#!/usr/bin/perl

# Barbara's samples

$dkPink = "255,0,127";    # female
$dkBlue = "0,0,204";	  # male

open(OUT, ">trackDb.RNA-BN.txt");
$prio = 300;

##### normalized depth #####
# write header supertrack header
print OUT "track\tdataRNAseqBN\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tRNAseq BNicol\n";
print OUT "longLabel\tRNA-seq data BNicol (aggregate normalized depth)\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tview View NORM=normDepth\n";
print OUT "subGroup2\tSex Sex Female-XX=Female-XX Male-XY=Male-XY\n";
print OUT "dimensions\tdimX=Sex\n";
print OUT "sortOrder\tSex=+\n";
print OUT "type\tbigWig\n\n";

# write header for depth tracks
print OUT "   track\tdataRNAseqBN_ViewDepth\n";
print OUT "   parent\tdataRNAseqBN\n";
print OUT "   shortLabel\tRNAseq BNicol\n";
print OUT "   longLabel\tRNA-seq data BNicol (aggregate normalized depth)\n";
print OUT "   view\tNORM\n";
print OUT "   visibility\tfull\n";
print OUT "   type\tbigWig\n";
print OUT "   allButtonPair\ton\n";
print OUT "   centerLabelsDense\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";

# write depth tracks
  $id = "BNicol_female";
  $bwfile = "DATA/$id.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "      track\t$id.RNA\n";
  print OUT "      parent\tdataRNAseqBN_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\n";
  print OUT "      longLabel\taggregate normalized RNA-seq depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$dkPink\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tSex=Female-XX view=NORM\n\n";

  $id = "BNicol_male";
  $bwfile = "DATA/$id.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "	   track\t$id.RNA\n";
  print OUT "	   parent\tdataRNAseqBN_ViewDepth\n";
  print OUT "	   bigDataUrl\t$bwfile\n";
  print OUT "	   shortLabel\t$id\n";
  print OUT "	   longLabel\taggregate normalized RNA-seq depth: $id\n";
  print OUT "	   type\tbigWig\n";
  print OUT "	   color\t$dkBlue\n";
  print OUT "	   priority\t$prio\n";
  print OUT "	   visibility\thide\n";
  print OUT "	   subGroups\tSex=Male-XY view=NORM\n\n";


close(OUT);