[Bioperl-l] BLOSUM Matrix parser

[Jason Stajich]

As it shows in the SYNOPSIS of Bio::Matrix::Generic.

my $score = $matrix->get_entry('W', 'R');


On Oct 13, 2004, at 10:34 PM, zayed albertyn wrote:

> Good Day Bioperl Enthusiasts,
>
> I have been working with amino acid scoring matrices, most notably
> BLOSUM62, and I was interested in a parser for this matrix.
>
> Following the bioperl documentation I came across Bio::Matrix::Scoring
> which I could load successfully and parse matrix parameters. However,
> I was unable to actually get slices of the matrix data. As I
> understand it Bio::Matrix::Scoring is supposed to inherit from
> Bio::Matrix::Generic. If I load the module and initialize a new object
> as below:
>
> use Bio::Matrix::IO;
> use Bio::Matrix::MatrixI;
>
> my $matrixfile = shift; #BLOSUM62 scoring matrix
>
> my $parser = new Bio::Matrix::IO(-format => 'scoring',
>                                    -file   => $matrixfile);
>
>
> How do I use Bio::Matrix::Generic to get slices of the matrix e.g. the
> BLOSUM62 score for any two arbitrarily chosen amino acids?
>
>
> Thanks
> Zayed
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>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/