Re^3: Position Weight Matrix of Set of Strings

The problem arises in this line my $n = $.;. $. (also known as $INPUT_LINE_NUMBER. See perlvar), is the record or line number of the last line read from a file.

In the original code that line came immediately after the while( my $line = <DATA> ) { loop, so $n was set to the number of lines in the file.

In your code/function, you are not reading from a file, therefore $. is 0, so $n gets set to 0, hence the error in this line:

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

As you are passing the data into the function as a list and assigning it to an array, the equivalent value is the number of elements in the array. Eg. scalar @data;. So, modifying your code as

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

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

    return;
}
[download]

Produces this output (assuming -l):

$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'
                 ]
        };

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
[download]

Not sure why you are outputting the results two different ways. It's also not typical to output from within a subroutine.

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.

Comment on Re^3: Position Weight Matrix of Set of Strings Select or Download Code

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Re^4: Position Weight Matrix of Set of Strings by neversaint (Deacon) on Sep 07, 2006 at 02:31 UTC
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.......	[reply] [d/l] [select]
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