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 = {})

Source

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

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)

Public Instance Methods

dump_parameters ()

Source

    # File lib/bio/appl/paml/common.rb
271 def dump_parameters
272   keyorder = DEFAULT_PARAMETERS_ORDER
273   keys = parameters.keys
274   str = String.new
275   keys.sort do |x, y|
276     (keyorder.index(x) || (keyorder.size + keys.index(x))) <=>
277       (keyorder.index(y) || (keyorder.size + keys.index(y)))
278   end.each do |key|
279     value = parameters[key]
280     # Note: spaces are required in both side of the "=".
281     str.concat "#{key.to_s} = #{value.to_s}\n" if value
282   end
283   str
284 end

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

Returns: string representation of the parameters (String)

load_parameters (str)

Source

    # File lib/bio/appl/paml/common.rb
249 def load_parameters(str)
250   hash = {}
251   str.each_line do |line|
252     param, value = parse_parameter(line)
253     hash[param] = value if param
254   end
255   self.parameters = hash
256 end

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)

query (alignment, tree = nil)

Source

    # File lib/bio/appl/paml/common.rb
118 def query(alignment, tree = nil)
119   astr = alignment.output(:phylipnon)
120   if tree then
121     tstr = [ sprintf("%3d %2d\n", tree.leaves.size, 1), "\n",
122              tree.output(:newick,
123                          { :indent => false,
124                            :bootstrap_style => :disabled,
125                            :branch_length_style => :disabled })
126            ].join('')
127   else
128     tstr = nil
129   end
130   str = _query_by_string(astr, tstr)
131   @report = self.class::Report.new(str)
132   @report
133 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 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:

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

Returns: Report object

query_by_string (alignment = nil, tree = nil)

Source

    # File lib/bio/appl/paml/common.rb
152 def query_by_string(alignment = nil, tree = nil)
153   _query_by_string(alignment, tree)
154 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 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)

run (control_file)

Source

   # File lib/bio/appl/paml/common.rb
96 def run(control_file)
97   exec_local([ control_file ])
98 end

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)

set_default_parameters ()

Source

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

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

Returns: parameters (Hash)