Bio::Tools::Run::Phylo::Hyphy::REL(3pm) User Contributed Perl Documentation Bio::Tools::Run::Phylo::Hyphy::REL(3pm)
NAME
Bio::Tools::Run::Phylo::Hyphy::REL - Wrapper around the Hyphy REL analysis
SYNOPSIS
use Bio::Tools::Run::Phylo::Hyphy::REL;
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 $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
$rel->alignment($aln);
$rel->tree($tree);
my ($rc,$results) = $rel->run();
DESCRIPTION
This is a wrapper around the REL 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.
This module will generate the correct list of options for interfacing with TemplateBatchFiles/Ghostrides/Wrapper.bf.
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 for REL 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 $obj = Bio::Tools::Run::Phylo::Hyphy::REL->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
Returns : Bio::Tools::Run::Phylo::Hyphy::REL
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
run
Title : run
Usage : my ($rc,$results) = $rel->run($aln);
Function: run the rel 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 : $rel->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::WrapperBase methods
no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
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 : $rel->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 v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::Hyphy::REL(3pm)