Re^6: Position Weight Matrix of Set of Strings

BrowserUk,
Given this set of sequences where base A doesn't exists (i.e, only CGT).

my @inst = ( 'GGTGTGCC', 
             'GCTGTGGG', 
             'GGTGGGCC' );
[download]

The code gives this matrix only:

T => 0 0 1 0 0.666666666666667 0 0 0 
C => 0 0.333333333333333 0 0 0 0 0.666666666666667 0.666666666666667
G => 1 0.666666666666667 0 1 0.333333333333333 1 0.333333333333333 0.3
+33333333333333
[download]

Note that it doesn't show matrix element of A:

A => 0 0 0 0 0 0 0 0
[download]

My question is how can I initialize your code above, so it can also includes matrix where the bases doesn't exist?
Given that there are only 4 alphabets [ATCG] required for the construction of matrix.

Regards,
Edward

Comment on Re^6: Position Weight Matrix of Set of Strings Select or Download Code

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Re^7: Position Weight Matrix of Set of Strings by BrowserUk (Patriarch) on Sep 19, 2006 at 01:23 UTC
Better? #! perl -slw use strict; use Data::Dumper; sub get_pwm { my @data = @_; my $l = length( $data[0] ); my %pwm = map{ $_ => [ (0) x length( $_[ 0 ] ) ] } qw[ A C G T ]; foreach my $line (@data) { ++$pwm{ substr $line, $_, 1 }[$_] for 0 .. $l - 1; } my $n = @data; @$_ = map { $_ ? $_ / $n : 0 } @{ $_ }[ 0 .. $l - 1 ] for values +%pwm; return \%pwm; } my @inst = ( 'GGTGTGCC', 'GCTGTGGG', 'GGTGGGCC' ); my $res = get_pwm(@inst); printf "%1s => [ %s ]\n", $_ => join ' ', map{ sprintf '%5.2f', $_ } @{ $res->{ $_ } } for keys %{ $res }; __END__ c:\test>530623.pl A => [ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ] T => [ 0.00 0.00 1.00 0.00 0.67 0.00 0.00 0.00 ] C => [ 0.00 0.33 0.00 0.00 0.00 0.00 0.67 0.67 ] G => [ 1.00 0.67 0.00 1.00 0.33 1.00 0.33 0.33 ] [download] Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal? "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply] [d/l]

Replies are listed 'Best First'.

Re^7: Position Weight Matrix of Set of Strings
by BrowserUk (Patriarch) on Sep 19, 2006 at 01:23 UTC

Better?

#! perl -slw
use strict;
use Data::Dumper;

sub get_pwm {
    my @data = @_;

    my $l = length( $data[0] );
    my %pwm = map{ $_ => [ (0) x length( $_[ 0 ] ) ] } qw[ A C G  T ];
    foreach my $line (@data) {
        ++$pwm{ substr $line, $_, 1 }[$_] for 0 .. $l - 1;
    }
    my $n = @data;
    @$_ = map { $_ ? $_ / $n : 0 } @{ $_ }[ 0 .. $l - 1 ]  for values 
+%pwm;

    return \%pwm;
}

my @inst = (
    'GGTGTGCC',
    'GCTGTGGG',
    'GGTGGGCC'
);

my $res = get_pwm(@inst);

printf "%1s => [ %s ]\n", $_ => join ' ', map{
        sprintf '%5.2f', $_
    } @{ $res->{ $_ } } for keys %{ $res };

__END__
c:\test>530623.pl
A => [  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 ]
T => [  0.00  0.00  1.00  0.00  0.67  0.00  0.00  0.00 ]
C => [  0.00  0.33  0.00  0.00  0.00  0.00  0.67  0.67 ]
G => [  1.00  0.67  0.00  1.00  0.33  1.00  0.33  0.33 ]
[download]

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

[reply]
[d/l]