| Bio::Matrix::IO(3pm) | User Contributed Perl Documentation | Bio::Matrix::IO(3pm) |
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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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.
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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
| 2018-10-27 | perl v5.26.2 |