Class Bio::PAML::Yn00
In: lib/bio/appl/paml/yn00.rb
lib/bio/appl/paml/yn00/report.rb
Parent: Common

Description

Bio::PAML::Yn00 is a wrapper for running PAML yn00 program.

Because most of the methods in this class are inherited from Bio::PAML::Common, see documents of Bio::PAML::Common for details.

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').alignment
  # Creates a Yn00 object
  baseml = Bio::PAML::Yn00.new
  # Sets parameters
  baseml.parameters[:verbose] = 1
  baseml.parameters[:icode] = 0
  # You can also set many parameters at a time.
  baseml.parameters.update({ :weighting => 0, :commonf3x4 => 0 })
  # Executes yn00 with the alignment
  report = yn00.query(alignment)

Methods

Classes and Modules

Class Bio::PAML::Yn00::Report

Constants

DEFAULT_PROGRAM = 'yn00'.freeze   Default program name
DEFAULT_PARAMETERS = { # Essential argumemts :seqfile => nil, :outfile => nil, # Optional arguments :verbose => 1, :icode => 0, :weighting => 0, :commonf3x4 => 0   Default parameters when running baseml.

The parameters whose values are different from the baseml defalut value (described in pamlDOC.pdf) in PAML 4.1 are:

 seqfile, outfile, treefile, ndata, noisy, verbose

Public Instance methods

Runs the program on the internal parameters with the specified sequence alignment. Note that parameters[:seqfile] and parameters[:outfile] are always modified.

For other important information, see the document of Bio::PAML::Common#query.


Arguments:

Returns:Report object

[Source]

    # File lib/bio/appl/paml/yn00.rb, line 83
83:     def query(alignment)
84:       super(alignment)
85:     end

Runs the program on the internal parameters with the specified sequence alignment as a String object.

For other important information, see the document of query and Bio::PAML::Common#query_by_string methods.


Arguments:

Returns:Report object

[Source]

    # File lib/bio/appl/paml/yn00.rb, line 97
97:     def query_by_string(alignment = nil)
98:       super(alignment)
99:     end

[Validate]