UNIX for Dummies Questions & Answers

AATGGTCCTG

A=2 C=2 G=3 T=3

A
A
T
G
G
T
C
C
T
G

#!/usr/bin/perl -w

use strict;
use warnings;

my ( $data, %count );

{

    # Slurp in all data at once
    local $/;
    open my $fh, '<', 'file.txt' or die "Can't open file.txt: $!";
    $data = <$fh>;
    close $fh;
}

# Remove any line breaks, spaces, tabs, ...
$data =~ s/[\s]//msg;

# Split between each character, and sum the occurences
$count{$_}++ foreach ( split( //, $data ) );

# Print a sorted list of characters and their occurences
print "$_=$count{$_} " foreach sort keys %count;