#!/usr/bin/perl
use warnings;
use strict;
use autodie;
use List::Util;

my $file = 'sequence.txt';
my $goal = 'GATC';

my $stats = process_file( $file, $goal );

# do something with stats ... 

# ----------------------------------------
# Subroutines
#
sub process_file {
    my ( $file, $goal ) = @_;

    open my $infh, '<', $file;
    my $stats = process_lines( $infh, $goal );
    close $infh;

    return $stats
}

sub process_lines {
    my ( $infh, $goal ) = @_;

    my @stats;
    while ( my $line - <$infh> ) {
        chomp $line;
        my $linestats = process_one_line( $line, $goal );
        push @stats, $linestats || 0;
    }
    return \@stats;
}

sub process_one_line {
    my ( $line, $goal ) = @_

    my @occurences;
    my ( $offset ) = ( 0 );
  SEEK:
    while ( 1 ) {
        $idx = index( $line, $goal, $offset );
        last SEEK if $idx == -1; # no more occurences
        push @occurences, $idx;
        $offset = $idx;
    }

    return calc_avg_distance( \@occurences, length $goal );
}

sub calc_avg_distance {
    my ( $occurences, $len ) = @_;

    return unless $occurences and scalar @$occurences;

    my $start = shift @$occurences;
    my @distances;

    while ( my $end = shift @$occurences ) {
        push @distances, ( $end - $start ) - $len;
        $start = $end;
    }
    my $sum = reduce { $a + $b }, @distances;
    my $n   = scalar @distances;
    return $sum / $n;
}
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