fxtract

#!/usr/bin/perl

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

=head1 NAME

fxtract

=head1 SYNOPSIS

 fxtract [options] genotype-file
  -h  help
    
 example: fxtract pscalare.gt
          fxtract pscalare.tg
          
 Extracts sample-ids and snp-ids from a gt or tg file.
       
=head1 DESCRIPTION

=cut

#option variables
my $help;
my $genotypeFile;
my $genotypeSkeletonFile;
my $headerProcessed;

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

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

$genotypeFile = $ARGV[0];
isGtOrTg($genotypeFile) || die "$genotypeFile not a genotype file";

if(!defined($genotypeSkeletonFile))
{
	my($name, $path, $ext) = fileparse($genotypeFile, '\..*');
	$genotypeSkeletonFile = "$name$ext" . "s";
}

open(GENO_SKELETON, ">$genotypeSkeletonFile") || die "Cannot open $genotypeSkeletonFile";

open(GENO, "$genotypeFile") || die "Cannot open $genotypeFile";
$headerProcessed = 0;

while (<GENO>)
{
    s/\r?\n?$//;
   
    if(!$headerProcessed)
    {		
        print GENO_SKELETON "$_\n";
        
        $headerProcessed = 1;
    }
    else
    {
    	my @fields = split('\t', $_, 2);
    
        print GENO_SKELETON "$fields[0]\n";
	}
}

close(GENO_SKELETON);
close(GENO);