#!/usr/bin/perl

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

%grpcolor = (
"WT" => "127,0,255", #dark purple
"KO" => "178,102,255", # light purple
);


# Step 1)  Write track view header.
$prio = 200;
open(OUT, ">trackDb.Glis2KO_kidney1w2w.txt");
print OUT "track\tYGRoh_G2KO_kidney1w2w\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tGlis2KO RNAseq, kidney 1wk/2wk\n";
print OUT "longLabel\tGlis2KO kidney 1wk/2wk RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview View COVN=depthNorm\n"; # COVR=depthRaw\n";
print OUT "subGroup2\tage Age";
foreach $age (@ages) { print OUT " $age=$age"; } print OUT "\n";
print OUT "subGroup3\tgt GT";
foreach $gt (@gts) { print OUT " $gt=$gt"; } print OUT "\n";
print OUT "subGroup4\treplicate Replicate";
foreach $rep (@reps) { print OUT " $rep=$rep"; } print OUT "\n";
print OUT "dimensions\tdimX=gt dimY=age dimA=replicate\n";
print OUT "sortOrder\tage=+ gt=+ 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_G2KO_kidney1w2wViewDepthN\n";
print OUT "   parent\tYGRoh_G2KO_kidney1w2w\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 $age (@ages) { foreach $gt (@gts) { foreach $rep (@reps) {
  $bwfile = "DATA/Glis2KO_kidney1wk2wk/G2KO-Kid-$age-$gt-$rep.depthNorm.bw";
  next unless (-e $bwfile);
  $tracktot++;
  $useColor = $grpcolor{$gt};
  $prio++;
  print OUT "      track\tG2$gt$rep.$age.ND\n";
  print OUT "      parent\tYGRoh_G2KO_kidney1w2wViewDepthN on\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\tG2$gt$rep\-$age\n";
  print OUT "      longLabel\tnormalized read depth: G2$gt$rep ($age)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$useColor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tage=$age gt=$gt replicate=$rep view=COVN\n\n";
} } }

close(OUT);

print "$tracktot tracks\n";