#!/usr/bin/perl

@gts = ("KO", "WT");
@cts = ("GC", "MC", "Naive", "PC");
@reps = (1,2,3);

$useColor = "0,0,153";


# Step 1)  Write track view header.
$prio = 100;
open(OUT, ">trackDb.txt");
print OUT "track\tKC_tracks\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tKC Tracks\n";
print OUT "longLabel\tKC ATACseq Depth\n";
print OUT "priority\t$prio\n";
print OUT "visibility\tfull\n";
print OUT "subGroup1\tview Views COVN=depthNorm\n";
print OUT "subGroup2\tgenotype Genotype "; foreach $gt (@gts) { print OUT "$gt=$gt "; } print OUT "\n";
print OUT "subGroup3\tcelltype CellType "; foreach $ct (@cts) { print OUT "$ct=$ct "; } print OUT "\n";
print OUT "subGroup4\treplicate Replicate "; foreach $rep (@reps) { print OUT "rep$rep=rep$rep "; } print OUT "\n";
print OUT "dimensions\tdimX=genotype dimY=celltype dimA=replicate\n";
print OUT "sortOrder\tgenotype=+ celltype=+ replicate=+\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\tKC_tracksViewDepthN\n";
print OUT "   parent\tKC_tracks\n";
print OUT "   shortLabel\tNormDepth\n";
print OUT "   longLabel\tNormalized ATAC-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\t0:100\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# Step 2b)  Write normalized depth tracks.
foreach $gt (@gts) { foreach $ct (@cts) { foreach $r (@reps) {
  $id = "MTA3c"."$gt-$ct.rep$r";
  $bwfile = "DATA/$id.mm9.footprint.norm.bigWig";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "      track\t$id.ND\n";
  print OUT "      parent\tKC_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\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tgenotype=$gt celltype=$ct replicate=rep$r view=COVN\n\n";
} } }


close(OUT);