#!perl -w
# This script converts the normalized data file generated by NimbleGen's
# array-CGH platform to the .dcn file accepted by DCNDenoise. The input file
# is [array id]_normalized.txt on NimbleGen's data CD/DVD. In fact,
# the log2 ratios in this file are the same as those in the [array id]_unavg.txt.
#
# 5/11/2006 Yuhang Wang yuhangw@engr.smu.edu
# V0.9
use strict;

if($#ARGV != 1 && $#ARGV != 0) {
  print "Usage: nimblegen2dcn.pl input_txt_file [ouput_dcn_file]\n";
  exit;
}

my $inputfile = $ARGV[0];

# Name for output .dcn file (extension is optional)
my $outputfile;
if($#ARGV == 1) { # If the user has entered a name for output .dcn file
  $outputfile = $ARGV[1];
}
else { # If the user did not enter it
  # The output .dcn file will be the same as the .txt file name
  # except it has a .dcn extension
  $outputfile = substr($ARGV[0], 0, index($ARGV[0], ".")).".dcn";
}

if($outputfile !~ /\./) { # If there is no extension in the output file name
  $outputfile .= ".dcn";
}

open(INPUT, $inputfile) or die "File \'$inputfile\' cannot be found\n";
open(OUTPUT, ">$outputfile");

my @DATA; # array of arrays

# Slurp in the whole file
while (<INPUT>)
{
  chomp;
  push @DATA, [ split "\t" ];
}

for (my $j = 1; $j < @DATA; $j++)
{
  my @slice = @{$DATA[$j]}[6,7,13];
  $slice[0] =~ s/chr0/chr/; 
  my $line = join "\t", @slice;
  print OUTPUT $line;
  print OUTPUT "\n";
}

close(INPUT);
close(OUTPUT);