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.txt
DESCRIPTION¶
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 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://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 : None
program_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 resides
See 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 : none
set_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 values
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 : none
save_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 to
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 : $evolver->cleanup();
Function: Will cleanup the tempdir directory after a PAML run
Returns : none
Args : none
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
indel¶
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)