#!/usr/bin/perl

@grps = ("Sham","CLPDCA","CLP");
@reps = ("rep1","rep2","rep3","rep4");

%useColor = ("Sham" => "0,0,204",   # blue
             "CLPDCA" => "0,102,0", # green
             "CLP" => "255,128,0"); # orange

# Step 1)  Write track view header.
$prio = 150;
open(OUT, ">trackDb.txt");
print OUT "track\tJMar_tracks\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tJMar sepsis RNAseq\n";
print OUT "longLabel\tJMartinez mouse liver sepsis RNAseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview View COVN=depthNorm\n";
print OUT "subGroup2\tgroup Group"; foreach $grp (@grps) { print OUT " $grp=$grp"; } print OUT "\n";
print OUT "subGroup3\treplicate Replicate"; foreach $r (@reps) { print OUT " $r=$r"; } print OUT "\n";
print OUT "dimensions\tdimX=group dimY=replicate\n";
print OUT "sortOrder\tgroup=+ 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\tJMar_tracksViewDepthN\n";
print OUT "   parent\tJMar_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 $grp (@grps) { foreach $r (@reps) {
  $id = "$grp"."-$r";
  $bwfile = "DATA/$id.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "      track\t$id.ND\n";
  print OUT "      parent\tJMar_tracksViewDepthN on\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\n";
  print OUT "      longLabel\tnormalized read depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$useColor{$grp}\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tgroup=$grp replicate=$r view=COVN\n\n";
} }

close(OUT);