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)