Bio::Matrix::IO::scoring

NAME

Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies

SYNOPSIS

  use Bio::Matrix::IO;
  my $parser = Bio::Matrix::IO->new(-format => 'scoring',
                                   -file   => 'BLOSUM50');
  my $matrix = $parser->next_matrix;

DESCRIPTION

Describe the object here

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::Matrix::IO::scoring->new();
 Function: Builds a new Bio::Matrix::IO::scoring object 
 Returns : an instance of Bio::Matrix::IO::scoring
 Args    :

next_matrix

 Title   : next_matrix
 Usage   : my $matrux = $parser->next_matrix
 Function: parses a scoring matrix (BLOSUM,PAM styles) 
 Returns : L<Bio::Matrix::Scoring>
 Args    : none

write_matrix

 Title   : write_matrix
 Usage   : $matio->write_matrix($matrix)
 Function: Write out a matrix in the BLOSUM/PAM format
 Returns : none
 Args    : L<Bio::Matrix::Scoring>