#!/usr/bin/perl

use warnings;
use strict;
use autodie;

use Data::Dumper;

@ARGV == 2 or die "Invalid number of arguments. Please re-run program and suppy as arguments \n1) the filter file and \n2) the input file.";

my ($filter_file, $input_file) = @ARGV;

open (my $FILTER,"<","$filter_file") or die "Cannot open filter file: $!";
my @filter_array;

<$FILTER>;

while (my $line = <$FILTER>)
{
	chomp $line;
	my @line_array = split(/\t/, $line);
	push (@filter_array, \@line_array);
} 

@filter_array = sort { $a->[5] <=> $b->[5]} @filter_array;
#print Dumper \@filter_array, "\n"; #[DEBUGGING]


my $num_elements = (@filter_array-1);
#print "$num_elements", "\n"; #[DEBUGGING]


open (IN,"<","$input_file") or die "Cannot open input file: $!";
open (OUTFILE, ">>", "OUTPUT_$input_file") or die "Cannot create an output file: $!";

for (my $i=0; $i<=$num_elements; $i++)
{
	my $search_string = $filter_array[$i][0];
#	print "$search_string", "\n";

	my $header = <IN>;
	my @header_titles = split /\t/, $header;
	my $extract_col = 0;

	for my $header_line (@header_titles)
	{
		last if $header_line =~ m/$search_string/;
		$extract_col++;
	}

	print "Extracting column $extract_col\n";

	while (my $row = <IN>)
	{
		last unless $row =~ /\S/;
		chomp $row;
		my @cells = split /\t/, $row;
#		print "$cells[$extract_col]\n";
			
			if ((eval "$cells[$extract_col] $filter_array[$i][1] $filter_array[$i][2]"))
			{
				print OUTFILE "$cells[$extract_col]", "\n";
			}
		
                

	}
}