db5ac43c0f7db0be135f2e3a1ca4f58c0e91ec80
fanhsu
  Tue Feb 8 11:19:36 2011 -0800
Updated buildDecipher from hg18 to hg19.
diff --git src/utils/decipher/buildDecipher src/utils/decipher/buildDecipher
index 814a043..8075969 100755
--- src/utils/decipher/buildDecipher
+++ src/utils/decipher/buildDecipher
@@ -1,32 +1,32 @@
 # get raw data file from DECIPHER
 
 cp $1  decipherRaw.txt -p
 
-hgsql hg18 -e 'delete from decipherRaw'
+hgsql hg19 -e 'delete from decipherRaw'
 
-hgsql hg18 -e \
+hgsql hg19 -e \
 'load data local infile "decipherRaw.txt" into table decipherRaw ignore 1 lines'
 
-hgsql hg18 -N -e 'select "chr", chr, start-1, end, id from decipherRaw ' |\
+hgsql hg19 -N -e 'select "chr", chr, start-1, end, id from decipherRaw ' |\
 sed -e 's/chr\t/chr/' |sort -u>j.tmp
 
 # fix some out of range of entries
 cat j.tmp|sed -e 's/243000000/242951149/' |\
 sed -e 's/115090019/114142980/' >decipher.bed
 rm j.tmp
 
 # Load decipher table
-hgLoadBed hg18 decipher decipher.bed
+hgLoadBed hg19 decipher decipher.bed
 
 # Create knownToDecipher table
-hgMapToGene -all hg18 decipher knownGene knownToDecipher
+hgMapToGene -all hg19 decipher knownGene knownToDecipher
 
 # Create knownCanonToDecipher table
 
-hgsql hg18 -N -e \
+hgsql hg19 -N -e \
 'select d.* from knownToDecipher d, knownCanonical c where c.transcript=d.name' >knownCanonToDecipher.tab
 
-hgsql hg18 -e 'delete from knownCanonToDecipher'
-hgsql hg18 -e 'load data local infile "knownCanonToDecipher.tab" into table knownCanonToDecipher'
+hgsql hg19 -e 'delete from knownCanonToDecipher'
+hgsql hg19 -e 'load data local infile "knownCanonToDecipher.tab" into table knownCanonToDecipher'