#!/usr/bin/perl

@conditions = ("KO30m", "KOUnt", "WT30m", "WTUnt");
@reps = ("1", "2", "3");
@ids = (); foreach $cnd (@conditions) { foreach $rep (@reps) { $id = "$cnd-$rep"; push @id, $ids; } }

%grpColor = ("KO30m" => "255,128,0", "KOUnt" => "255,51,255", "WT30m" => "0,204,0", "WTUnt" => "0,0,204");  # orange, pink, green, blue


# Step 1)  Write track view header.
$prio = 100;
open(OUT, ">trackDb.txt");
print OUT "track\tGM_tracks\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tGM Tracks\n";
print OUT "longLabel\tGMuse RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview Views COVN=depthNorm\n"; # COVR=depthRaw\n";
print OUT "subGroup2\tcondition Condition";
foreach $cnd (@conditions) { print OUT " $cnd=$cnd"; } print OUT "\n";
print OUT "subGroup3\treplicate Replicate";
foreach $rep (@reps) { print OUT " $rep=$rep"; } print OUT "\n";
print OUT "dimensions\tdimX=condition dimY=replicate\n";
print OUT "sortOrder\tcondition=+ replicate=+ view=-\n";
print OUT "configurable\ton\n";
print OUT "type\tbed 3\n\n";


# Step 2a)  Write header for normalized depth track grouping.
print OUT "   track\tGM_tracksViewDepthN\n";
print OUT "   parent\tGM_tracks\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.
foreach $cnd (@conditions) { foreach $rep (@reps) {
  $id = "$cnd-$rep";
  $bwfile = "DATA/$id.mm10.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  $thiscolor = $grpColor{$cnd};
  print OUT "      track\t$id.ND\n";
  print OUT "      parent\tGM_tracksViewDepthN on\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\n";
  print OUT "      longLabel\tnormalized read depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$thiscolor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tcondition=$cnd replicate=$rep view=COVN\n\n";
} }

close(OUT);