trio_whole_exome_parse_peddy_ped_csv.pl

#!/usr/bin/perl -w

=head1 NAME

trio_whole_exome_parse_peddy_ped_csv.pl

=head1 AUTHOR

Alison Meynert (alison.meynert@igmm.ed.ac.uk)

=head1 DESCRIPTION

Checks the parent-child and parent-parent relationships from peddy output.

=cut

use strict;

use Getopt::Long;
use IO::File;

my $usage = qq{USAGE:
$0 [--help]
  --output  Output directory
  --ped     Pedigree file for project
  --project Project id
  --batch   Batch id
};

my $help = 0;
my $ped_file;
my $project_id;
my $out_dir;
my $batch_id;

GetOptions(
    'help'      => \$help,
    'project=s' => \$project_id,
    'ped=s'     => \$ped_file,
    'output=s'  => \$out_dir,
    'batch=s'   => \$batch_id
) or die $usage;

if ($help || !$project_id || !$ped_file || !$out_dir || !$batch_id)
{
    print $usage;
    exit(0);
}

# Read in the pedigree file
my $in_fh = new IO::File;
$in_fh->open($ped_file, "r") or die "Could not open $ped_file\n$!";

my %ped;
while (my $line = <$in_fh>)
{
	chomp $line;
	my ($family_id, $individual_id, $father_id, $mother_id, $sex, $aff) = split(/\t/, $line);
	$ped{$family_id}{'count'}++;
	$ped{$family_id}{$individual_id}{'father'} = $father_id;
	$ped{$family_id}{$individual_id}{'mother'} = $mother_id;
	if ($aff == 2)
	{
		$ped{$family_id}{'aff'} = $individual_id;
	}
}

$in_fh->close();

my $out_file = "$out_dir/qc/$project_id.ped_check.txt";