#!usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my %HoH;
my @AoH;
my $substring = 'ATG';

sub get_first_index {
    my %hash;
    my ($found, $string) = @_;
    my @tags = ('TAG', 'TAA', 'TGA');

    my @indexes;
    foreach my $tag (@tags) {
	my $position = index($string, $tag, $found + 2);
	push @indexes, $position if ($position != -1);
    }

    # hash slice
    @hash{@indexes} = @tags;

    # sort has based on the lowest key first
    my @sorted = (sort {$a <=> $b} keys %hash);

    # remove the rest of the keys as we only want first occurence
    my $array_size = @sorted;
    delete $hash{$_} for @sorted [1..$array_size - 1];
    return \%hash;
}

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my $found = index($_, $substring);
    while ($found != -1) {
	my $hash_result = get_first_index( $found, $_ );
	# choose one or the other what ever you prefer
	$HoH{"Found $substring at $found"} = $hash_result if (%$hash_result);
	push @AoH, "Found $substring at $found" ,$hash_result if (%$hash_result);
	my $offset = $found + 1;
	$found = index( $_, $substring, $offset );
    }
} continue {
    close ARGV if eof; # reset $.
}

my @keys = keys %HoH;

print scalar @keys . "\n";

# print Dumper \@AoH;
# print Dumper \%HoH;

__END__

$ perl bio.pl sequence.fa
23

##</code><code>##

$ cat sequence.fa | grep -bo ATG
16:ATG
50:ATG
133:ATG
232:ATG
252:ATG
287:ATG
305:ATG
363:ATG
394:ATG
489:ATG
575:ATG
651:ATG
689:ATG
724:ATG
854:ATG
859:ATG
954:ATG
1014:ATG
1044:ATG
1051:ATG
1145:ATG
1228:ATG
1249:ATG
1272:ATG
tinyos@tinyOMN:~/Monks$ cat sequence.fa | grep -bo ATG | wc -l
24

##</code><code>##

#!usr/bin/perl
use say;
use strict;
use warnings;
use Data::Dumper;

my %HoH;
my @AoH;
my $substring = 'ATG';

sub get_first_index {
    my %hash;
    my ($found, $string) = @_;
    my @tags = ('TAG', 'TAA', 'TGA');

    my @indexes;
    while (my $tag = shift @tags) {
	my $position = index($string, $tag, $found + 2);
	push @indexes, $position if ($position != -1);
    }

    # hash slice, we destroy the array above so we need to replace it
    @hash{@indexes} = ('TAG', 'TAA', 'TGA');

    # sort has based on the lowest key first
    my @sorted = (sort {$a <=> $b} keys %hash);

    # remove the rest of the keys as we only want first occurence
    my $array_size = @sorted;
    delete $hash{$_} for @sorted [1..$array_size - 1];
    return \%hash;
}

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my $found = index($_, $substring);
    while ($found != -1) {
	my $hash_result = get_first_index( $found, $_ );
	# choose one or the other what ever you prefer
	$HoH{"Found $substring at $found"} = $hash_result if (%$hash_result);
	push @AoH, "Found $substring at $found" ,$hash_result if (%$hash_result);
	my $offset = $found + 1;
	$found = index( $_, $substring, $offset );
    }
} continue {
    close ARGV if eof; # reset $.
}

my @keys = keys %HoH;

print scalar @keys . "\n";

# print Dumper \@AoH;
# print Dumper \%HoH;