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#
# test/unit/bio/appl/paml/test_codeml.rb - Unit test for Bio::PAML::Codeml
#
# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
# License:: The Ruby License
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/appl/paml/codeml'
module Bio; module TestPAMLCodeml
module TestCodemlData
TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'paml', 'codeml')).cleanpath.to_s
def self.example_control
File.join TEST_DATA, 'control_file.txt'
end
end #module TestCodemlData
class TestCodemlInitialize < Test::Unit::TestCase
def test_new_with_one_argument
factory = Bio::PAML::Codeml.new('echo')
assert_instance_of(Bio::PAML::Codeml, factory)
assert_equal('echo', factory.instance_eval { @program })
end
def test_new_with_two_argument
factory = Bio::PAML::Codeml.new('echo', { :test => 'value' })
assert_instance_of(Bio::PAML::Codeml, factory)
assert_equal('echo', factory.instance_eval { @program })
assert_equal('value', factory.parameters[:test])
end
def test_new_with_parameters
factory = Bio::PAML::Codeml.new(nil, { :test => 'value' })
assert_instance_of(Bio::PAML::Codeml, factory)
assert_equal('codeml', factory.instance_eval { @program })
assert_equal('value', factory.parameters[:test])
end
def test_new_without_argument
factory = Bio::PAML::Codeml.new
assert_instance_of(Bio::PAML::Codeml, factory)
assert_equal('codeml', factory.instance_eval { @program })
end
end #class TestCodemlInitialize
class TestCodeml < Test::Unit::TestCase
def setup
@codeml = Bio::PAML::Codeml.new
end
def test_parameters
params = { :verbose => 1 }
@codeml.parameters = params
assert_equal(params, @codeml.parameters)
end
def test_load_parameters
str = " seqfile = test.aa \n verbose = 1 \n"
params = { :seqfile => 'test.aa', :verbose => '1' }
assert_equal(params, @codeml.load_parameters(str))
end
def test_set_default_parameters
assert_equal(Bio::PAML::Codeml::DEFAULT_PARAMETERS,
@codeml.set_default_parameters)
# modifying parameters should not affect DEFAULT_PARAMETERS
@codeml.parameters[:only_for_test] = 'this is test'
assert_not_equal(Bio::PAML::Codeml::DEFAULT_PARAMETERS,
@codeml.parameters)
end
def test_dump_parameters
params = { :seqfile => 'test.aa', :verbose => '1' }
@codeml.parameters = params
assert_equal("seqfile = test.aa\nverbose = 1\n",
@codeml.dump_parameters)
end
end #class TestCodeml
class TestCodemlControlGeneration < Test::Unit::TestCase
TEST_DATA = TestCodemlData::TEST_DATA
def generate_control_file
@tempfile_control = Tempfile.new('codeml_control')
@tempfile_control.close(false)
@tempfile_outfile = Tempfile.new('codeml_test')
@tempfile_outfile.close(false)
test_control = @tempfile_control.path
Bio::PAML::Codeml.create_control_file({
:model => 1,
:fix_kappa => 1,
:aaRatefile => File.join(TEST_DATA, 'wag.dat'),
:seqfile => File.join(TEST_DATA, 'abglobin.aa'),
:treefile => File.join(TEST_DATA, 'abglobin.trees'),
:outfile => @tempfile_outfile.path,
}, test_control)
test_control
end
private :generate_control_file
def setup
@example_control = generate_control_file
end
def teardown
@tempfile_control.close(true)
@tempfile_outfile.close(true)
end
def test_control_file_generated
assert_not_nil(File.size?(@example_control))
end
def test_expected_parameters_set_in_control_file
produced_control = File.open(@example_control) do |f|
f.inject(Hash.new) do |hash,line|
hash.store(*line.strip.split(' = '))
hash
end
end
assert_equal(File.join(TEST_DATA, 'abglobin.aa'),
produced_control['seqfile'])
assert_equal('1', produced_control['fix_kappa'])
assert_equal('1', produced_control['model'])
end
end #class TestCodemlControlGeneration
class TestControlFileUsage < Test::Unit::TestCase
def setup
@codeml = Bio::PAML::Codeml.new
@codeml.load_parameters(File.read(TestCodemlData.example_control))
end
def test_parameters_should_be_loaded_from_control
assert_not_nil(@codeml.parameters)
end
def test_correct_parameters_should_be_loaded
assert_equal('abglobin.aa', @codeml.parameters[:seqfile])
assert_equal('1', @codeml.parameters[:fix_kappa])
assert_equal('1', @codeml.parameters[:model])
end
end #class TestControlFileUsage
class TestExpectedErrorsThrown < Test::Unit::TestCase
def test_error_thrown_if_seqfile_does_not_specified
codeml = Bio::PAML::Codeml.new('echo')
codeml.load_parameters(File.read(TestCodemlData.example_control))
codeml.parameters[:seqfile] = nil
assert_raises RuntimeError do
codeml.query_by_string()
end
end
end #class TestExpectedErrorsThrown
end; end #module TestPAMLCodeml; module Bio
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