| Bio::Tools::Run::Phylo::Hyphy::Base(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Hyphy::Base(3pm) |
Bio::Tools::Run::Phylo::Hyphy::Base - Hyphy wrapping base methods
FIXME
HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information.
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
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.
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:
http://redmine.open-bio.org/projects/bioperl/
Email avilella-at-gmail-dot-com
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Valid and default values are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the python wrapper or provided by the author.
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
Title : valid_values
Usage : $factory->valid_values()
Function: returns the possible parameters
Returns: an array holding all possible parameters (this needs to be specified per child class).
Returns an empty array in the base class.
Args : None
Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy object
Returns : Bio::Tools::Run::Phylo::Hyphy
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
Title : prepare
Usage : my $rundir = $hyphy->prepare($aln);
Function: prepare the analysis using the default or updated parameters
the alignment parameter must have been set
Returns : value of rundir
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
Title : create_wrapper Usage : $self->create_wrapper Function: It will create the wrapper file that interfaces with the analysis bf file Example : Returns : Args :
Title : run Usage : my ($rc,$results) = $BatchFile->run(); Function: run the Hyphy analysis using the specified batchfile and its ordered parameters Returns : Return code, Hash Args : none
Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional)
Title : alignment
Usage : $hyphy->alignment($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::SimpleAlign>
Title : tree
Usage : $hyphy->tree($tree);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI>
Args : [optional] $tree => L<Bio::Tree::TreeI>,
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::Tree::Tree>
Title : get_parameters Usage : my %params = $self->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none
Title : set_parameter
Usage : $hyphy->set_parameter($param,$val);
Function: Sets a hyphy parameter, will be validated against
the valid values.
The checks can be ignored if one turns off param checks like this:
$hyphy->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
then no warning will be reported
Args : $param => name of the parameter
$value => value to set the parameter to
See also: L<no_param_checks()>
Title : set_default_parameters
Usage : $obj->set_default_parameters();
Function: (Re)set the default parameters from the defaults
(the first value in each array in the valid_values() array)
Returns : none
Args : none
Title : update_ordered_parameters Usage : $hyphy->update_ordered_parameters(0); Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable) Returns : none Args : boolean: keep existing parameter values
Title : outfile_name
Usage : my $outfile = $hyphy->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
Title : version Usage : $obj->version() Function: Returns the version string from HYPHY Returns : string Args : none
Title : hyphy_lib_dir Usage : $obj->hyphy_lib_dir() Function: Returns the HYPHY_LIB_DIRECTORY from HYPHY Returns : string Args : none
| 2018-09-14 | perl v5.26.2 |