NAME
Bio::Tools::Run::Phylo::PAML::Evolver - Wrapper aroud the PAML program evolver
SYNOPSIS
use Bio::Tools::Run::Phylo::PAML::Evolver;
my $evolver = Bio::Tools::Run::Phylo::PAML::Evolver->new();
# Get a $tree object somehow
$evolver->tree($tree);
# FIXME: evolver generates a tree (first run with option 1 or 2)?
# One or more alns are created
my @alns = $evolver->run();
####
# Or with all the data coming from a previous PAML run
my $parser = Bio::Tools::Phylo::PAML->new
(
-file => "$inputfile",
);
my $result = $parser->next_result();
my $tree = $result->next_tree;
$evolver->tree($tree);
my @codon_freqs = $result->get_CodonFreqs();
$evolver->set_CodonFreqs(\@codon_freqs);
my $val = $evolver->prepare();
# FIXME: something similar for nucleotide frequencies:
# Option (5) Simulate nucleotide data sets (use MCbase.dat)?
# FIXME: something similar for aa parameters:
# Option (7) Simulate amino acid data sets (use MCaa.dat)?
# FIXME: With an initial RootSeq.txtDESCRIPTION
This is a wrapper around the evolver program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information.
This module is more about generating the properl MCmodel.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place.
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/MailList.shtml - About the mailing listsSupport
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://bioperl.org/bioperl-bugs/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 evolver programs are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the example MCcodon.dat file and pamlDOC documentation provided by the author.
Stub:
option1 specifies something.
option2 specifies something else.
INCOMPLETE DOCUMENTATION OF ALL METHODS
program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : Noneprogram_dir
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Evolver->new();
Function: Builds a new Bio::Tools::Run::Phylo::PAML::Evolver object
Returns : Bio::Tools::Run::Phylo::PAML::Evolver
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object (FIXME: optional if this is done in a first run)
-params => a hashref of PAML parameters (all passed to set_parameter)
-executable => where the evolver executable residesSee also: Bio::Tree::TreeI
prepare
Title : prepare
Usage : my $rundir = $evolver->prepare($aln);
Function: prepare the evolver 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]run
Title : run
Usage : my ($rc,$parser) = $evolver->run();
Function: run the evolver analysis using the default or updated parameters
the alignment parameter must have been set
Returns : Return code, L<Bio::Tools::Phylo::PAML>
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 analysis run is stored.
Returns : value of error_string
Args : newvalue (optional)alignment
Title : alignment
Usage : $evolver->align($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 : $evolver->tree($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:
branchLengths: 0, 1 or 2
out
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 : noneset_parameter
Title : set_parameter
Usage : $evolver->set_parameter($param,$val);
Function: Sets a evolver 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:
$evolver->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 : $evolver->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 valuesBio::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)set_CodonFreqs
Title : set_CodonFreqs
Usage : $obj->set_CodonFreqs($newval)
Function: Get/Set the Codon Frequence table
Returns : value of set_CodonFreqs (a scalar)
Args : on set, new value (a scalar or undef, optional)get_CodonFreqs
Title : get_CodonFreqs
Usage : my @codon_freqs = $evolver->get_CodonFreqs()
Function: Get the Codon freqs
Returns : Array
Args : nonesave_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)outfile_name
Title : outfile_name
Usage : my $outfile = $evolver->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value totempdir
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 : nonecleanup
Title : cleanup
Usage : $evolver->cleanup();
Function: Will cleanup the tempdir directory after a PAML run
Returns : none
Args : noneio
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : noneindel
Title : indel
Usage : $obj->indel($newval)
Function: this is only useful if using evolver_indel instead of main
evolver package:
Exploring the Relationship between Sequence Similarity and
Accurate Phylogenetic Trees Brandi L. Cantarel, Hilary
G. Morrison and William Pearson
Example :
Returns : value of indel (a scalar)
Args : on set, new value (a scalar or undef, optional)