#!/usr/bin/perl

#use strict;
use warnings;



#print "Enter the input file name: ";
#my $filename = <STDIN>;
#chomp ($filename);

@ARGV == 1 or die "Invalid number of arguments. Please supply as arguments: \n1) the input file listing all data to be used.";
my ($input_file) = @ARGV;

open (IN, "$input_file") or die "Cannot open file: $!";
#head -1 <IN>;
#my $firstline = IN;

my $x=0;
my @keys;
my @holder;
my @array_hash;
my $threshold=.03;
my $blank = "-";
my $nonsyn = "nonsynonymous";

open (OUTFILE, ">TEST_$input_file") or die "Cannot create an output file: $!";
while(my $line = <IN>)
{
	print OUTFILE head -1;
	chomp($line);
	$x++;
	if ($x==1)
	{
		(@keys)=split(/\t/, $line);
	}
	else
	{
		my $y=0;
		(@holder) = split(/\t/, $line);
		my %hash;
		for my $column (@holder)
		{
			$hash{$keys[$y]}=$column;
			$y++;
		}

#		-ne print OUTFILE; exit;
#		my $first = shift (@array_hash);
#		print OUTFILE $first;

		if ($hash{"1000_Genomes"} ne $blank)
		{
			if ($hash{"1000_Genomes"} <=  $threshold)
                	{
                		if ($hash{"Syn/Nonsyn"} eq $nonsyn)
				{        
			 		print OUTFILE $line, "\n";
				}
                	}
		}
                if ($hash{"1000_Genomes"} eq $blank)
                {
                       # if ($hash{"1000_Genomes"} <=  $threshold)
                       # {
                                if ($hash{"Syn/Nonsyn"} eq $nonsyn)
                                {
                                        print OUTFILE $line, "\n";
                                }
                       # }
                }

	}

}