Bio::Matrix::IO - A factory for Matrix parsing
use Bio::Matrix::IO; my $parser = Bio::Matrix::IO->new(-format => 'scoring', -file => 'BLOSUMN50'); my $matrix = $parser->next_matrix;
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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 :
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
Title : format Usage : $format = $obj->format() Function: Get the matrix format Returns : matrix format Args : none
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
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
Title : _load_format_module Usage : *INTERNAL Matrix::IO stuff* Function: Loads up (like use) a module at run time on demand
Title : _guess_format Usage : $obj->_guess_format($filename) Returns : guessed format of filename (lower case) Args : filename