Class: Bio::PAML::Baseml

Inherits:

Common

• Object
• Common
• Bio::PAML::Baseml

Defined in:

lib/bio/appl/paml/baseml.rb,
lib/bio/appl/paml/baseml/report.rb

Overview

Description

Bio::PAML::Baseml is a wrapper for running PAML baseml program.

Because most of the methods in this class are inherited from Bio::PAML::Common, see documents of Bio::PAML::Common for details.

Examples

Example 1:

require 'bio'
# Reads multi-fasta formatted file and gets a Bio::Alignment object.
alignment = Bio::FlatFile.open(Bio::Alignment::MultiFastaFormat,
                               'example.fst').alignment
# Reads newick tree from a file
tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').tree
# Creates a Baseml object
baseml = Bio::PAML::Baseml.new
# Sets parameters
baseml.parameters[:runmode] = 0
baseml.parameters[:RateAncestor] = 1
# You can also set many parameters at a time.
baseml.parameters.update({ :alpha => 0.5, :fix_alpha => 0 })
# Executes baseml with the alignment and the tree
report = baseml.query(alignment, tree)

Defined Under Namespace

Classes: Report

Constant Summary

DEFAULT_PROGRAM =

Default program name

'baseml'.freeze

DEFAULT_PARAMETERS =

Default parameters when running baseml.

The parameters whose values are different from the baseml defalut value (described in pamlDOC.pdf) in PAML 4.1 are:

seqfile, outfile, treefile, ndata, noisy, verbose

{
  # Essential argumemts
  :seqfile             => nil,
  :outfile             => nil,
  # Optional arguments
  :treefile            => nil,
  :noisy               => 0,
  :verbose             => 1,
  :runmode             => 0,
  :model               => 5,
  :Mgene               => 0,
  :ndata               => 1,
  :clock               => 0,
  :fix_kappa           => 0,
  :kappa               => 2.5,
  :fix_alpha           => 1,
  :alpha               => 0.0,
  :Malpha              => 0,
  :ncatG               => 5,
  :fix_rho             => 1,
  :rho                 => 0.0,
  :nparK               => 0,
  :nhomo               => 0,
  :getSE               => 0,
  :RateAncestor        => 0,
  :Small_Diff          => 1e-6,
  :cleandata           => 1,
  :fix_blength         => 0,
  :method              => 0
}

Constants inherited from Common

Common::DEFAULT_PARAMETERS_ORDER

Instance Attribute Summary

Attributes inherited from Common

#command, #data_stdout, #exit_status, #output, #parameters, #report, #supplemental_outputs

Method Summary

Methods inherited from Common

#dump_parameters, #initialize, #load_parameters, #query, #query_by_string, #run, #set_default_parameters

Constructor Details

This class inherits a constructor from Bio::PAML::Common