| Bio::Tools::Run::Phylo::Hyphy::BatchFile(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Hyphy::BatchFile(3pm) |
Bio::Tools::Run::Phylo::Hyphy::BatchFile - Wrapper for custom execution of Hyphy batch files
my $aln = Bio::Align::AlignI->new(); my $treeio = Bio::TreeIO->new(-format => "nexus", -file => "$tree_file"); my $tree = $treeio->next_tree(); my $bf_exec = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new(-params => {'bf' => "hyphybatchfile.bf", 'order' => ["Universal", "Custom", $aln, "001001", $tree]}); $bf_exec->set_parameter('3', "012012"); my ($rc,$parser) = $bf_exec->run();
This module creates a generic interface to processing of HBL files in HyPhy ([Hy]pothesis Testing Using [Phy]logenies), a package by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information.
Instances of this module require only a link to the batch file and an ordered list of parameters, as described in the HyPhy documentation "SelectionAnalyses.pdf."
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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
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
Title : update_ordered_parameters Usage : $BatchFile->update_ordered_parameters(); Function: updates all of the parameters needed for the ordered input redirect in HBL. Returns : nothing Args : none
Title : run Usage : my ($rc,$results) = $BatchFile->run(); Function: run the Hyphy analysis using the specified batchfile and its ordered parameters Returns : Return code, Hash Args : none
Title : 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
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
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
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
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
| 2021-01-06 | perl v5.32.0 |