Bio::Matrix::IO.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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
 
 

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