81ed6a428f3655d2f32f1cc523993632955e2e6f
chmalee
  Fri Jul 24 17:04:40 2020 -0700
Fix up LOVD otto script after code review, refs #25925

diff --git src/hg/utils/otto/lovd/checkAndLoad.sh src/hg/utils/otto/lovd/checkAndLoad.sh
index a6a58b2..d5770fc 100755
--- src/hg/utils/otto/lovd/checkAndLoad.sh
+++ src/hg/utils/otto/lovd/checkAndLoad.sh
@@ -1,78 +1,63 @@
 #!/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`
-#new18Cc=`cat lovd.hg18.bed | $TAWK '(NF!=6)' | wc -l`
 if [ "$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
 
-#if [ "$new18Cc" -ne "0" ]; then
-#        echo LVOD hg18 $today: found rows with not six columns, quitting
-#        exit 255
-#fi
-
-# compare old and new line counts and abort if no increase
-$KENTBIN/bedClip lovd.hg38.bed /cluster/data/hg38/chrom.sizes stdout | sed -e 's/^chrM/chrMT/g' > lovd.hg38.clipped.bed
-$KENTBIN/bedClip lovd.hg19.bed /cluster/data/hg19/chrom.sizes stdout | sed -e 's/^chrM/chrMT/g' > lovd.hg19.clipped.bed
-echo 
-cat lovd.hg38.clipped.bed | awk '(($3-$2)<50)' > lovd.hg38.short.bed
-cat lovd.hg19.clipped.bed | awk '(($3-$2)<50)' > lovd.hg19.short.bed
-echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t' >> lovd.hg38.short.bed
-echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t' >> lovd.hg19.short.bed
-cat lovd.hg38.clipped.bed | awk '(($3-$2)>=50)' > lovd.hg38.long.bed
-cat lovd.hg19.clipped.bed | awk '(($3-$2)>=50)' > lovd.hg19.long.bed
-echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t' >> lovd.hg38.long.bed
-echo -e 'chrM\t0\t16571\tCheck chrMT\tPlease look at chrMT, not chrM, for LOVD annotations.\t' >> lovd.hg19.long.bed
-old38ShortLc=`$KENTBIN/hgsql hg38 -e "SELECT COUNT(*) from lovdShort" -NB`
-old38LongLc=`$KENTBIN/hgsql hg38 -e "SELECT COUNT(*) from lovdLong" -NB`
-new38ShortLc=`wc -l lovd.hg38.short.bed | cut -d' ' -f1 `
-new38LongLc=`wc -l lovd.hg38.long.bed | cut -d' ' -f1 `
-old19ShortLc=`$KENTBIN/hgsql hg19 -e "SELECT COUNT(*) from lovdShort" -NB`
-old19LongLc=`$KENTBIN/hgsql hg19 -e "SELECT COUNT(*) from lovdLong" -NB`
-new19ShortLc=`wc -l lovd.hg19.short.bed | cut -d' ' -f1 `
-new19LongLc=`wc -l lovd.hg19.long.bed | cut -d' ' -f1 `
-
-echo hg38 short rowcount: old $old38ShortLc new: $new38ShortLc
-echo hg38 long rowcount: old $old38LongLc new: $new38LongLc
-echo hg19 short rowcount: old $old19ShortLc new: $new19ShortLc
-echo hg19 long rowcount: old $old19LongLc new: $new19LongLc
+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
 
-echo $old38ShortLc $new38ShortLc | awk '{if (($2-$1)/$1 > 0.1) {printf "validate on hg38 LOVD short failed: old count: %d, new count: %d\n", $1,$2; exit 1;}}'
-echo $old38LongLc $new38LongLc | awk '{if (($2-$1)/$1 > 0.1) {printf "validate on hg38 LOVD long failed: old count: %d, new count: %d\n", $1,$2; exit 1;}}'
-echo $old19ShortLc $new19ShortLc | awk '{if (($2-$1)/$1 > 0.1) {printf "validate on hg19 LOVD short failed: old count: %d, new count: %d\n", $1,$2; exit 1;}}'
-echo $old19LongLc $new19LongLc | awk '{if (($2-$1)/$1 > 0.1) {printf "validate on hg19 LOVD long failed: old count: %d, new count: %d\n", $1,$2; exit 1;}}'
+    cat lovd.${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
+    fi
 
+    oldShortLc=`$KENTBIN/hgsql ${db} -e "SELECT COUNT(*) from lovdShort" -NB`
+    oldLongLc=`$KENTBIN/hgsql ${db} -e "SELECT COUNT(*) from lovdLong" -NB`
+    newShortLc=`wc -l lovd.${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,$2; exit 1;}}'
     # bedDetail4.sql was generated like this:
     # egrep -v 'score|strand|thick|reserved|block|chromStarts' /cluster/home/max/kent/src/hg/lib/bedDetail.sql > bedDetail4.sql 
-# need to use bedClip as current files include invalid coords which LOVD won't fix.
-#$KENTBIN/bedClip lovd.hg19.bed /cluster/data/hg19/chrom.sizes lovd.hg19.clipped.bed
-cat lovd.hg38.short.bed | $KENTBIN/hgLoadBed hg38 lovdShort stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
-cat lovd.hg38.long.bed | $KENTBIN/hgLoadBed hg38 lovdLong stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
-cat lovd.hg19.short.bed | $KENTBIN/hgLoadBed hg19 lovdShort stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
-cat lovd.hg19.long.bed | $KENTBIN/hgLoadBed hg19 lovdLong stdin -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
-#$KENTBIN/bedClip lovd.hg18.bed /cluster/data/hg18/chrom.sizes stdout | $KENTBIN/hgLoadBed hg18 lovd stdin  -tab -sqlTable=../bedDetail4.sql -renameSqlTable -noBin
+    cat lovd.${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
+done
+
 echo LOVD update: OK