2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3
gperez2
  Wed Sep 27 13:56:11 2023 -0700
Making VISTA Enhancers into native track, refs #16044

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index ba346b1..ebf4557 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35110,15 +35110,41 @@
 mkdir fantom5
 cd fantom5
 # Making symlinks for big files
 for file in $(ls /hive/data/outside/fantom5/riken_f5/hg19/*.b*) ; do ln -s $file; done
 cd /hive/data/outside/fantom5/riken_f5/hg19/
 cp trackDb.txt fantom5.ra
 vi fantom5.ra
 # Indented subtracks
 # Changing bigDataUrl
 # Removing non-alpha characters
 cd ~/kent/src/hg/makeDb/trackDb/human/hg19
 cp /hive/data/outside/fantom5/riken_f5/hg19/fantom5.ra .
 vi trackDb.ra
 #include fantom5.ra alpha
 #############################################################################
+# VISTA Enhancers track refs #16044  (2023-09-20 Gerardo)
+cd /hive/data/outside/
+mkdir vistaEnhancers; cd vistaEnhancers
+mkdir hg19; cd hg19
+wget -O enhancerbrowser.datadownload.txt 'https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?page=1;action=search;form=search;page_size=100;search.form=no;show=1;search.result=yes;search.sequence=1'
+cat enhancerbrowser.datadownload.txt \
+        | grep ">" \
+        | sed -e 's#^<pre>##' \
+        | sed -e 's#</pre>$##' \
+        | grep "^>Human" \
+        | sed -e 's#^>Human|##' \
+        | tr :- ' ' \
+        | sed -e 's/positive/positive\t255,0,0/'\
+        | sed -e 's/negative/negative\t0,0,255/' \
+        | awk '{print $1"\t"($2-1)"\t"$3"\ths"$6"\t0\t.\t"$2"\t"$3"\t"$9"\t"$8"\t"$6}' \
+        | grep -P -v "^chr\t" \
+        > vistaEnhancers.bed
+bedSort vistaEnhancers.bed sortedVistaEnhancers.bed
+bedToBigBed -tab -type=bed9+ -as=vistaEnhancers.as sortedVistaEnhancers.bed https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes vistaEnhancers.bb
+cd /gbdb/hg19
+mkdir vistaEnhancers; cd vistaEnhancers
+# Making symlink for big files
+ln -s /hive/data/outside/vistaEnhancers/hg19/vistaEnhancers.bb
+cd ~/kent/src/hg/makeDb/trackDb/human/hg19
+vi trackDb.ra
+#############################################################################