#!/usr/bin/perl

@grps = ("CON1", "CON2", "GLIS2over");
@reps = ("1", "2", "3", "4");

%grpcolor = (
"CON1" => "0,153,0", # green
"CON2" => "0,153,0", # green
"GLIS2over" => "0,153,0" # green
);


# Step 1)  Write track view header.
$prio = 300;
open(OUT, ">trackDb.Glis2over_IMCD3.txt");
print OUT "track\tYGRoh_G2OV_IMCD3\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tGlis2over RNAseq, IMCD3\n";
print OUT "longLabel\tGlis2over IMCD3 RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview View COVN=depthNorm\n"; # COVR=depthRaw\n";
print OUT "subGroup2\tgroup Group";
foreach $grp (@grps) { print OUT " $grp=$grp"; } print OUT "\n";
print OUT "subGroup3\treplicate Replicate";
foreach $rep (@reps) { print OUT " $rep=$rep"; } print OUT "\n";
print OUT "dimensions\tdimX=group dimY=replicate\n";
print OUT "sortOrder\tgroup=+ replicate=+\n";
print OUT "configurable\ton\n";
print OUT "type\tbigWig\n\n";

# Step 2a)  Write header for normalized depth track grouping.
print OUT "   track\tYGRoh_G2OV_IMCD3ViewDepthN\n";
print OUT "   parent\tYGRoh_G2OV_IMCD3\n";
print OUT "   shortLabel\tNormDepth\n";
print OUT "   longLabel\tNormalized RNA-seq Depth\n";
print OUT "   view\tCOVN\n";
print OUT "   visibility\tfull\n";
print OUT "   type\tbigWig\n";
print OUT "   allButtonPair\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 "   viewLimits\t0:300\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# Step 2b)  Write normalized depth tracks.
$tracktot = 0;
foreach $grp (@grps) { foreach $rep (@reps) {
  $id = "$grp\-$rep";
  $bwfile = "DATA/Glis2over_IMCD3/$id.depthNorm.bw";
  next unless (-e $bwfile);
  $tracktot++;
  $useColor = $grpcolor{$grp};
  $prio++;
  print OUT "      track\t$id.IMCD3.ND\n";
  print OUT "      parent\tYGRoh_G2OV_IMCD3ViewDepthN on\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\-IMCD3\n";
  print OUT "      longLabel\tnormalized read depth: $id (IMCD3)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$useColor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tgroup=$grp replicate=$rep view=COVN\n\n";
} }

close(OUT);

print "$tracktot tracks\n";