#!/usr/bin/perl


#because everyone says its important to include in code
use warnings;
use strict;
use Data::Dumper;

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

#link to input file from command line - 2 arguments or error displayed; Set to respective variables
@ARGV == 2 or die "Invalid number or arguments. Program will now terminate.";
my ($filter_file, $input_file) = @ARGV;

###############################################
#   STORE CRITERIA FOR FILTERING INPUT FILE   #
###############################################
open (FILTER,"$filter_file");
my @filter;

<FILTER>; # read one line from the file

while (<FILTER>)
{ # read other lines
	chomp; # remove "\n" from the end of the line
	 push @filter,[(split /\t/,$_)]; # create an array of the line by splitting it by <TAB>, make a reference of it and push the reference to the @filter array
}

@filter = sort { $a->[4] <=> $b->[4] } @filter; # sort the array 

#--------------------------------------------------------------------------
#PRINTS REFERENCES TO ARRAY FROM LEAST TO GREATEST REGARDING 'ORDER' COLUMN
#print Dumper \@filter; 
#print $filter[0]->[0], "\n";
#--------------------------------------------------------------------------

###############################################
#   LOAD INPUT FILE FOR PROCESSING            #
###############################################
open (IN, "$input_file") or die "Cannot open file: $!";

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

#*********************************************
#set relationship operators to variables
# HOW ?!?!?!?!?!?!?!
#*********************************************

#open output file - Given name:  OUTPUT_"input_file" or error displayed if file cannot be created
open (OUTFILE, ">OUTPUT_$input_file") or die "Cannot create an output file: $!";

#Column headers stored as keys; Can be called to retrieve data in specified column
#Hashes are put into an array; each hash is an array row;
while(my $line = <IN>)
{
        chomp($line);
        $x++;
        if ($x==1)
        {
                print OUTFILE $line, "\n";
                (@keys)=split(/\t/, $line);
        }
        else
        {
                my $y=0;
                (@holder) = split(/\t/, $line);
                my %hash;
                for my $column (@holder)
                {
                        $hash{$keys[$y]}=$column;
                        $y++;
                }
		#********************************************************************
		#HOW TO COMBINE PROCESSING BLANKS AND RELATIONSHIPS IN ONE STEP??????
		#********************************************************************
		if ($hash{$filter[0]->[0]} eq $blank)
		{
			print OUTFILE $line, "\n";
		}
		if ($hash{$filter[0]->[0]} le $filter[0]->[2])
		{
			print OUTFILE $line, "\n";
		}

		if ($hash{$filter[1]->[0]} eq $blank)
		{
			print OUTFILE $line, "\n";
		}
		if ($hash{$filter[1]->[0]} eq $filter[1]->[2])
		{
			print OUTFILE $line, "\n";
		}

	}
}

##</code><code>##

column relationship value filter_or_append order
a      <=           0.3   filter           1
b      =            abc   append           3
c      <=           0.3   filter           2

##</code><code>##

if ($hash{$filter[0]->[0]} le $filter[0]->[2])
		{
			print OUTFILE $line, "\n";
		}

##</code><code>##

 if ($hash{$filter[0]->[0]} $filter[0]->[1] $filter[0]->[2])
		{
			print OUTFILE $line, "\n";
		}