Sha256: 0bfb12ff0ea0ab154678f114ce90346bb0fbd88c2b83fa4f03017460b450ca78
Contents?: true
Size: 1.33 KB
Versions: 14
Compression:
Stored size: 1.33 KB
Contents
#
# test/unit/bio/appl/paml/codeml/test_report.rb - Unit test for Bio::PAML::Codeml::Report
#
# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
# License:: The Ruby License
#
require 'pathname'
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/appl/paml/codeml/report'
module Bio; module TestPAMLCodeml
class TestCodemlReport < Test::Unit::TestCase
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
def setup
str = File.read(File.join(TEST_DATA, 'output.txt'))
@example_report = Bio::PAML::Codeml::Report.new(str)
end
def test_tree_log_likelihood
assert_equal(-1817.465211, @example_report.tree_log_likelihood)
end
def test_tree_length
assert_equal(0.77902, @example_report.tree_length)
end
def test_alpha
assert_equal(0.58871, @example_report.alpha)
end
def test_tree
tree = "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
assert_equal(tree, @example_report.tree)
end
end
end; end #module TestPAMLCodeml; module Bio
Version data entries
14 entries across 14 versions & 4 rubygems