b73a4247460859687b16ae03aa9b848f56576aa1
max
  Tue Sep 17 02:40:05 2019 -0700
ottomatizing mastermind, refs #24157

diff --git src/hg/utils/otto/mastermind/buildMastermind.sh src/hg/utils/otto/mastermind/buildMastermind.sh
new file mode 100755
index 0000000..9f6434b
--- /dev/null
+++ src/hg/utils/otto/mastermind/buildMastermind.sh
@@ -0,0 +1,31 @@
+#wget 'https://mastermind.genomenon.com/cvr/download?format=csv' -O - > mastermind.2018.11.26.csv.gz
+#unzip mastermind.2018.11.26.csv.zip
+#mv mastermind_cited_variants_reference-2018.11.26-csv/ 2018-11-26
+#hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > chromAlias.tab
+#ln -s `pwd`/mastermind.bb /gbdb/hg19/bbi/mastermind.bb
+#python mastermindToBed.py 2018-11-26/mastermind_cited_variants_reference-2018.11.26.csv 
+#bedSort mastermind.bed mastermind.bed
+#bedToBigBed -type=bed9+ -as=mastermind.as -tab mastermind.bed //hive/data/genomes/hg19/chrom.sizes  mastermind.bb
+
+set -e -o pipefail
+cd /hive/data/outside/otto/mastermind
+date=`date --iso-8601`
+mkdir -p hg19 hg38
+mkdir -p archive/$date
+hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > hg19/chromAlias.tab
+hgsql hg38 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > hg38/chromAlias.tab
+wget 'https://mastermind.genomenon.com/cvr/download?build=grch37&format=csv' -O archive/$date/hg19.zip
+wget 'https://mastermind.genomenon.com/cvr/download?build=grch38&format=csv' -O archive/$date/hg38.zip
+unzip -o archive/$date/hg19.zip -d archive/$date
+unzip -o archive/$date/hg38.zip -d archive/$date
+python mastermindToBed.py hg19/chromAlias.tab archive/$date/mastermind_cited_variants_reference-*-grch37.csv hg19/mastermind.bed
+python mastermindToBed.py hg38/chromAlias.tab archive/$date/mastermind_cited_variants_reference-*-grch38.csv hg38/mastermind.bed
+bedSort hg19/mastermind.bed hg19/mastermind.bed
+bedSort hg38/mastermind.bed hg38/mastermind.bed
+bedToBigBed -type=bed9+ -as=mastermind.as -tab hg19/mastermind.bed /hive/data/genomes/hg19/chrom.sizes  hg19/mastermind.new.bb
+bedToBigBed -type=bed9+ -as=mastermind.as -tab hg38/mastermind.bed /hive/data/genomes/hg38/chrom.sizes  hg38/mastermind.new.bb
+curl -s https://mastermind.genomenon.com/cvr/version | cut -d\" -f4 > mastermindRelease.new.txt
+mv mastermindRelease.new.txt mastermindRelease.txt
+mv hg19/mastermind.new.bb hg19/mastermind.bb
+mv hg38/mastermind.new.bb hg38/mastermind.bb
+