# # = test/unit/bio/appl/test_pts1.rb - Unit test for Bio::PTS1 # # Copyright:: Copyright (C) 2006 # Mitsuteru Nakao # License:: The Ruby License # # $Id: test_pts1.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $ # require 'pathname' libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s $:.unshift(libpath) unless $:.include?(libpath) require 'test/unit' require 'bio/appl/pts1' module Bio class TestPTS1Constant < Test::Unit::TestCase def test_FUNCTION keys = ['METAZOA-specific','FUNGI-specific','GENERAL'].sort assert_equal(keys, Bio::PTS1::FUNCTION.keys.sort) end end class TestPTS1New < Test::Unit::TestCase def test_metazoa pts1 = Bio::PTS1.new_with_metazoa_function assert_equal('METAZOA-specific', pts1.function) end def test_fungi pts1 = Bio::PTS1.new_with_fungi_function assert_equal('FUNGI-specific', pts1.function) end def test_general pts1 = Bio::PTS1.new_with_general_function assert_equal('GENERAL', pts1.function) end end class TestPTS1 < Test::Unit::TestCase def setup @seq =<AB000464 MRTGGDNAGPSHSHIKRLPTSGLSTWLQGTQTCVLHLPTGTRPPAHHPLLGYSSRRSYRL LENPAAGCWARFSFCQGAAWDWDLEGVQWLRALAGGVSTAPSAPPGNLVFLSVSIFLCGS LLLETCPAYFSSLDPD* END @serv = Bio::PTS1.new end def test_function_set @serv.function("GENERAL") assert_equal("GENERAL", @serv.function) end def test_function_show assert_equal("METAZOA-specific", @serv.function) end def test_function_set_number_1 @serv.function(1) assert_equal("METAZOA-specific", @serv.function) end def test_function_set_number_2 @serv.function(2) assert_equal("FUNGI-specific", @serv.function) end def test_function_set_number_3 @serv.function(3) assert_equal("GENERAL", @serv.function) end def test_exec report = @serv.exec(@seq) assert_equal(Bio::PTS1::Report, report.class) end def test_exec_with_faa report = @serv.exec(Bio::FastaFormat.new(@seq)) assert_equal(Bio::PTS1::Report, report.class) end end class TestPTS1Report < Test::Unit::TestCase def setup serv = Bio::PTS1.new seq = ">hoge\nAVSFLSMRRARL\n" @report = serv.exec(seq) end def test_output_size assert_equal(1634, @report.output.size) end def test_entry_id assert_equal("hoge", @report.entry_id) end def test_prediction assert_equal("Targeted", @report.prediction) end def test_cterm assert_equal("AVSFLSMRRARL", @report.cterm) end def test_score assert_equal("7.559", @report.score) end def test_fp assert_equal("2.5e-04", @report.fp) end def test_sppta assert_equal("-5.833", @report.sppta) end def test_spptna assert_equal("-1.698", @report.spptna) end def test_profile assert_equal("15.091", @report.profile) end end end