Re^4: Position Weight Matrix of Set of Strings

Dear BrowserUK,
I was trying your code above with this set of strings:

my @inst = ( 'CAGGTG',
             'CAGGTG' );

my $res1 = get_pwm(@inst);
[download]

But why it returns this answer:

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

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' ] 
};
[download]

It seems that the code didn't supply 0 when the bases is not present in a particular column as it should after it found 1.
I thought from this line of the code should do that job, but seems not.

    @$_ = map { $_ ? $_ / $n : 0 } @$_ for values %pwm;
[download]

Please advice.

---
neversaint and everlastingly indebted.......

Comment on Re^4: Position Weight Matrix of Set of Strings Select or Download Code

Replies are listed 'Best First'.
Re^5: Position Weight Matrix of Set of Strings by BrowserUk (Patriarch) on Sep 07, 2006 at 03:55 UTC
Try this `#! perl -slw use strict; use Data::Dumper; sub get_pwm { my @data = @_; my $l = length( $data[0] ); my %pwm; 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 = ( 'CAGGTG', 'CAGGTG' ); my $res = get_pwm(@inst); print "$_ => @{ $res->{ $_ } }" for keys %{ $res }; __END__ c:\test>530623 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` [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]
Re^6: Position Weight Matrix of Set of Strings by monkfan (Curate) on Sep 19, 2006 at 01:05 UTC
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	[reply] [d/l] [select]
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]