NAME
Bio::Matrix::IO - A factory for Matrix parsing
SYNOPSIS
my $parser = Bio::Matrix::IO->new(-format => 'scoring',
-file => 'BLOSUMN50');
my $matrix = $parser->next_matrix;
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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
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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:
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 :
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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>;
print $fh $matrix;
Returns : filehandle tied to the Bio::SeqIO::Fh class
Args :
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fh
Title : fh
Usage : $obj->fh
Function: Get a filehandle type access to the matrix parser
Example : $fh = $obj->fh;
$matrix = <$fh>;
print $fh $matrix;
Returns : filehandle tied to Bio::Matrix::IO class
Args : none
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Title : format
Usage : $format = $obj->format()
Function: Get the matrix format
Returns : matrix format
Args : none
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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
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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
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Title : _load_format_module
Usage : *INTERNAL Matrix::IO stuff*
Function: Loads up (like use) a module at run time on demand
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Title : _guess_format
Usage : $obj->_guess_format($filename)
Returns : guessed format of filename (lower case)
Args : filename
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