#!/usr/bin/perl

@grps = ("AIF-WWW-F","AIF-WWW-M","AIF-KKW-M","AIF-KKK-M");
@reps = ("0","1","2","3","4");
@strands = ("plus","minus");

%grpcolor = (
"AIF-WWW-F" => "255,51,153", # pink
"AIF-WWW-M" => "0,0,204",    # blue
"AIF-KKW-M" => "255,128,0",  # orange
"AIF-KKK-M" => "0,153,0"     # green
);


# Step 1)  Write track view header.
$prio = 100;
open(OUT, ">trackDb.tripleKO-May2021.txt");
print OUT "track\tKR_tKO_May2021\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\ttripleKO RNAseq, mouse gonad\n";
print OUT "longLabel\ttripleKO RNAseq, mouse gonad; RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview View COVN=depthNorm\n"; # COVR=depthRaw\n";
print OUT "subGroup2\tgt Genotype"; 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 "subGroup4\tstr Strand"; foreach $str (@strands) { print OUT " $str=$str"; } print OUT "\n";
print OUT "dimensions\tdimX=gt dimY=replicate dimA=str\n";
print OUT "sortOrder\tgt=+ replicate=+ str=-\n";
print OUT "configurable\ton\n";
print OUT "type\tbigWig\n\n";

# Step 2a)  Write header for normalized depth track grouping.
print OUT "   track\tKR_tKO_May2021ViewDepthN\n";
print OUT "   parent\tKR_tKO_May2021\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) { foreach $str (@strands) {
  $id = "$grp\-rep$rep";
  $bwfile = "DATA/RNA_tripleKO_May2021/$id.depthNorm.$str.bw";
  next unless (-e $bwfile);
  $tracktot++;
  $useColor = $grpcolor{$grp};
  $prio++;
  print OUT "      track\t$id.$str.ND\n";
  print OUT "      parent\tKR_tKO_May2021ViewDepthN on\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id $str\n";
  print OUT "      longLabel\tnormalized read depth: $id ($str strand)\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=$grp replicate=$rep str=$str view=COVN\n\n";
} } }

close(OUT);

print "$tracktot tracks\n";