Dear BrowserUK,

First of all I would like to apologize for coming back to you again.

Your code worked fine as you presented.
But when I attempted to put your code above as a function:
use Data::Dumper;

my @inst = ( 'AAA', 'ATG', 'TTT', 'GTC' );
get_pwm(@inst);

sub get_pwm {

    my @data = @_;
    my %pwm;
    foreach my $line (@data) {

        ++$pwm{ substr $line, $_, 1 }[$_] for 0 .. length($line) - 1;
    }

    my $n = $.;
    @$_ = map { $_ ? $_ / $n : 0 } @$_ for values %pwm;  # Line 26

    print Dumper \%pwm;
    print "$_ => @{ $pwm{ $_ } }" for keys %pwm;

    return;
}

[download]
It gives: 
Use of uninitialized value in division (/) at pwm.pl line 26.
Illegal division by zero at pwm.pl line 26.
Attempt to free temp prematurely: SV 0x8f6a3f8, Perl interpreter: 0x8f
+53008.
Attempt to free unreferenced scalar: SV 0x8f6a3f8, Perl interpreter: 0
+x8f53008.

[download]
How can I overcome the problem above.

Regards,
Edward

In reply to Re^2: Position Weight Matrix of Set of Strings by monkfan
in thread Position Weight Matrix of Set of Strings by monkfan

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