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) click to toggle source

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

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

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

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

Public Instance Methods

options() click to toggle source

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

# File lib/bio/appl/paml/codeml.rb, line 133
def options
  warn 'The method Codeml#options will be changed to be used for command line arguments in the future. Instead, use Codeml#parameters.'
  parameters
end
options=(hash) click to toggle source

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

# File lib/bio/appl/paml/codeml.rb, line 140
def options=(hash)
  warn 'The method Codeml#options=() will be changed to be used for command line arguments in the future. Instead, use Codeml#parameters=().'
  self.parameters=(hash)
end
query(alignment, tree = nil, aarate = nil) click to toggle source

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:

Returns

Report object

Calls superclass method
# File lib/bio/appl/paml/codeml.rb, line 183
def query(alignment, tree = nil, aarate = nil)
  begin
    aaratefile = prepare_aaratefile(aarate)
    ret = super(alignment, tree)
  ensure
    finalize_aaratefile(aaratefile)
  end
  ret
end
query_by_string(alignment = nil, tree = nil, aarate = nil) click to toggle source

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
# File lib/bio/appl/paml/codeml.rb, line 212
def query_by_string(alignment = nil, tree = nil, aarate = nil)
  begin
    aaratefile = prepare_aaratefile(aarate)
    ret = super(alignment, tree)
  ensure
    finalize_aaratefile(aaratefile)
  end
  ret
end