5f856345200f8861b168c85d45e267010d6b55e4
chmalee
  Mon Aug 3 16:40:33 2020 -0700
Update LOVD to bigBed, refs #25841

diff --git src/hg/utils/otto/lovd/checkAndLoad.sh src/hg/utils/otto/lovd/checkAndLoad.sh
index d5770fc..718c221 100755
--- src/hg/utils/otto/lovd/checkAndLoad.sh
+++ src/hg/utils/otto/lovd/checkAndLoad.sh
@@ -1,63 +1,64 @@
 #!/bin/sh -e
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/otto/lovd/check.sh
 #	This script is used via a cron job 
 
 umask 002
 WORKDIR="/hive/data/outside/otto/lovd"
 TAWK=/cluster/bin/scripts/tawk
 KENTBIN=/cluster/bin/x86_64/
 
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in lovd release, Can not find the directory: ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 today=`date +%F`
 cd $today
 
 # count columns and make sure new files have 6 columns
-new38Cc=`cat lovd.hg38.bed | $TAWK '(NF!=6)' | wc -l`
-new19Cc=`cat lovd.hg19.bed | $TAWK '(NF!=6)' | wc -l`
+new38Cc=`cat lovd.hg38.bed | $TAWK '(NF!=7)' | wc -l`
+new19Cc=`cat lovd.hg19.bed | $TAWK '(NF!=7)' | wc -l`
 if [ "$new38Cc" -ne "0" ]; then
         echo LVOD hg38 $today: found rows with not six columns, quitting
         exit 255
 fi
 if [ "$new19Cc" -ne "0" ]; then
         echo LVOD hg19 $today: found rows with not six columns, quitting
         exit 255
 fi
 
 for db in hg38 hg19
 do
     if [ ${db} == "hg19" ]
     then
         $KENTBIN/bedClip lovd.${db}.bed /cluster/data/${db}/chrom.sizes stdout | sed -e 's/^chrM/chrMT/g' > lovd.${db}.clipped.bed
     else
         $KENTBIN/bedClip lovd.${db}.bed /cluster/data/${db}/chrom.sizes lovd.${db}.clipped.bed
     fi
 
-    cat lovd.${db}.clipped.bed | awk '(($3-$2)<50)' > lovd.${db}.short.bed
-    cat lovd.${db}.clipped.bed | awk '(($3-$2)>=50)' > lovd.${db}.long.bed
     if [ ${db} == "hg19" ]
     then
-        echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t' >> lovd.${db}.short.bed
-        echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t' >> lovd.${db}.long.bed
+        echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t\t' >> lovd.${db}.short.bed
+        echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t\t' >> lovd.${db}.long.bed
     fi
+    sort -k1,1 -k2,2n lovd.${db}.clipped.bed | awk '(($3-$2)<50)' > lovd.${db}.short.bed
+    sort -k1,1 -k2,2n lovd.${db}.clipped.bed | awk '(($3-$2)>=50)' > lovd.${db}.long.bed
 
-    oldShortLc=`$KENTBIN/hgsql ${db} -e "SELECT COUNT(*) from lovdShort" -NB`
-    oldLongLc=`$KENTBIN/hgsql ${db} -e "SELECT COUNT(*) from lovdLong" -NB`
+    oldShortLc=`bigBedToBed ../release/${db}/lovd.${db}.short.bb stdout | wc -l`
+    oldLongLc=`bigBedToBed ../release/${db}/lovd.${db}.long.bb stdout | wc -l`
     newShortLc=`wc -l lovd.${db}.short.bed | cut -d' ' -f1`
     newLongLc=`wc -l lovd.${db}.long.bed | cut -d' ' -f1`
     echo ${db} short rowcount: old $oldShortLc new: $newShortLc
     echo ${db} long rowcount: old $oldLongLc new: $newLongLc
     echo $oldShortLc $newShortLc | awk -v d=${db} '{if (($2-$1)/$1 > 0.1) {printf "validate on %s LOVD short failed: old count: %d, new count: %d\n", d,$1,$2; exit 1;}}'
     echo $oldLongLc $newLongLc | awk -v d=${db} '{if (($2-$1)/$1 > 0.1) {printf "validate on %s LOVD long failed: old count: %d, new count: %d\n", d,$1,$2; exit 1;}}'
-    # bedDetail4.sql was generated like this:
-    # egrep -v 'score|strand|thick|reserved|block|chromStarts' /cluster/home/max/kent/src/hg/lib/bedDetail.sql > bedDetail4.sql 
-    cat lovd.${db}.short.bed | $KENTBIN/hgLoadBed ${db} lovdShort stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
-    cat lovd.${db}.long.bed | $KENTBIN/hgLoadBed ${db} lovdLong stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
+
+    bedToBigBed -type=bed4+3 -tab -as=../lovd.as lovd.${db}.short.bed /cluster/data/${db}/chrom.sizes lovd.${db}.short.bb
+    bedToBigBed -type=bed4+3 -tab -as=../lovd.as lovd.${db}.long.bed /cluster/data/${db}/chrom.sizes lovd.${db}.long.bb
+    mkdir -p ${WORKDIR}/release/${db}
+    cp lovd.${db}.{short,long}.bb ${WORKDIR}/release/${db}/
 done
 
 echo LOVD update: OK