trio_whole_exome_create_parameter_files.pl

#!/usr/bin/perl -w

=head1 NAME

trio_whole_exome_create_parameter_files.pl

=head1 AUTHOR

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

=head1 DESCRIPTION

Creates the files:
  $prefix.family_ids.txt - format <pcr_plate_id>_<family_id>
  $prefix_$family_id.ped - select only the individuals in a given family,
                           prefix <family_id> with <pcr_plate_id> and
                           add suffix <family_id> to <individual_id>

=cut

use strict;

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

my $usage = qq{USAGE:
$0 [--help]
  --prefix Output prefix for files
  --ped    Pedigree file for project
  --suffix Sample suffix
};

my $help = 0;
my $ped_file;
my $output_prefix;
my $sample_suffix;

GetOptions(
    'help'     => \$help,
    'prefix=s' => \$output_prefix,
    'suffix=s' => \$sample_suffix,
    'ped=s'    => \$ped_file
) or die $usage;

if ($help || !$output_prefix || !$sample_suffix || !$ped_file)
{
    print $usage;
    exit(0);
}

# Read in the file_list.tsv file(s) from the Edinburgh Genomics project delivery folder
my %family;
while (my $line = <>)
{
	next if ($line =~ /^File/);
	next if ($line =~ /unassigned/);
	chomp $line;

	my @tokens = split(/\t/, $line);
	my $sample_dir = $tokens[7];

	# remove the sample suffix
	$sample_dir =~ /(.+)$sample_suffix/;
	my $sample_full_id = $1;

	my ($pcr_plate_id, $individual_id, $family_id) = split('_', $sample_full_id);

	$family{$family_id}{'pcr_plate_id'} = $pcr_plate_id;
	$family{$family_id}{'individual_id'}{$individual_id}++;
}