NAME

Bio::Matrix::IO - A factory for Matrix parsing

SYNOPSIS

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'scoring',
                                  -file   => 'BLOSUMN50');

my $matrix = $parser->next_matrix;

DESCRIPTION

This is a general factory framework for writing parsers for Matricies. This includes parsing output from distance output like PHYLIP's ProtDist. Additionally it should be possible to fit parsers for PWM and PSSMs once their Matrix objects are written.

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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->new();
Function: Builds a new Bio::Matrix::IO object 
Returns : an instance of Bio::Matrix::IO
Args    :

newFh

Title   : newFh
Usage   : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format')
          $matrix = <$fh>;   # read a matrix object
          print $fh $matrix; # write a matrix object
Returns : filehandle tied to the Bio::SeqIO::Fh class
Args    :

fh

Title   : fh
Usage   : $obj->fh
Function: Get a filehandle type access to the matrix parser
Example : $fh = $obj->fh;      # make a tied filehandle
          $matrix = <$fh>;     # read a matrix object
          print $fh $matrix;   # write a matrix object
Returns : filehandle tied to Bio::Matrix::IO class
Args    : none

format

Title   : format
Usage   : $format = $obj->format()
Function: Get the matrix format
Returns : matrix format
Args    : none

next_matrix

Title   : next_matrix
Usage   : my $matrix = $matixio->next_matrix;
Function: Parse the next matrix from the data stream
Returns : L<Bio::Matrix::MatrixI> type object or undef when finished
Args    : none

write_matrix

Title   : write_matrix
Usage   : $io->write_matrix($matrix)
Function: Writes a matrix out to the data stream
Returns : none
Args    : Array of Bio::Matrix::MatrixI object
         - note that not all matricies can be converted to 
           each format, beware with mixing matrix types and output formats

_load_format_module

Title   : _load_format_module
Usage   : *INTERNAL Matrix::IO stuff*
Function: Loads up (like use) a module at run time on demand

_guess_format

Title   : _guess_format
Usage   : $obj->_guess_format($filename)
Returns : guessed format of filename (lower case)
Args    : filename

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq