class Bio::PAML::Common

Description

Bio::PAML::Common is a basic wrapper class for PAML programs. The class provides methods for generating the necessary configuration file, and running a program.

Constants

DEFAULT_PARAMETERS

Default parameters. Should be redefined in subclass.

DEFAULT_PARAMETERS_ORDER

Preferred order of parameters.

DEFAULT_PROGRAM

Default program. Should be redifined in subclass.

Attributes

command[R]

the last executed command (Array of String)

data_stdout[R]

the last output to the stdout (String)

exit_status[R]

the last exit status of the program

output[R]

the last result of the program (String)

parameters[RW]

Parameters described in the control file. (Hash) Each key of the hash must be a Symbol object, and each value must be a String object or nil.

report[R]

Report object created from the last result

supplemental_outputs[R]

contents of supplemental output files (Hash). Each key is a file name and value is content of the file.

Public Class Methods

new(program = nil, params = {}) click to toggle source

Creates a wrapper instance, which will run using the specified binary location or the command in the PATH. If program is specified as nil, DEFAULT_PROGRAM is used. Default parameters are automatically loaded and merged with the specified parameters.


Arguments:

  • (optional) program: path to the program, or command name (String)

  • (optional) params: parameters (Hash)

# File lib/bio/appl/paml/common.rb, line 73
def initialize(program = nil, params = {})
  @program = program || self.class::DEFAULT_PROGRAM
  set_default_parameters
  self.parameters.update(params)
end

Public Instance Methods

dump_parameters() click to toggle source

Shows parameters (content of control file) as a string. The string can be used for control file.


Returns

string representation of the parameters (String)

# File lib/bio/appl/paml/common.rb, line 270
def dump_parameters
  keyorder = DEFAULT_PARAMETERS_ORDER
  keys = parameters.keys
  str = ''
  keys.sort do |x, y|
    (keyorder.index(x) || (keyorder.size + keys.index(x))) <=>
      (keyorder.index(y) || (keyorder.size + keys.index(y)))
  end.each do |key|
    value = parameters[key]
    # Note: spaces are required in both side of the "=".
    str.concat "#{key.to_s} = #{value.to_s}\n" if value
  end
  str
end
load_parameters(str) click to toggle source

Loads parameters from the specified string. Note that all previous parameters are erased. Returns the parameters as a hash.


Arguments:

  • (required) str: contents of a PAML control file (String)

Returns

parameters (Hash)

# File lib/bio/appl/paml/common.rb, line 248
def load_parameters(str)
  hash = {}
  str.each_line do |line|
    param, value = parse_parameter(line)
    hash[param] = value if param
  end
  self.parameters = hash
end
query(alignment, tree = 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 is modified when tree is specified.

To prevent overwrite of existing files by PAML, this method automatically creates a temporary directory and the program is run inside the directory. After the end of the program, the temporary directory is automatically removed.


Arguments:

Returns

Report object

# File lib/bio/appl/paml/common.rb, line 117
def query(alignment, tree = nil)
  astr = alignment.output(:phylipnon)
  if tree then
    tstr = [ sprintf("%3d %2d\n", tree.leaves.size, 1), "\n",
             tree.output(:newick,
                         { :indent => false,
                           :bootstrap_style => :disabled,
                           :branch_length_style => :disabled })
           ].join('')
  else
    tstr = nil
  end
  str = _query_by_string(astr, tstr)
  @report = self.class::Report.new(str)
  @report
end
query_by_string(alignment = nil, tree = 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 and parameters are modified when alignment and tree are specified respectively.

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

For other information, see the document of query method.


Arguments:

  • (optional) alignment: String

  • (optional) tree: String or nil

Returns

contents of output file (String)

# File lib/bio/appl/paml/common.rb, line 151
def query_by_string(alignment = nil, tree = nil)
  _query_by_string(alignment, tree)
end
run(control_file) click to toggle source

Runs the program on the parameters in the passed control file. No parameters checks are performed. All internal parameters are ignored and are kept untouched. The output and report attributes are cleared in this method.

Warning about PAML's behavior: PAML writes supplemental output files in the current directory with fixed file names which can not be changed with parameters or command-line options, for example, rates, rst, and rub. This behavior may ovarwrite existing files, especially previous supplemental results.


Arguments:

  • (optional) control_file: file name of control file (String)

Returns

messages printed to the standard output (String)

# File lib/bio/appl/paml/common.rb, line 95
def run(control_file)
  exec_local([ control_file ])
end
set_default_parameters() click to toggle source

Loads system-wide default parameters. Note that all previous parameters are erased. Returns the parameters as a hash.


Returns

parameters (Hash)

# File lib/bio/appl/paml/common.rb, line 262
def set_default_parameters
  self.parameters = self.class::DEFAULT_PARAMETERS.merge(Hash.new)
end