@a=@c=@t=@g=@n=@a2=@c2=@t2=@g2=@n2=();

##</code><code>##

(@a, @c, @t, @g, @n, @a2, @c2, @t2, @g2, @n2) = ();

##</code><code>##

for (my $k=0;$k<$number_positions; $k++) {
    my (@a,@c,@t,@g,@n,@a2,@c2,@t2,@g2,@n2);

##</code><code>##

if ($letter1=~ /[aA]/) { ... }
... 

##</code><code>##

if (uc $letter1 eq 'A') { ... }
if (uc $letter1 eq 'C') { ... }
if (uc $letter1 eq 'T') { ... }
if (uc $letter1 eq 'G') { ... }
# ...

##</code><code>##

$letter1 = uc $letter1;

if ($letter1 eq 'A') { ... }
if ($letter1 eq 'C') { ... }
if ($letter1 eq 'T') { ... }
# ...

##</code><code>##

for (my $k=0;$k<$number_positions; $k++) {
    my (%base1, %base2);
    # ...
        $letter1 = uc $letter1;
        $letter2 = uc $letter2;

        push @${$base1{$letter1}}, $letter1;
        push @${$base2{$letter2}}, $letter2;

##</code><code>##

for (my $k=0;$k<$number_positions; $k++) {
    my (%base1, %base2);
    # ...
        $base1{uc $letter1}++;
        $base2{uc $letter2}++;

##</code><code>##

"$number_a" + "$number_c" + "$number_t" + "$number_g" + "$number_n"

##</code><code>##

$number_a + $number_c + $number_t + $number_g + $number_n

##</code><code>##

$base1{A} + $base1{C} + $base1{T} + $base1{G} + $base1{N}

##</code><code>##

my $total1 = $base1{A} + $base1{C} + $base1{T} + $base1{G} + $base1{N};

##</code><code>##

my %percent1 = (
    A => ($base{A} * 100) / $total1,
    C => ($base{C} * 100) / $total1,
    T => ($base{T} * 100) / $total1,
    G => ($base{G} * 100) / $total1,
    N => ($base{N} * 100) / $total1,
);

##</code><code>##

my %percent1 = map { $_ => ( $base{$_} * 100) / $total1 } 'A', 'C', 'T', 'G', 'N';

##</code><code>##

my %percent1 = map { $_ => ( $base1{$_} * 100) / $total1 } qw(A C T G N);

##</code><code>##

#!/usr/bin/perl

use warnings;
use strict;

chomp(my $input = <STDIN>);
open(INPUT, "$input") or die "Cannot open file: $!";

chomp(my $number_positions = <STDIN>);

chomp(my $patient_number = <STDIN>);

chomp(my $output = <STDIN>);
open(OUTPUT, ">$output.txt") or die "Cannot open file: $!";

my @prettybase = <INPUT>;
close(INPUT);

for my $k (0 .. $number_positions - 1) {
	my (%base1, %base2);

	for my $i (0 .. $patient_number) {
		my ($position, $patient, $letter1, $letter2) =
			split (/\t/, $prettybase[$i]);

		$base1{uc $letter1}++;
		$base2{uc $letter2}++;
	}

	my $total1 = $base1{A} + $base1{C} + $base1{T} + $base1{G} + $base1{N};
	my %percent1 = map { $_ => ( $base1{$_} * 100) / $total1 } qw(A C T G N);

	my $total2 = $base2{A} + $base2{C} + $base2{T} + $base2{G} + $base2{N};
	my %percent2 = map { $_ => ( $base2{$_} * 100) / $total2 } qw(A C T G N);

	print OUTPUT "Position\#\: $patient\n";
	print OUTPUT "\tAllele 1  Allele 1 percentage\n";
	for(qw(A C T G N)) {
		print OUTPUT "$_:\t$base1{$_}\t$percent1{$_}\%\n\n";
	}
	print OUTPUT "\tAllele 2  Allele 2 percentage\n";
	for(qw(A C T G N)) {
		print OUTPUT "$_:\t$base2{$_}\t$percent2{$_}\%\n\n";
	}
}
close(OUTPUT);