a3f91e95e311015f0e6bfab4818083d1c029b28b
fanhsu
  Mon Dec 6 13:58:56 2010 -0800
Created to check, download, and process DECIPHER data.
diff --git src/utils/decipher/buildDecipher src/utils/decipher/buildDecipher
new file mode 100755
index 0000000..814a043
--- /dev/null
+++ src/utils/decipher/buildDecipher
@@ -0,0 +1,32 @@
+# get raw data file from DECIPHER
+
+cp $1  decipherRaw.txt -p
+
+hgsql hg18 -e 'delete from decipherRaw'
+
+hgsql hg18 -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 ' |\
+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
+
+# Create knownToDecipher table
+hgMapToGene -all hg18 decipher knownGene knownToDecipher
+
+# Create knownCanonToDecipher table
+
+hgsql hg18 -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'
+
+