class Bio::PAML::Codeml

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').next_entry.alignment
# Reads newick tree from a file
tree = Bio::FlatFile.open(Bio::Newick, 'example.tree').next_entry.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)

Constants

DEFAULT_PARAMETERS

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

DEFAULT_PROGRAM

Default program name

Public Class Methods

create_config_file (parameters, filename)

Source

    # File lib/bio/appl/paml/codeml.rb
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 soon be removed. Instead, use create_control_file(parameters, filename).

create_control_file (parameters, filename)

Source

    # File lib/bio/appl/paml/codeml.rb
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

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

Public Instance Methods

options ()

Source

    # File lib/bio/appl/paml/codeml.rb
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.

options= (hash)

Source

    # File lib/bio/appl/paml/codeml.rb
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

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

query (alignment, tree = nil, aarate = nil)

Source

    # File lib/bio/appl/paml/codeml.rb
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 and tree.

Note that parameters and parameters are always modified, and parameters and parameters are modified when tree and aarate are specified respectively.

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

Arguments:

(required) alignment: Bio::Alignment object or similar object
(optional) tree: Bio::Tree object
(optional) aarate: String or nil

Returns: Report object

Calls superclass method

query_by_string (alignment = nil, tree = nil, aarate = nil)

Source

    # File lib/bio/appl/paml/codeml.rb
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

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

Note that parameters is always modified, and parameters, parameters, and parameters 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)

Calls superclass method