illumina2helixtree

#!/usr/bin/perl

use warnings;
use strict;
use fralib;
use Getopt::Long;
use Pod::Usage;

=head1 NAME

illumina2tg

=head1 SYNOPSIS

 illumina2tg [options] <filename>
  -h  help
  -m  SNP annotation file
    
 example: illumina2tg -m pscalare.mk pscalare.txt
 
 Converts an Illumina matrix file with [ACGT][ACGT] and -- encoding to a tgfile.
       
=head1 DESCRIPTION

=cut

#option variables
my $help;
my $snpAnnotationFile;
my $illuminaGenotypeFile;
my $genotypeFile;
my @col2snp;
my %SNP;
my $colNo;
my %anno2col;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions ('h'=>\$help) || scalar(@ARGV) != 1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

$illuminaGenotypeFile = $ARGV[0];

open(IN, "$illuminaGenotypeFile") || die "Cannot open $illuminaGenotypeFile\n";

$genotypeFile = "helixtree-$illuminaGenotypeFile";

open(OUT, ">$genotypeFile") || die "Cannot open $genotypeFile\n";

while (<IN>)
{
    s/\r?\n?$//;
   
    if($.==1)
    {
    	$colNo = s/\t/\t/g + 1;
    	    		
        print OUT "$_\n";
    }
    else
    {
    	my @fields = split('\t', $_, $colNo);
    
        print OUT "$fields[0]";

		my $snp = $fields[0];

		for my $col (1..$#fields)
		{
			my $genotype = $fields[$col];
			
			if ($genotype ne '--')
			{
				$genotype =~ /([ACGT])([ACGT])/;
				print OUT "\t$1_$2";
			}
			else
			{
				print OUT "\t?_?";
			}
		}

        print OUT "\n";
    }
}

close(OUT);
close(IN);