#!/usr/bin/perl

$thisdiet = $ARGV[0];

@diets = ("LF", "HF", "HF-LF");
@contexts = ("CpG", "CHx");
$dir = "/ddn/gs1/home/grimmsa/ruifang/WGBS_analysis/FIX/files_coverage";

$tool = "/ddn/gs1/home/grimmsa/tools/ucsc/wigToBigWig";
$cs = "/ddn/gs1/shared/fargod/reference_genomes/mm10_lambda/mm10ordered_lambda.chromSizes";

foreach $d (@diets) { foreach $ctxt (@contexts) {
  if ($thisdiet ne "") { next unless ($d eq $thisdiet); }
  next if (-e "$d.mm10.methpct.$ctxt.plus.wig");
  next if (-e "$d.mm10.methpct.$ctxt.minus.wig");
  $infile = "$dir/$d.mm10.methpct.$ctxt.wig";
  open(OUTP, ">$d.mm10.methpct.$ctxt.plus.wig");
  open(OUTM, ">$d.mm10.methpct.$ctxt.minus.wig");
  open(IN, "$infile");
  while (<IN>) {
    if ($_ =~ /^variableStep/) { print OUTP "$_"; print OUTM "$_"; next; }
    @ar = split/\s+/, $_;
    next if ($ar[1] == 0);
    if ($ar[1] < 0) { $v = -1*$ar[1]; print OUTM "$ar[0]\t$v\n"; }
    else { print OUTP "$_"; }
  }
  close(IN); close(OUTP); close(OUTM);
  system "$tool $d.mm10.methpct.$ctxt.plus.wig $cs $d.mm10.methpct.$ctxt.plus.bigwig";
  system "$tool $d.mm10.methpct.$ctxt.minus.wig $cs $d.mm10.methpct.$ctxt.minus.bigwig";
} }