3e50c8a867b33f2ea89bc9f26eb7e13dbcde51e1
chmalee
  Fri Jul 17 09:12:14 2020 -0700
Adding hg38 to lovd otto build

diff --git src/hg/utils/otto/lovd/checkAndLoad.sh src/hg/utils/otto/lovd/checkAndLoad.sh
index 5d971ee..a6a58b2 100755
--- src/hg/utils/otto/lovd/checkAndLoad.sh
+++ src/hg/utils/otto/lovd/checkAndLoad.sh
@@ -1,58 +1,78 @@
 #!/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
 
+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;}}'
 
 # 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
 echo LOVD update: OK