710f5b14245de8fc6cdf47e281f7f83178ab5205
braney
  Thu Sep 20 08:55:56 2012 -0700
checking in the scripts that Fan was actually using to update decipher (#8840)
diff --git src/utils/decipher/buildDecipher src/utils/decipher/buildDecipher
index 8075969..f1f0f32 100755
--- src/utils/decipher/buildDecipher
+++ src/utils/decipher/buildDecipher
@@ -1,32 +1,33 @@
 # get raw data file from DECIPHER
 
-cp $1  decipherRaw.txt -p
+#cp $1  decipherRaw.txt -p
+cat $1|grep -v '#' >  decipherRaw.txt 
 
 hgsql hg19 -e 'delete from decipherRaw'
 
 hgsql hg19 -e \
 'load data local infile "decipherRaw.txt" into table decipherRaw ignore 1 lines'
 
 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 hg19 decipher decipher.bed
 
 # Create knownToDecipher table
 hgMapToGene -all hg19 decipher knownGene knownToDecipher
 
 # Create knownCanonToDecipher table
 
 hgsql hg19 -N -e \
 'select d.* from knownToDecipher d, knownCanonical c where c.transcript=d.name' >knownCanonToDecipher.tab
 
 hgsql hg19 -e 'delete from knownCanonToDecipher'
 hgsql hg19 -e 'load data local infile "knownCanonToDecipher.tab" into table knownCanonToDecipher'