From 448ebcd4f71fc53013ea4ee42082b1bf65cac7c8 Mon Sep 17 00:00:00 2001
From: Sebastien Vigneau <sebastien.vigneau@gmail.com>
Date: Fri, 10 Jan 2014 15:14:49 -0500
Subject: [PATCH] first commit

---
 bedgraph_to_wig.pl | 130 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100755 bedgraph_to_wig.pl

diff --git a/bedgraph_to_wig.pl b/bedgraph_to_wig.pl
new file mode 100755
index 0000000..1e20fd4
--- /dev/null
+++ b/bedgraph_to_wig.pl
@@ -0,0 +1,130 @@
+#!/usr/bin/perl
+
+# Description: This script converts bedGraph to fixedStep wig format with defined step size. Input file may be compressed as .gz.
+# Coordinates in bedGraph input are assumed to be 0-based (http://genome.ucsc.edu/goldenPath/help/bedgraph.html).
+# Coordinates in wig output are 1-based (http://genome.ucsc.edu/goldenPath/help/wiggle.html). 
+
+# Usage: bedgraph_to_wig.pl --bedgraph input.bedgraph --wig output.wig --step step_size [--compact]
+# --bedgraph : specify input file in bedGraph format.
+# --wig : specify output file in fixedStep format.
+# --step : specify step size. Note that span is set to be identical to step.
+# --compact : if selected, steps with value equal to 0 will not be printed. This saves space but was not allowed in original wig format, thus some scripts using wig file as input may not understand it.
+
+# Credits: This script was written by Sebastien Vigneau (sebastien.vigneau@gmail.com) in Alexander Gimelbrant lab (Dana-Farber Cancer Institute). The inspiration for this script comes from Dave Tang's own version (http://davetang.org/wiki/tiki-index.php?page=wig).
+
+
+use strict;
+use warnings;
+use Getopt::Long;
+use List::Util qw[min max];
+
+my $usage = "Usage: $0 --bedgraph <infile.bedgraph> --wig <outfile.wig> --step <step_size> [--compact]\n";
+
+# Parse command line arguments
+
+my $infile; # bedGraph input file name
+my $outfile; # wig output file name
+my $step; # wig step size
+my $compact; # if selected, steps with value equal to 0 will not be printed
+
+GetOptions (
+  "bedgraph=s" => \$infile,
+  "wig=s" => \$outfile,
+  "step=i" => \$step,
+  "compact" => \$compact,
+) or die ("Error in command line arguments!\n$usage\n");
+
+# Open input file. If it is compressed with gunzip, uncompress it.
+
+if ($infile =~ /\.gz$/){
+  open(IN,'-|',"gunzip -c $infile") || die "Could not open $infile: $!\n";
+} else {
+  open(IN,'<',$infile) || die "Could not open $infile: $!\n";
+}
+
+# Open output file.
+
+open(OUT,'>',$outfile) || die "Could not open $outfile: $!\n";
+
+
+# bedGraph to wig conversion starts here.
+
+# Print main header.
+
+print OUT "track type=wiggle_0 name=\"$infile\" description=\"$infile\" visibility=full\n";
+
+# Initialize variables.
+
+my $cur_chr = 0; # chromosome being processed
+my $cur_pos = 0; # position of current step
+my $next_pos = $cur_pos + $step; # position of next step
+my $exp_pos = 0; # expected position if no step was skipped; used with --compact option
+my $cur_val = 0; # value for current step
+
+while (<IN>) {
+
+  chomp;
+
+  # Skip comment lines
+  next if (/^track/);
+  next if (/^#/);
+
+  # Parse relevant information in current line 
+  # e.g: chr1 3000400 3000500 2
+  my ($chr, $start, $end, $val) = split(/\t/);
+  
+  # Print header for new chromosome and initialize variables.
+  if ($chr ne $cur_chr) {
+    $cur_chr = $chr;
+    $cur_pos = 0;
+    $next_pos = $cur_pos + $step;
+    $cur_val = 0;
+    if (!$compact) { # If --compact option selected, header will be printed immediately before non-null value.
+      print OUT "fixedStep chrom=$chr start=", $cur_pos + 1, " step=$step span=$step\n";
+      # +1 was added to convert from 0-based to 1-based coordinates.
+    }
+  }
+  
+  # Print values when gap in bedGraph file is greater than step.
+  while ($start >= $next_pos) {
+    print_wig_line($cur_chr, \$cur_pos, \$next_pos, \$exp_pos, \$cur_val, $chr, $start, $end, $val, $step);
+  }
+  
+  # Print values when step overlaps with bedGraph interval and bedGraph interval is longer than step.
+  while ($end >= $next_pos) {
+    $cur_val += $val * ($next_pos - max($cur_pos, $start));
+    print_wig_line($cur_chr, \$cur_pos, \$next_pos, \$exp_pos, \$cur_val, $chr, $start, $end, $val, $step);
+  }
+
+  # Update value when end of bedGraph interval is contained within step.
+  if ($end < $next_pos) {
+    $cur_val += $val * ($end - max($cur_pos, $start));
+  }
+
+}
+
+close(IN);
+close(OUT);
+
+exit(0);
+
+
+# Print or skip line in wig file depending on --compact option and value; update variables for next step.
+sub print_wig_line {
+  my ($cur_chr, $cur_pos, $next_pos, $exp_pos, $cur_val, $chr, $start, $end, $val, $step) = @_;
+  if (!$compact) { # Always print if --compact option was not selected.
+    my $cur_ave_val = $$cur_val / $step;
+    print OUT "$cur_ave_val\n";
+  } elsif ($$cur_val != 0) { # Skips printing if --compact option selected and value is null.
+    if ($$cur_pos != $$exp_pos) { # Adds header if previous step had null value and was skipped in print out.
+      print OUT "fixedStep chrom=$chr start=", $$cur_pos + 1, " step=$step span=$step\n";
+      # +1 was added to convert from 0-based to 1-based coordinates.
+    }
+    my $cur_ave_val = $$cur_val / $step;
+    print OUT "$cur_ave_val\n";
+    $$exp_pos = $$next_pos;
+  }
+  $$cur_pos = $$next_pos;
+  $$next_pos = $$cur_pos + $step;
+  $$cur_val = 0;
+}