#!/usr/bin/perl
use strict;
use warnings;

use Benchmark;

use Data::Dumper;

my $DNAlength= 600000;
my $sequencelength= 3;
my $testfilename= 'DNA.tst';
my $bufsize= 1024;

# create testdata
open(my $testfile, ">$testfilename") or die "$testfilename: $!";
my $buffer = '';
for (my $i=$DNAlength; $i; --$i) {
    $buffer.= qw(A C G T)[rand 4];
    if (length($buffer) > $bufsize) {
        print $testfile $buffer;
        $buffer = '';
    }
}
print $testfile $buffer;
close $testfile;

a1: {
    # Start collecting data
    my %DNA_sequence_count;
    
    my $a1_0=new Benchmark;
    open($testfile, $testfilename) or die "$testfilename: $!";
    my $kept=0;
    while (1) {
        my $read_bytes = read($testfile, $buffer, $bufsize-$kept);
        last unless $read_bytes;
        my $end_buffer = $read_bytes-$sequencelength;
        for (my $i=0; $i <= $end_buffer; ++$i) {
            ++$DNA_sequence_count{substr($buffer, $i, $sequencelength)
+};
        }
        $kept= $sequencelength-1;
        $buffer= substr($buffer, $end_buffer+1, $kept);
    }
    close $testfile;
    my $a1_n=new Benchmark;
    
    print "the file code took:",timestr(timediff($a1_n, $a1_0)),"\n";
}

a2: {
    # Start collecting data
    my %DNA_sequence_count;
    
    my $a2_0=new Benchmark;
    open($testfile, $testfilename) or die "$testfilename: $!";
    my $allbuffered= <$testfile>;
    close $testfile;
    my $end_buffer= length($allbuffered)-$sequencelength+1;
    for (my $i=0; $i <= $end_buffer; ++$i) {
            ++$DNA_sequence_count{substr($allbuffered, $i, $sequencele
+ngth)};
    }
    my $a2_n=new Benchmark;

    print "the scalar code took:",timestr(timediff($a2_n, $a2_0)),"\n"
+;
}

a3: {
    # Start collecting data
    my %DNA_sequence_count;
    
    my $a3_0=new Benchmark;
    open($testfile, $testfilename) or die "$testfilename: $!";
    my $allbuffered= <$testfile>;
    close $testfile;
    ++$DNA_sequence_count{$1.$2} while $allbuffered=~ /(.)(?=(..))/g;
    my $a3_n=new Benchmark;

    print "the regex code took:",timestr(timediff($a3_n, $a3_0)),"\n";
}
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