#!/usr/bin/perl

@gts = ("WT", "cKO");
@diets = ("LID", "ND");
@reps = ("1", "2", "3", "4");
$age = "10wk";

@grps = (); foreach $diet (@diets) { foreach $gt (@gts) { $grp = "$diet"."-$gt"; push @grps, $grp; } }

$datadir = "DATA/Aug2020-10wk";

%grpcolor = (
"ND-WT" => "0,0,255", #dark blue
"LID-WT" => "51,153,255", # light blue
"ND-cKO" => "76,0,153", # dark purple
"LID-cKO" => "178,102,255" # light purple
);


# Step 1)  Write track view header.
$prio = 100;
open(OUT, ">trackDb-Aug2020.txt");
print OUT "track\tHSK_mmThy_RNA1\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\t$age mouse thyroid RNAseq\n";
print OUT "longLabel\t$age mouse thyroid RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview View COVN=depthNorm\n"; # COVR=depthRaw\n";
print OUT "subGroup2\tgenotype genotype"; foreach $gt (@gts) { print OUT " $gt=$gt"; } print OUT "\n";
print OUT "subGroup3\tdiet diet"; foreach $diet (@diets) { print OUT " $diet=$diet"; } print OUT "\n";
print OUT "subGroup4\treplicate replicate"; foreach $r (@reps) { print OUT " rep$r=rep$r"; } print OUT "\n";
print OUT "dimensions\tdimX=genotype dimY=diet dimA=replicate\n";
print OUT "sortOrder\tgenotype=+ diet=+ 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\tHSK_mmThy_RNA1ViewDepthN\n";
print OUT "   parent\tHSK_mmThy_RNA1\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\t150:30:11\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 $diet (@diets) { foreach $gt (@gts) {
  $grp = "$diet"."-$gt"; 
  $usecolor = $grpcolor{$grp};
  foreach $r (@reps) {
    $id = "$grp"."-rep$r";
    $useid = "$grp"."-$age"."-rep$r";
    $bwfile = "$datadir/$id.depthNorm.bw";
    next unless (-e $bwfile);
    $tracktot++;
    $prio++;
    print OUT "      track\t$useid.ND\n";
    print OUT "      parent\tHSK_mmThy_RNA1ViewDepthN on\n";
    print OUT "      bigDataUrl\t$bwfile\n";
    print OUT "      shortLabel\t$useid\n";
    print OUT "      longLabel\tnormalized read depth: $useid\n";
    print OUT "      type\tbigWig\n";
    print OUT "      color\t$usecolor\n";
    print OUT "      priority\t$prio\n";
    print OUT "      visibility\thide\n";
    print OUT "      subGroups\tgenotype=$gt diet=$diet replicate=rep$r view=COVN\n\n";
  }
} }

close(OUT);

print "$tracktot tracks\n";