d0aad7f66c2fee0fa9366c3b3caf4d761750c055
braney
  Tue Aug 17 10:27:07 2021 -0700
first version of Gencode genes (knownGene version) for mm39

diff --git src/hg/utils/otto/knownGene/buildFoldUtr.sh src/hg/utils/otto/knownGene/buildFoldUtr.sh
new file mode 100755
index 0000000..e68abb1
--- /dev/null
+++ src/hg/utils/otto/knownGene/buildFoldUtr.sh
@@ -0,0 +1,52 @@
+#!/bin/sh -ex
+cd $dir
+{
+# MAKE FOLDUTR TABLES 
+# First set up directory structure and extract UTR sequence on hgwdev
+cd $dir
+rm -rf rnaStruct
+mkdir -p rnaStruct
+
+cd rnaStruct
+ln -s /cluster/data/$db/$db.2bit $tempDb.2bit
+mkdir -p utr3/split utr5/split utr3/fold utr5/fold
+# these commands take some significant time
+utrFa -nibPath=`pwd` $tempDb knownGene utr3 utr3/utr.fa
+utrFa -nibPath=`pwd` $tempDb knownGene utr5 utr5/utr.fa
+
+# Split up files and make files that define job.
+faSplit sequence utr3/utr.fa 10000 utr3/split/s
+faSplit sequence utr5/utr.fa 10000 utr5/split/s
+ls -1 utr3/split > utr3/in.lst
+ls -1 utr5/split > utr5/in.lst
+cd utr3
+cat << _EOF_ > template
+#LOOP
+rnaFoldBig split/\$(path1) fold
+#ENDLOOP
+_EOF_
+gensub2 in.lst single template jobList
+cp template ../utr5
+cd ../utr5
+
+gensub2 in.lst single template jobList
+
+# Do cluster runs for UTRs
+ssh $cpuFarm "cd $dir/rnaStruct/utr3; para make jobList"
+ssh $cpuFarm "cd $dir/rnaStruct/utr5; para make jobList"
+
+ssh $cpuFarm "cd $dir/rnaStruct/utr3; para time"
+ssh $cpuFarm "cd $dir/rnaStruct/utr5; para time"
+
+# Load database
+    cd $dir/rnaStruct/utr5
+    hgLoadRnaFold $tempDb foldUtr5 fold
+    cd ../utr3
+    hgLoadRnaFold -warnEmpty $tempDb foldUtr3 fold
+
+# Clean up
+    rm -r split fold err batch.bak
+    cd ../utr5
+    rm -r split fold err batch.bak
+echo "BuildFoldUtr successfully finished"
+} > doFoldUtr.log < /dev/null 2>&1