RE: Position Weight Matrix of Set of Strings with Perl

[Wijaya Edward]

Dear Rob,
 
I was trying your script with this set of strings:
 
__DATA__
CAGGTG
CAGGTG
 
But how come it returns:
 
$VAR1 = {
    'A' => [ 0, '0.5' ], 
    'T' => [ 0, 0, 0, 0, '0.5' ], 
    'C' => [ '0.5' ],    
    'G' => [ 0, 0, '0.5', '0.5', 0, '0.5' ]
};

Instead of the correct:

$VAR1 = {
    'A' => [ '0', '1', '0', '0', '0', '0' ],
    'T' => [ '0', '0', '0', '0', '1', '0' ],
    'C' => [ '1', '0', '0', '0', '0', '0' ],
    'G' => [ '0', '0', '1', '1', '0', '1' ] 
};


Hope to hear from you again.


Regards,
Edward WIJAYA
SINGAPORE

 


 

________________________________

From: Rob Dixon [mailto:[EMAIL PROTECTED]
Sent: Wed 9/6/2006 8:14 PM
To: beginners@perl.org
Subject: Re: Position Weight Matrix of Set of Strings with Perl



use strict;
use warnings;

my %pwm;

while (<DATA>) {
   my $col = 0;
   foreach my $c (/\S/g) {
     $pwm{$c}[$col++]++;
   }
}

foreach my $freq (values %pwm) {
   $_ = $_ ? $_ / keys %pwm : 0 foreach @$freq;
}

use Data::Dumper;
print Dumper \%pwm;


__END__
AAA
ATG
TTT
GTC


OUTPUT


$VAR1 = {
           'A' => [
                    '0.5',
                    '0.25',
                    '0.25'
                  ],
           'T' => [
                    '0.25',
                    '0.75',
                    '0.25'
                  ],
           'C' => [
                    0,
                    0,
                    '0.25'
                  ],
           'G' => [
                    '0.25',
                    0,
                    '0.25'
                  ]
         };

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