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 |
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.
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)
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 |
OBSOLETE. This method will soon be removed. Instead, use create_control_file(parameters, filename).
# 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.
# 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
OBSOLETE. This method should not be used. Instead, use parameters.
# 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).
# 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 |
# 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:
Returns: | contents of output file (String) |
# 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