#!/usr/bin/perl

$stroot = "RNA8";
$shortLab = "RNAseq Sertoli D,L,Media Mar2025";
$longLab = "RNAseq Normalized Depth Tracks - Sertoli D,L,Media Mar2025";

$prio = 270;

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

$datadir = "data/NOV0701-Sertoli";
$trackname = "trackDb.$stroot.txt";

@grps = ("D","L","Media");
@reps = (1,2,3,4);
@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\tgrp Group"; foreach $grp (@grps) { print OUT " $grp=$grp"; } print OUT "\n";
print OUT "subGroup3\trep Replicate"; foreach $r (@reps) { print OUT " $r=$r"; } print OUT "\n";
print OUT "subGroup4\tstr Strand"; foreach $str (@strands) { print OUT " $str=$str"; } print OUT "\n";
print OUT "dimensions\tdimX=grp dimY=rep dimA=str\n";
print OUT "sortOrder\tview=+ grp=+ rep=+ str=+\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 $grp (@grps) { foreach $r (@reps) { foreach $str (@strands) {
  $id = "$grp$r";
  $label_id = $id;
#  $label_id = "$grpLabel{$grp}-rep$r";
  $ss = uc(substr($str, 0, 1));
  $bwfile = "$datadir/$id.depthRPM.$str.bw";
  unless (-e $bwfile) { print "WARNING: Did not find \'$bwfile\'.\n"; next; }
  $prio++;
  print OUT "      track\t$label_id.$ss\n";
  print OUT "      parent\tdata$stroot\_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$label_id ($str)\n";
  print OUT "      longLabel\tSertoli $grp\-rep$r RPM-normalized depth ($str)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t0,0,0\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tview=RNA grp=$grp rep=$r str=$str\n\n";
} } }

print OUT "\n\n";

close(OUT);