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/download.sh src/hg/utils/otto/lovd/download.sh
index 789821d..14c6be7 100755
--- src/hg/utils/otto/lovd/download.sh
+++ src/hg/utils/otto/lovd/download.sh
@@ -1,38 +1,29 @@
 #!/bin/sh -e
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/lovd/check.sh
 #	This script is used via a cron job 
 
 #	cron jobs need to ensure this is true
 umask 002
 
 WORKDIR="/hive/data/outside/otto/lovd"
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in lovd release, Can not find the directory: ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 today=`date +%F`
 mkdir -p $today
 cd $today
 
 # http request needs to come from hgwdev IP address otherwise file not found error
-wget -q 'http://varcache.lovd.nl/bed/hg38?add_id_ncbi=1&add_annotation=1' -O - | grep -v track | grep -v ^$ > lovd.hg38.bed
-wget -q 'http://varcache.lovd.nl/bed/hg19?add_id_ncbi=1&add_annotation=1' -O - | grep -v track | grep -v ^$ > lovd.hg19.bed
-wget -q 'http://varcache.lovd.nl/bed/hg18?add_id_ncbi=1&add_annotation=1' -O - | grep -v track | grep -v ^$ > lovd.hg18.bed
-
-sed -i s/^/chr/g lovd.hg38.bed
-sed -i s/^/chr/g lovd.hg19.bed
-sed -i s/^/chr/g lovd.hg18.bed
-
-# effect:;lovd_count:1
-sed -i 's/effect:/Variant Effect: /g' lovd.hg38.bed
-sed -i 's/effect:/Variant Effect: /g' lovd.hg19.bed
-sed -i 's/effect:/Variant Effect: /g' lovd.hg18.bed
-
-sed -i 's/;lovd_count:/<br>Number of LOVD Installations reporting this variant: /g' lovd.hg38.bed
-sed -i 's/;lovd_count:/<br>Number of LOVD Installations reporting this variant: /g' lovd.hg19.bed
-sed -i 's/;lovd_count:/<br>Number of LOVD Installations reporting this variant: /g' lovd.hg18.bed
+for db in hg38 hg19
+do
+    wget -q 'http://varcache.lovd.nl/bed/'${db}'?add_id_ncbi=1&add_annotation=1' -O - | grep -v track | grep -v ^$ > lovd.${db}.bed
+    sed -i s/^/chr/g lovd.${db}.bed
+    sed -i 's/effect:/Variant Effect: /g' lovd.${db}.bed
+    sed -i 's/;lovd_count:/<br>Number of LOVD Installations reporting this variant: /g' lovd.${db}.bed
+done