#!/usr/bin/perl

$stroot = "RNA9";
$shortLab = "RNAseq embGonad Syro May2025";
$longLab = "RNAseq Normalized Depth Tracks - embGonad Syro May2025";

$prio = 300;

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

$datadir = "data/NS20163-embGonad";
$trackname = "trackDb.$stroot.txt";

@sexes = ("M","F");
@treatments = ("Syro","Ctrl");
@indiv = (1,2,3,4,5);

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

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\tsex Sex"; foreach $s (@sexes) { print OUT " $s=$s"; } print OUT "\n";
print OUT "subGroup3\ttrt Treatment"; foreach $t (@treatments) { print OUT " $t=$t"; } print OUT "\n";
print OUT "subGroup4\tindiv Individual"; foreach $r (@indiv) { print OUT " $r=$r"; } print OUT "\n";
print OUT "dimensions\tdimX=sex dimY=trt\n";
print OUT "sortOrder\tview=+ sex=+ trt=+ indiv=+\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 $s (@sexes) { foreach $t (@treatments) { foreach $r (@indiv) {
  $id = "$s$r"."_$t";
  $label_id = "$id.Syro";
  if ($t eq "Ctrl") { $shortuse = "$id\[Syro]"; } else { $shortuse = $id; }
  $bwfile = "$datadir/$id.depthRPM.bw";
  unless (-e $bwfile) { print "WARNING: Did not find \'$bwfile\'.\n"; next; }
  $prio++;
  print OUT "      track\t$label_id\n";
  print OUT "      parent\tdata$stroot\_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$shortuse\n";
  print OUT "      longLabel\tembGonad (Syro dataset) $id RPM-normalized depth\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t0,0,0\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tview=RNA sex=$s trt=$t indiv=$r\n\n";
} } }

print OUT "\n\n";

close(OUT);