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Contents
#
# = bio/appl/paml/codeml/report.rb - Codeml report parser
#
# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
#
# License:: The Ruby License
#
# == Description
#
# This file contains a class that implement a simple interface to Codeml output file
#
# == References
#
# * http://abacus.gene.ucl.ac.uk/software/paml.html
#
require 'bio/appl/paml/codeml'
module Bio::PAML
class Codeml
# == Description
#
# A simple class for parsing codeml output.
#
# WARNING: This data is parsed using a regex from the output file, and
# so will take the first result found. If using multiple tree's, your
# milage may vary. See the source for the regular expressions.
#
# require 'bio'
#
# report = Bio::PAML::Codeml::Report.new(File.open(codeml_output_file).read)
# report.gene_rate # => Rate of gene evolution as defined be alpha
# report.tree_lengh # => Estimated phylogetic tree length
class Report < Bio::PAML::Common::Report
attr_reader :tree_log_likelihood, :tree_length, :alpha, :tree
def initialize(codeml_report)
@tree_log_likelihood = pull_tree_log_likelihood(codeml_report)
@tree_length = pull_tree_length(codeml_report)
@alpha = pull_alpha(codeml_report)
@tree = pull_tree(codeml_report)
end
private
def pull_tree_log_likelihood(text)
text[/lnL\(.+\):\s+(-?\d+(\.\d+)?)/,1].to_f
end
def pull_tree_length(text)
text[/tree length\s+=\s+ (-?\d+(\.\d+)?)/,1].to_f
end
def pull_alpha(text)
text[/alpha .+ =\s+(-?\d+(\.\d+)?)/,1].to_f
end
def pull_tree(text)
text[/([^\n]+)\n\nDetailed/m,1]
end
end # End Report
end # End Codeml
end # End Bio::PAML
Version data entries
15 entries across 15 versions & 4 rubygems