| Bio::Tools::Run::Phylo::Hyphy::SLAC(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Hyphy::SLAC(3pm) |
Bio::Tools::Run::Phylo::Hyphy::SLAC - Wrapper around the Hyphy SLAC analysis
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();
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.
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
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.
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/
Email avilella-at-gmail-dot-com
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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 $obj = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object
Returns : Bio::Tools::Run::Phylo::Hyphy::SLAC
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
Title : run
Usage : my ($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]
Title : create_wrapper Usage : $self->create_wrapper Function: It will create the wrapper file that interfaces with the analysis bf file Example : Returns : Args :
| 2023-01-22 | perl v5.36.0 |