class Bio::PAML::Codeml::PositiveSites

List for the positive selection sites. PAML returns:

Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: PITG_23265T0)

        Pr(w>1)     post mean +- SE for w

17 I      0.988*        3.293
18 H      1.000**       17.975
23 F      0.991**       6.283

(…)

131 V      1.000**       22.797
132 R      1.000**       10.800

(newline)

these can be accessed using normal iterators. Also special methods are available for presenting this data

Attributes

descr[R]

Public Class Methods

new(search, buf, num_codons) click to toggle source

    # File lib/bio/appl/paml/codeml/report.rb
537 def initialize search, buf, num_codons
538   @num_codons = num_codons
539   if buf.index(search)==nil
540     raise ReportError,"No NB sites found for #{search}" 
541   end
542   # Set description of this class
543   @descr = search
544   lines = buf.split("\n")
545   # find location of 'search'
546   start = 0
547   lines.each_with_index do | line, i |
548     if line.index(search) != nil
549       start = i
550       break
551     end
552   end
553   raise ReportError,"Out of bound error for <#{buf}>" if lines[start+6]==nil
554   lines[start+6..-1].each do | line |
555     break if line.strip == ""
556     fields = line.split
557     push PositiveSite.new(fields)
558   end
559   num = size()
560   @buf = lines[start..start+num+7].join("\n")
561 end

Public Instance Methods

graph() click to toggle source

Generate a graph - which is a simple string pointing out the positions showing evidence of positive selection pressure.

>> c.sites.graph[0..32]
=> "                **    *       * *"

    # File lib/bio/appl/paml/codeml/report.rb
569 def graph
570   graph_to_s(lambda { |site| "*" })
571 end

graph_omega() click to toggle source

Generate a graph - which is a simple string pointing out the positions showing evidence of positive selection pressure, with dN/dS values (high values are an asterisk *)

>> c.sites.graph_omega[0..32]
=> "                24    3       3 2"

    # File lib/bio/appl/paml/codeml/report.rb
580 def graph_omega
581   graph_to_s(lambda { |site| 
582       symbol = "*"
583       symbol = site.omega.to_i.to_s if site.omega.abs <= 10.0
584       symbol
585   })
586 end

graph_seq() click to toggle source

Graph of amino acids of first sequence at locations

    # File lib/bio/appl/paml/codeml/report.rb
589 def graph_seq
590   graph_to_s(lambda { |site |
591     symbol = site.aaref
592     symbol
593   })
594 end

to_s() click to toggle source

Return the positive selection information as a String

    # File lib/bio/appl/paml/codeml/report.rb
597 def to_s
598   @buf
599 end