/ 
BioPerl-Run-1.007000
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Phylo::Hyphy::Base

NAME

Bio::Tools::Run::Phylo::Hyphy::Base - Hyphy wrapping base methods

SYNOPSIS

FIXME

DESCRIPTION

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.

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:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Albert Vilella

Email avilella-at-gmail-dot-com

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Default Values

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.

program_name

Title   : program_name
Usage   : $factory->program_name()
Function: holds the program name
Returns:  string
Args    : None

valid_values

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

program_dir

Title   : program_dir
Usage   : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns:  string
Args    :

new

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

prepare

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]

create_wrapper

Title   : create_wrapper
Usage   : $self->create_wrapper
Function: It will create the wrapper file that interfaces with the analysis bf file
Example :
Returns :
Args    :

run

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

error_string

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)

alignment

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>

tree

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>

get_parameters

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

set_parameter

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()>

set_default_parameters

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

update_ordered_parameters

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

outfile_name

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

version

Title   : version
Usage   : $obj->version()
Function:  Returns the version string from HYPHY
Returns : string
Args    : none

hyphy_lib_dir

Title   : hyphy_lib_dir
Usage   : $obj->hyphy_lib_dir()
Function: Returns the HYPHY_LIB_DIRECTORY from HYPHY
Returns : string
Args    : none