#!/usr/bin/perl

@gts = ("WT", "KO");
@reps = ("1", "2", "3", "4", "5");

%grpcolor = (
"WT" => "0,0,255", #dark blue
"KO" => "51,153,255", # light blue
);


# Step 1)  Write track view header.
$prio = 100;
open(OUT, ">trackDb.Glis3KO_kidneyP7.txt");
print OUT "track\tYGRoh_G3KO_kidneyP7\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tGlis3KO RNAseq\n";
print OUT "longLabel\tGlis3KO kidney P7 RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview View COVN=depthNorm\n"; # COVR=depthRaw\n";
print OUT "subGroup2\tgt GT";
foreach $gt (@gts) { print OUT " $gt=$gt"; } print OUT "\n";
print OUT "subGroup3\treplicate Replicate";
foreach $rep (@reps) { print OUT " $rep=$rep"; } print OUT "\n";
print OUT "dimensions\tdimX=gt dimY=replicate\n";
print OUT "sortOrder\tgt=+ 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_G3KO_kidneyP7ViewDepthN\n";
print OUT "   parent\tYGRoh_G3KO_kidneyP7\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\t0:500\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# Step 2b)  Write normalized depth tracks.
$tracktot = 0;
foreach $gt (@gts) { foreach $rep (@reps) {
  $id = "$gt$rep";
  $bwfile = "DATA/Glis3KO_kidneyP7/$id.depthNorm.bw";
  next unless (-e $bwfile);
  $tracktot++;
  $useColor = $grpcolor{$gt};
  $prio++;
  print OUT "      track\tG3KOP7.$id.ND\n";
  print OUT "      parent\tYGRoh_G3KO_kidneyP7ViewDepthN on\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\tG3$id\-P7\n";
  print OUT "      longLabel\tnormalized read depth: G3$id (P7)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$useColor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tgt=$gt replicate=$rep view=COVN\n\n";
} }

close(OUT);

print "$tracktot tracks\n";