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

diff --git src/hg/makeDb/doc/mm9.txt src/hg/makeDb/doc/mm9.txt
index d33cfe9..bb2b6dc 100644
--- src/hg/makeDb/doc/mm9.txt
+++ src/hg/makeDb/doc/mm9.txt
@@ -12658,15 +12658,41 @@
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -target2Bit=/hive/data/genomes/mm9/mm9.2bit \
         -targetSizes=/hive/data/genomes/mm9/chrom.sizes \
         -query2Bit=/hive/data/genomes/mm39/mm39.2bit \
         -querySizes=/hive/data/genomes/mm39/chrom.sizes \
         -ooc=/hive/data/genomes/mm9/11.ooc \
          mm9 mm39) > doLiftOverToMm39.log 2>&1
     # performed in two steps
     # real    212m47.631s
     # real    128m9.574s
 
     # see if the liftOver menus function in the browser from mm9 to mm39
 
 ##############################################################################
+# VISTA Enhancers track refs #16044  (2023-09-20 Gerardo)
+cd /hive/data/outside/
+mkdir vistaEnhancers; cd vistaEnhancers
+mkdir mm9; cd mm9
+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 "^>Mouse" \
+        | sed -e 's#^>Mouse|##' \
+        | 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"\tmm"$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/mm9/bigZips/mm9.chrom.sizes vistaEnhancers.bb
+cd /gbdb/mm9
+mkdir vistaEnhancers; cd vistaEnhancers
+# Making symlink for big files
+ln -s /hive/data/outside/vistaEnhancers/mm9/vistaEnhancers.bb
+cd ~/kent/src/hg/makeDb/trackDb/mouse/mm9
+vi trackDb.ra
+#############################################################################