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Contents
#
# = bio/appl/paml/codeml/rates.rb - Codeml rates report file 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 rates estimation file
#
# == References
#
# * http://abacus.gene.ucl.ac.uk/software/paml.html
#
require 'delegate'
require 'bio/appl/paml/codeml'
module Bio::PAML
class Codeml
# == Description
#
# A simple class for parsing the codeml rates file.
#
# WARNING: The order of the parsed data should be correct, however will
# not necessarily correspond to the position in the alignment. For instance
# codeml ignores columns that contains gaps, and therefore there will not
# be any estimated rate data.
#
# == Usage
#
# site_rates = Bio::PAML::Codeml::Rates.new(File.open(@tmp_dir + "/rates").read)
# site_rate.first[:freq] # => Number of times that column appears
# site_rate.[5][:rate] # => Estimated rate of evolution
# site_rate.last[:data] # => The content of the column, as a string
#
# # This class delegates to an array, so will respond to all array methods
# site_rates.max {|x,y| x[:rate] <=> y[:rate] } # => Fastest evolving column
# site_rates.detect {|x| x[:freq] > 1 } # => Columns appearing more than once
class Rates < DelegateClass(Array)
def initialize(rates)
super(parse_rates(rates))
end
private
def parse_rates(text)
re = /\s+(\d+)\s+(\d+)\s+([A-Z\*]+)\s+(\d+\.\d+)\s+(\d)/
array = Array.new
text.each_line do |line|
if re =~ line
match = Regexp.last_match
array[match[1].to_i] = {
:freq => match[2].to_i,
:data => match[3],
:rate => match[4].to_f }
end
end
array.compact
end
end
end
end
Version data entries
29 entries across 29 versions & 4 rubygems