Bio::Tools::Run::Phylo::Hyphy::REL.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://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 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