class Bio::PAML::Codeml::Model

Model class contains one of the models of a codeml run (e.g. M0) which is used as a test hypothesis for positive selection. This class is used by Codeml::Report.

Public Class Methods

new(buf) click to toggle source

Create a model using the relevant information from the codeml result data (text buffer)

    # File lib/bio/appl/paml/codeml/report.rb
405 def initialize buf
406   @buf = buf
407 end

Public Instance Methods

alpha() click to toggle source

Return codeml alpha of model, when available

    # File lib/bio/appl/paml/codeml/report.rb
438 def alpha
439   return nil if @buf !~ /alpha/
440   @buf[/alpha .+ =\s+(-?\d+(\.\d+)?)/,1].to_f
441 end

classes() click to toggle source

Return classes when available. For M3 it parses

dN/dS (w) for site classes (K=3) p: 0.56413 0.35613 0.07974 w: 0.00928 1.98252 23.44160

and turns it into an array of Hash

>> m3.classes[0]
=> {:w=>0.00928, :p=>0.56413}

    # File lib/bio/appl/paml/codeml/report.rb
463 def classes
464   return nil if @buf !~ /classes/
465   # probs = @buf.scan(/\np:\s+(\w+)\s+(\S+)\s+(\S+)/)
466   probs = @buf.scan(/\np:.*?\n/).to_s.split[1..3].map { |f| f.to_f }
467   ws = @buf.scan(/\nw:.*?\n/).to_s.split[1..3].map { |f| f.to_f }
468   ret = []
469   probs.each_with_index do | prob, i |
470     ret.push  :p => prob, :w => ws[i] 
471   end
472   ret
473 end

dN_dS()

Alias for: omega

kappa() click to toggle source

Return codeml kappa of model, when available

    # File lib/bio/appl/paml/codeml/report.rb
432 def kappa
433   return nil if @buf !~ /kappa/
434   @buf[/kappa \(ts\/tv\)\s+=\s+ (-?\d+(\.\d+)?)/,1].to_f
435 end

lnL() click to toggle source

Return codeml log likelihood of model

    # File lib/bio/appl/paml/codeml/report.rb
420 def lnL
421   @buf[/lnL\(.+\):\s+(-?\d+(\.\d+)?)/,1].to_f
422 end

modelnum() click to toggle source

Return the model number

    # File lib/bio/appl/paml/codeml/report.rb
410 def modelnum
411   @buf[0..0].to_i
412 end

name() click to toggle source

Return the model name, e.g. ‘M0’ or ‘M7’

    # File lib/bio/appl/paml/codeml/report.rb
415 def name
416   'M'.to_s+modelnum.to_s
417 end

omega() click to toggle source

Return codeml omega of model

    # File lib/bio/appl/paml/codeml/report.rb
425 def omega
426   @buf[/omega \(dN\/dS\)\s+=\s+ (-?\d+(\.\d+)?)/,1].to_f
427 end

Also aliased as: dN_dS

to_s() click to toggle source

Return the model information as a String

    # File lib/bio/appl/paml/codeml/report.rb
476 def to_s
477   @buf
478 end

tree() click to toggle source

Return codeml tree

    # File lib/bio/appl/paml/codeml/report.rb
449 def tree
450   @buf[/([^\n]+)\n\nDetailed/m,1]
451 end

tree_length() click to toggle source

Return codeml treee length

    # File lib/bio/appl/paml/codeml/report.rb
444 def tree_length
445   @buf[/tree length\s+=\s+ (-?\d+(\.\d+)?)/,1].to_f
446 end