Bio::Tools::Run::PhyloUserpContributed PBio::Tools::Run::Phylo::Hyphy::SLAC(3)NAMEBio::Tools::Run::Phylo::Hyphy::SLAC - Wrapper around the Hyphy SLAC
analysis
SYNOPSIS
use Bio::Tools::Run::Phylo::Hyphy::SLAC;
use Bio::AlignIO;
use Bio::TreeIO;
my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/hyphy1.fasta');
my $aln = $alignio->next_aln;
my $treeio = Bio::TreeIO->new(
-format => 'newick', -file => 't/data/hyphy1.tree');
my $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
$slac->alignment($aln);
$slac->tree($tree);
my ($rc,$results) = $slac->run();
DESCRIPTION
This is a wrapper around the SLAC analysis of 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://bugzilla.open-bio.org/
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 for SLAC 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.
INCOMPLETE DOCUMENTATION OF ALL METHODS
new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object
Returns : Bio::Tools::Run::Phylo::Hyphy::SLAC
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
run
Title : run
Usage : my ($rc,$results) = $slac->run($aln);
Function: run the slac analysis using the default or updated parameters
the alignment parameter must have been set
Returns : Return code, hash
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 :
set_default_parameters
Title : set_default_parameters
Usage : $hyphy->set_default_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
Bio::Tools::Run::Phylo::Hyphy::Base methods
program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
prepare
Title : prepare
Usage : my $rundir = $slac->prepare($aln);
Function: prepare the slac 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]
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 : $slac->align($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Args : [optional] L<Bio::Align::AlignI>
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 : $slac->tree($tree, %params);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI>
Args : [optional] $tree => L<Bio::Tree::TreeI>,
[optional] %parameters => hash of tree-specific parameters:
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 : $slac->set_parameter($param,$val);
Function: Sets a slac parameter, will be validated against
the valid values as set in the %VALIDVALUES class variable.
The checks can be ignored if one turns off param checks like this:
$slac->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 : $slac->set_default_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
update_ordered_parameters
Title : update_ordered_parameters
Usage : $slac->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
Bio::Tools::Run::WrapperBase methods
save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
cleanup
Title : cleanup
Usage : $slac->cleanup();
Function: Will cleanup the tempdir directory after a run
Returns : none
Args : none
io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
perl v5.14.12011-0Bio::Tools::Run::Phylo::Hyphy::SLAC(3)
