Class Bio::PAML::Common
In: lib/bio/appl/paml/common.rb
lib/bio/appl/paml/common_report.rb
Parent: Object

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.

Methods

Classes and Modules

Class Bio::PAML::Common::Report

Constants

DEFAULT_PARAMETERS = {}   Default parameters. Should be redefined in subclass.
DEFAULT_PROGRAM = nil   Default program. Should be redifined in subclass.
DEFAULT_PARAMETERS_ORDER = %w( seqfile outfile treefile noisy verbose runmode seqtype CodonFreq ndata clock aaDist aaRatefile model NSsites icode Mgene fix_kappa kappa fix_omega omega fix_alpha alpha Malpha ncatG fix_rho rho nparK nhomo getSE RateAncestor Small_Diff cleandata fix_blength method ).collect { |x| x.to_sym }   Preferred order of parameters.

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

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)

[Source]

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

Public Instance methods

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


Returns:string representation of the parameters (String)

[Source]

     # File lib/bio/appl/paml/common.rb, line 270
270:     def dump_parameters
271:       keyorder = DEFAULT_PARAMETERS_ORDER
272:       keys = parameters.keys
273:       str = ''
274:       keys.sort do |x, y|
275:         (keyorder.index(x) || (keyorder.size + keys.index(x))) <=>
276:           (keyorder.index(y) || (keyorder.size + keys.index(y)))
277:       end.each do |key|
278:         value = parameters[key]
279:         # Note: spaces are required in both side of the "=".
280:         str.concat "#{key.to_s} = #{value.to_s}\n" if value
281:       end
282:       str
283:     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)

[Source]

     # File lib/bio/appl/paml/common.rb, line 248
248:     def load_parameters(str)
249:       hash = {}
250:       str.each_line do |line|
251:         param, value = parse_parameter(line)
252:         hash[param] = value if param
253:       end
254:       self.parameters = hash
255:     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] 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

[Source]

     # File lib/bio/appl/paml/common.rb, line 117
117:     def query(alignment, tree = nil)
118:       astr = alignment.output(:phylipnon)
119:       if tree then
120:         tstr = [ sprintf("%3d %2d\n", tree.leaves.size, 1), "\n",
121:                  tree.output(:newick,
122:                              { :indent => false,
123:                                :bootstrap_style => :disabled,
124:                                :branch_length_style => :disabled })
125:                ].join('')
126:       else
127:         tstr = nil
128:       end
129:       str = _query_by_string(astr, tstr)
130:       @report = self.class::Report.new(str)
131:       @report
132:     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] and parameters[:treefile] 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)

[Source]

     # File lib/bio/appl/paml/common.rb, line 151
151:     def query_by_string(alignment = nil, tree = nil)
152:       _query_by_string(alignment, tree)
153:     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)

[Source]

    # File lib/bio/appl/paml/common.rb, line 95
95:     def run(control_file)
96:       exec_local([ control_file ])
97:     end

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


Returns:parameters (Hash)

[Source]

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

[Validate]