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/

valid_values¶

 Title   : valid_values
 Usage   : $factory->valid_values()
 Function: returns the possible parameters
 Returns:  an array holding all possible parameters. The default
values are always the first one listed.  These descriptions are
essentially lifted from the python wrapper or provided by the author.
 Args    : None

new¶

 Title   : new
 Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new();
 Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::BatchFile object
 Returns : Bio::Tools::Run::Phylo::Hyphy::BatchFile
 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)
                      this hashref should include   'bf' => custombatchfile.bf
                                                    'order' => [array of ordered parameters]
           -executable => where the hyphy executable resides

See also: Bio::Tree::TreeI, Bio::Align::AlignI

update_ordered_parameters¶

 Title   : update_ordered_parameters
 Usage   : $BatchFile->update_ordered_parameters();
 Function: updates all of the parameters needed for the ordered input redirect in HBL.
 Returns : nothing
 Args    : none

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

create_wrapper¶

 Title   : create_wrapper
 Usage   : $self->create_wrapper
 Function: Creates the wrapper file for the batchfile specified in the hash, saves it to the hash as '_wrapper'.
 Returns : nothing
 Args    : none

set_parameter¶

Title : set_parameter Usage : $hyphy->set_parameter($param,$val); Function: Sets the named parameter $param to $val if it is a non-numeric parameter
If $param is a number, sets the corresponding value of the ordered redirect array (starts from 1). Returns : boolean if set was successful Args : $param => name of the parameter
$value => value to set the parameter to

batchfile¶

Title : batchfile Usage : $hyphy->batchfile($bf_name); Function: Gets/sets the batchfile that is run by $hyphy. Returns : The batchfile path. Args : $bf_name => path of new batchfile

make_batchfile_with_contents¶

Title : make_batchfile_with_contents Usage : $hyphy->make_batchfile_with_contents($bf_string); Function: Creates a temporary file with the specified string of contents for the batchfile. Returns : The batchfile path. Args : $bf_string => contents for the batchfile

set_default_parameters¶

 Title   : set_default_parameters
 Usage   : $BatchFile->set_default_parameters(0);
 Function: (Re)set the default parameters from the defaults
           (the first value in each array in the
            valid_values)
 Returns : none
 Args    : boolean: keep existing parameter values