c221127385169ec659bcf7e598bd4ef83189b264
braney
  Fri Sep 21 12:41:07 2012 -0700
got it working in /hive/data/outside/otto/decipher (#8840)
diff --git src/utils/decipher/buildDecipher src/utils/decipher/buildDecipher
index f1f0f32..76a4806 100755
--- src/utils/decipher/buildDecipher
+++ src/utils/decipher/buildDecipher
@@ -1,32 +1,33 @@
 # get raw data file from DECIPHER
 
 #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'
+'load data local infile "decipherRaw.txt" into table decipherRaw'
 
 hgsql hg19 -N -e 'select "chr", chr, start-1, end, id from decipherRaw ' |\
 sed -e 's/chr\t/chr/' |sort -u>j.tmp
 
+cp j.tmp decipher.bed
 # 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
+#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'