#!/usr/bin/env perl

# author: bliako
# for: https://perlmonks.org/?node_id=1227228
# date: 14/12/2018

use strict;
use warnings;

# our $biologists = new alchemists() and fork until pop(@the::bubble); do not tell until tied $all;

# Below, set the complete pathname of the file with DNA strings
my $filename = "dna.txt";

# a DNA string is a sequence (any order) of A,C,G,T of at
# least 5 items in length. Adjust 5 to suit you and
# not detect TATA FOR NOW
# or GATTAGA or ATTAC or CACA or GAGA or TAGA
# similar detection to https://perlmonks.org/?node_id=1227232 by 1nickt
my $regex = q/([ACGT]{5,})/;

#
# nothing to change below
#
my $FH;
open($FH, '<', $filename) or die "opening file: $!";
# slurp the file
my $contents = undef;
{local $/ = undef; $contents = <$FH> } close $FH;

print "Possible DNA:\n$1\nEnd\n\n" while $contents =~ /$regex/gi