimLocation
+cd cleanUpOmimLocation
+
+echo cleaning omimLocation ...
+
+hgsql $1 -N -e \
+'select distinct name from omimLocation' |sort -u >j.all
+
+hgsql $1 -N -e \
+'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=1' >j.1
+hgsql $1 -N -e \
+'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=2' >j.2
+hgsql $1 -N -e \
+'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=3' >j.3
+hgsql $1 -N -e \
+'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=4' >j.4
+
+cat j.1 j.2 j.3 j.4 |sort -u >j.1234
+
+diff j.all j.1234 |grep "<" |sed -e "s/</do1 ${1}/" >doall
+
+#cat doall
+
+cat << '_EOF_' > do1
+hgsql $1 -e "delete from omimLocation where name='${2}'"
+'_EOF_'
+
+#sleep 3
+#echo after sleep
+
+chmod +x do1
+chmod +x doall
+./doall
+
+##############################################################
+
+# remember to check in new mim2gene.sql
+