XMS::WeightMatrix - Perl module for creating weightmatrices for DNA motifs in XMS format
use XMS::WeightMatrix; my $wm = XMS::Weightmatrix->new(@matrix); # @matrix is reference to array of arrays $wm->toXML(); # wm is weightmatrix is xms format $wm->toString(); # wm is weightmatrix is string/raw format $wm->WeightForSymbol("adenine",rowindex) # Get weight for "adenine" residue at row number rowindex $wm->setWeightForSymbol("adenine",rowindex,weight) # Set weight for "adenine" residue at row number rowindex
The WeightMatrix package can be used to create the XMS format for a given position weight matrix. It can also be sued to obtain weights or to set new weights.
new()
toXML()
toString()
WeightForSymbol()
setWeightForSymbol()
$w = XMS::WeightMatrix-
new() returns a new String handle.
$x = $w-
toXML() converts the array into a XMS format weightmatrix.
$s = $w-
toString() converts the array into a string format weightmatrix.
$ws = $w-
= item $sws = $w-setWeightForSymbol([symbol, rownumber,weight]);> setWeightForSymbol allows to set weight for a nucleotide (A, T, G or C) at a particular position in the matrix.
$sws = $w-
This module has external dependencies on the following modules: Exporter XML::Writer, IO::File XML::Reader
Nothing.
perl(1), XML::Writer, XML::Reader
Harpreet Saini, hsaini@ebi.ac.uk
Copyright (C) 2009 by harpreet saini
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.9 or, at your option, any later version of Perl 5 you may have available.
To install XMS::Motif, copy and paste the appropriate command in to your terminal.
cpanm
cpanm XMS::Motif
CPAN shell
perl -MCPAN -e shell install XMS::Motif
For more information on module installation, please visit the detailed CPAN module installation guide.