#!/usr/bin/perl -w
use strict;


my $file1 = $ARGV[0];
my $file2 = $ARGV[1];
open (FILE1, $file1) or die "Uh oh.. unable to find file $file1"; ##Opens input file
open (FILE2, $file2) or die "Unable to find $file2";

my @maxent_unchanged = <FILE1>; #loads inputfile1 data into array
close FILE1;

my @maxent_with_variant = <FILE2>; ## loads ref genome
close FILE2;


my @NM;
my @max_score_unchanged;
my %max_unchanged;
foreach my $line(@maxent_unchanged) {

	if ($line =~ m/[a-z]/i) {
	push (@NM, $line);
	}
		else { 
	push (@max_score_unchanged, $line);
	}
}

my $i = 0;
foreach my $lines(@maxent_unchanged) {
$max_unchanged{$NM[$i]} = $max_score_unchanged[$i]; 
$i++;
}



my @NM_ID;
my @max_score_changed;
my %max_changed;
foreach my $line(@maxent_with_variant) {

	if ($line =~ m/[a-z]/i) {
	push (@NM_ID, $line);
	}
		else { 
	push (@max_score_changed, $line);
	}
}

my $i = 0;
foreach my $lines(@maxent_with_variant) {
$max_changed{$NM_ID[$i]} = $max_score_changed[$i]; 
$i++;
}

print %max_unchanged;
print "\n";
print "\n";
print "\n";
print %max_changed;



my @calc;
foreach my $key (keys(%max_changed)) {
my $value1 = $max_unchanged{$key};
my $value2 = $max_changed{$key};
my $calc = $value1 - $value2;
push (@calc, $calc);
}

use Data::Dumper;
print Dumper @calc;