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The Zenautics Matrix Project 0.01 Beta (Default branch)
04-21-2008
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Bio::Matrix::IO(3pm) User Contributed Perl Documentation Bio::Matrix::IO(3pm) 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://redmine.open-bio.org/projects/bioperl/ 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 perl v5.14.2 2012-03-02 Bio::Matrix::IO(3pm)