#!/usr/bin/perl

$stroot = "RNA2";
$shortLab = "RNAseq Astro P28-Pilot Jan2025";
$longLab = "RNAseq Normalized Depth Tracks - Astrocyte P28 Pilot Jan2025";

$prio = 130;

##############################################################

$datadir = "data/AstroNS51552";
$trackname = "trackDb.$stroot.txt";

@ids = ("p28WT-Astro","p28G3KO-Astro");
#@reps = (1,2,3);
#@strands = ("plus","minus");

##############################################################

open(OUT, ">$trackname");

##### normalized depth #####
# write header supertrack header
print OUT "track\tdata$stroot\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\t$shortLab\n";
print OUT "longLabel\t$longLab\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tview View RNA=RNA\n";
#print OUT "subGroup2\tgt Genotypes"; foreach $gt (@gts) { print OUT " $gt=$gt"; } print OUT "\n";
#print OUT "subGroup3\ttrt Treatment"; foreach $trt (@trts) { print OUT " $trt=$trt"; } print OUT "\n";
#print OUT "subGroup4\trep Replicate"; foreach $r (@reps) { print OUT " $r=$r"; } print OUT "\n";
#print OUT "subGroup5\tstr Strand"; foreach $str (@strands) { print OUT " $str=$str"; } print OUT "\n";
#print OUT "dimensions\tdimX=gt dimY=trt dimA=str\n";
#print OUT "sortOrder\tview=+ gt=+ trt=+ rep=+ str=+\n";
print OUT "subGroup2\tsample Sample"; foreach $id (@ids) { print OUT " $id=$id"; } print OUT "\n";
print OUT "dimensions\tdimX=sample\n";
print OUT "sortOrder\tview=+ sample=+\n";
print OUT "configurable\ton\n";
print OUT "type\tbigWig\n\n";

# write header for RNAseq tracks
print OUT "   track\tdata$stroot\_ViewDepth\n";
print OUT "   parent\tdata$stroot\n";
print OUT "   shortLabel\t$shortLab\n";
print OUT "   longLabel\t$longLab\n";
print OUT "   view\tRNA\n";
print OUT "   visibility\tfull\n";
print OUT "   type\tbigWig\n";
print OUT "   allButtonPair\ton\n";
print OUT "   centerLabelsDense\ton\n";
print OUT "   dragAndDrop\ton\n";
print OUT "   alwaysZero\ton\n";
print OUT "   graphTypeDefault\tbar\n";
print OUT "   maxHeightPixels\t150:40:11\n";
print OUT "   autoScale\tgroup\n";
#print OUT "   viewLimits\t0:5\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write RNAseq depth tracks
foreach $id (@ids) {
  $bwfile = "$datadir/$id.depthRPM.bw";
  unless (-e $bwfile) { print "WARNING: Did not find \'$bwfile\'.\n"; next; }
  $prio++;
  print OUT "      track\t$id\n";
  print OUT "      parent\tdata$stroot\_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id (pilot)\n";
  print OUT "      longLabel\t$id RPM-normalized depth (pilot)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t0,0,0\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tview=RNA id=$id\n\n";
}

print OUT "\n\n";

close(OUT);