Class Bio::PAML::Codeml
In: lib/bio/appl/paml/codeml.rb
lib/bio/appl/paml/codeml/rates.rb
lib/bio/appl/paml/codeml/report.rb
Parent: Common

Description

Bio::PAML::Codeml is a wrapper for estimating evolutionary rate using the CODEML tool. The class provides methods for generating the necessary configuration file, and running codeml with the specified binary. Codeml output is returned when codeml is run. Bio::PAML::Codeml::Report and Bio::PAML::Codeml::Rates provide simple classes for parsing and accessing the Codeml report and rates files respectively.

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 Codeml object
  codeml = Bio::PAML::Codeml.new
  # Sets parameters
  codeml.parameters[:runmode] = 0
  codeml.parameters[:RateAncestor] = 1
  # You can also set many parameters at a time.
  codeml.parameters.update({ :alpha => 0.5, :fix_alpha => 0 })
  # Executes codeml with the alignment and the tree
  report = codeml.query(alignment, tree)

Example 2 (Obsolete usage):

  # Create a control file, setting some Codeml options
  # Default parameters are used otherwise, see RDoc for defaults
  # The names of the parameters correspond to those specified
  # in the Codeml documentation
  control_file = Tempfile.new('codeml_ctl')
  control_file.close(false)
  # Prepare output file as a temporary file
  output_file = Tempfile.new('codeml_test')
  output_file.close(false)
  Bio::PAML::Codeml.create_control_file(config_file.path, {
    :model       => 1,
    :fix_kappa   => 1,
    :aaRatefile  => TEST_DATA + '/wag.dat',
    :seqfile     => TEST_DATA + '/abglobin.aa',
    :treefile    => TEST_DATA + '/abglobin.trees',
    :outfile     => output_file.path,
  })

  # Create an instance of Codeml specifying where the codeml binary is
  codeml = Bio::PAML::Codeml.new('/path/to/codeml')

  # Run codeml using a control file
  # Returns the command line output
  codeml_output = codeml.run(control_file)

Methods

Classes and Modules

Class Bio::PAML::Codeml::Rates
Class Bio::PAML::Codeml::Report

Constants

DEFAULT_PROGRAM = 'codeml'.freeze   Default program name
DEFAULT_PARAMETERS = { # Essential argumemts :seqfile => nil, :outfile => nil, # Optional arguments :treefile => nil, :noisy => 0, :verbose => 1, :runmode => 0, :seqtype => 2, :CodonFreq => 2, :ndata => 1, :clock => 0, :aaDist => 0, :aaRatefile => 'wag.dat', :model => 2, :NSsites => 0, :icode => 0, :Mgene => 0, :fix_kappa => 0, :kappa => 2, :fix_omega => 0, :omega => 0.4, :fix_alpha => 0, :alpha => 0.0, :Malpha => 0, :ncatG => 3, :fix_rho => 1, :rho => 0.0, :getSE => 0, :RateAncestor => 0, :Small_Diff => 0.5e-6, :cleandata => 1, :fix_blength => 0, :method => 0   Default parameters when running codeml.

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

 seqfile, outfile, treefile, ndata, noisy, verbose, cleandata

Public Class methods

OBSOLETE. This method will soon be removed. Instead, use create_control_file(parameters, filename).

[Source]

     # File lib/bio/appl/paml/codeml.rb, line 160
160:     def self.create_config_file(parameters, filename)
161:       warn "The method Codeml.create_config_file(parameters, filename) will soon be removed. Instead, use Codeml.create_control_file(filename, parameters)."
162:       create_control_file(parameters, filename)
163:     end

Obsolete. This method will be removed in the future. Helper method for creating a codeml control file. Note that default parameters are automatically merged.

[Source]

     # File lib/bio/appl/paml/codeml.rb, line 148
148:     def self.create_control_file(parameters, filename)
149:       parameters = DEFAULT_PARAMETERS.merge(parameters)
150:       File.open(filename, 'w') do |file|
151:         parameters.each do |key, value|
152:           file.puts "#{key.to_s} = #{value.to_s}" if value
153:         end
154:       end
155:       filename
156:     end

Public Instance methods

OBSOLETE. This method should not be used. Instead, use parameters.

[Source]

     # File lib/bio/appl/paml/codeml.rb, line 133
133:     def options
134:       warn 'The method Codeml#options will be changed to be used for command line arguments in the future. Instead, use Codeml#parameters.'
135:       parameters
136:     end

OBSOLETE. This method should not be used. Instead, use parameters=(hash).

[Source]

     # File lib/bio/appl/paml/codeml.rb, line 140
140:     def options=(hash)
141:       warn 'The method Codeml#options=() will be changed to be used for command line arguments in the future. Instead, use Codeml#parameters=().'
142:       self.parameters=(hash)
143:     end

Runs the program on the internal parameters with the specified sequence alignment and tree.

Note that parameters[:seqfile] and parameters[:outfile] are always modified, and parameters[:treefile] and parameters[:aaRatefile] are modified when tree and aarate are specified respectively.

For other important information, see the document of Bio::PAML::Common#query.


Arguments:

Returns:Report object

[Source]

     # File lib/bio/appl/paml/codeml.rb, line 183
183:     def query(alignment, tree = nil, aarate = nil)
184:       begin
185:         aaratefile = prepare_aaratefile(aarate)
186:         ret = super(alignment, tree)
187:       ensure
188:         finalize_aaratefile(aaratefile)
189:       end
190:       ret
191:     end

Runs the program on the internal parameters with the specified sequence alignment data string and tree data string.

Note that parameters[:outfile] is always modified, and parameters[:seqfile], parameters[:treefile], and parameters[:aaRatefile] are modified when alignment, tree, and aarate are specified respectively.

It raises RuntimeError if seqfile is not specified in the argument or in the parameter.

For other important information, see the document of query method.


Arguments:

  • (optional) alignment: String
  • (optional) tree: String or nil
  • (optional) aarate: String or nil
Returns:contents of output file (String)

[Source]

     # File lib/bio/appl/paml/codeml.rb, line 212
212:     def query_by_string(alignment = nil, tree = nil, aarate = nil)
213:       begin
214:         aaratefile = prepare_aaratefile(aarate)
215:         ret = super(alignment, tree)
216:       ensure
217:         finalize_aaratefile(aaratefile)
218:       end
219:       ret
220:     end

[Validate]