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#
# test/unit/bio/db/kegg/test_module.rb - Unit test for Bio::KEGG::MODULE
#
# Copyright:: Copyright (C) 2010 Kozo Nishida <kozo-ni@is.naist.jp>
# Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>
# 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/db/kegg/module'
module Bio
class TestKeggModule < Test::Unit::TestCase
def setup
filename = File.join(BioRubyTestDataPath, 'KEGG/M00118.module')
entry = File.read(filename)
@obj = Bio::KEGG::MODULE.new(entry)
end
def test_new
assert_instance_of(Bio::KEGG::MODULE, @obj)
end
def test_entry_id
assert_equal('M00118', @obj.entry_id)
end
def test_name
assert_equal('Pentose interconversion, arabinose/ribulose/xylulose/xylose', @obj.name)
end
def test_definition
expected = "K00011 K01804 K00853 (K01786,K03080) K03331 K05351 K00854 K00011 K01805 K01783 (K00853,K00875) K00039"
assert_equal(expected, @obj.definition)
end
def test_keggclass
assert_equal('Metabolism; Central metabolism; Other carbohydrate metabolism', @obj.keggclass)
end
def test_pathways_as_strings
expected = ["ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039) Pentose and glucuronate interconversions"]
assert_equal(expected, @obj.pathways_as_strings)
end
def test_pathways_as_hash
expected = { "ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039)" =>
"Pentose and glucuronate interconversions" }
assert_equal(expected, @obj.pathways_as_hash)
end
def test_pathways
expected = { "ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039)" =>
"Pentose and glucuronate interconversions" }
assert_equal(expected, @obj.pathways)
end
def test_orthologs_as_strings
expected =
[ "K00011 aldehyde reductase [EC:1.1.1.21] [RN:R01758 R01759]",
"K01804 L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]",
"K00853 L-ribulokinase [EC:2.7.1.16] [RN:R02439]",
"K01786,K03080 L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4] [RN:R05850]",
"K03331 L-xylulose reductase [EC:1.1.1.10] [RN:R01904]",
"K05351 D-xylulose reductase [EC:1.1.1.9] [RN:R01896]",
"K00854 xylulokinase [EC:2.7.1.17] [RN:R01639]",
"K00011 aldehyde reductase [EC:1.1.1.21] [RN:R01431]",
"K01805 xylose isomerase [EC:5.3.1.5] [RN:R01432]",
"K01783 ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]",
"K00853,K00875 ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]",
"K00039 ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]"
]
assert_equal(expected, @obj.orthologs_as_strings)
end
def test_orthologs_as_hash
expected = {
"K00039" => "ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]",
"K00853" => "L-ribulokinase [EC:2.7.1.16] [RN:R02439]",
"K00854" => "xylulokinase [EC:2.7.1.17] [RN:R01639]",
"K05351" => "D-xylulose reductase [EC:1.1.1.9] [RN:R01896]",
"K00853,K00875" => "ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]",
"K03331" => "L-xylulose reductase [EC:1.1.1.10] [RN:R01904]",
"K00011" => "aldehyde reductase [EC:1.1.1.21] [RN:R01431]",
"K01786,K03080" =>
"L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4] [RN:R05850]",
"K01804" => "L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]",
"K01783" => "ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]",
"K01805" => "xylose isomerase [EC:5.3.1.5] [RN:R01432]"
}
assert_equal(expected, @obj.orthologs_as_hash)
end
def test_orthologs
expected = {
"K00039" => "ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]",
"K00853" => "L-ribulokinase [EC:2.7.1.16] [RN:R02439]",
"K00854" => "xylulokinase [EC:2.7.1.17] [RN:R01639]",
"K05351" => "D-xylulose reductase [EC:1.1.1.9] [RN:R01896]",
"K00853,K00875" => "ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]",
"K03331" => "L-xylulose reductase [EC:1.1.1.10] [RN:R01904]",
"K00011" => "aldehyde reductase [EC:1.1.1.21] [RN:R01431]",
"K01786,K03080" =>
"L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4] [RN:R05850]",
"K01804" => "L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]",
"K01783" => "ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]",
"K01805" => "xylose isomerase [EC:5.3.1.5] [RN:R01432]"
}
assert_equal(expected, @obj.orthologs)
end
def test_orthologs_as_array
expected =
[ "K00011",
"K00039",
"K00853",
"K00854",
"K00875",
"K01783",
"K01786",
"K01804",
"K01805",
"K03080",
"K03331",
"K05351"
]
assert_equal(expected, @obj.orthologs_as_array)
end
def test_reactions_as_strings
expected = [ "R01903 C00312 -> C00532",
"R01758,R01759 C00532 -> C00259",
"R01761 C00259 -> C00508",
"R02439 C00508 -> C01101",
"R05850 C01101 -> C00231",
"R01904 C00312 -> C00379",
"R01896 C00379 -> C00310",
"R01639 C00310 -> C00231",
"R01431 C00379 -> C00181",
"R01432 C00181 -> C00310",
"R01529 C00199 -> C00231",
"R01526 C00231 -> C00309",
"R01895 C00309 -> C00474"
]
assert_equal(expected, @obj.reactions_as_strings)
end
def test_reactions_as_hash
expected = {
"R01529" => "C00199 -> C00231",
"R01431" => "C00379 -> C00181",
"R01639" => "C00310 -> C00231",
"R01761" => "C00259 -> C00508",
"R01903" => "C00312 -> C00532",
"R01904" => "C00312 -> C00379",
"R01432" => "C00181 -> C00310",
"R01758,R01759" => "C00532 -> C00259",
"R01895" => "C00309 -> C00474",
"R01896" => "C00379 -> C00310",
"R02439" => "C00508 -> C01101",
"R05850" => "C01101 -> C00231",
"R01526" => "C00231 -> C00309"
}
assert_equal(expected, @obj.reactions_as_hash)
end
def test_reactions
expected = {
"R01529" => "C00199 -> C00231",
"R01431" => "C00379 -> C00181",
"R01639" => "C00310 -> C00231",
"R01761" => "C00259 -> C00508",
"R01903" => "C00312 -> C00532",
"R01904" => "C00312 -> C00379",
"R01432" => "C00181 -> C00310",
"R01758,R01759" => "C00532 -> C00259",
"R01895" => "C00309 -> C00474",
"R01896" => "C00379 -> C00310",
"R02439" => "C00508 -> C01101",
"R05850" => "C01101 -> C00231",
"R01526" => "C00231 -> C00309"
}
assert_equal(expected, @obj.reactions)
end
def test_compounds_as_strings
expected = [ "C00312 L-Xylulose",
"C00532 L-Arabitol",
"C00259 L-Arabinose",
"C00508 L-Ribulose",
"C01101 L-Ribulose 5-phosphate",
"C00231 D-Xylulose 5-phosphate",
"C00379 Xylitol",
"C00310 D-Xylulose",
"C00181 D-Xylose",
"C00199 D-Ribulose 5-phosphate",
"C00309 D-Ribulose",
"C00474 Ribitol"
]
assert_equal(expected, @obj.compounds_as_strings)
end
def test_compounds_as_hash
expected = {
"C00231" => "D-Xylulose 5-phosphate",
"C00474" => "Ribitol",
"C00309" => "D-Ribulose",
"C00199" => "D-Ribulose 5-phosphate",
"C01101" => "L-Ribulose 5-phosphate",
"C00310" => "D-Xylulose",
"C00508" => "L-Ribulose",
"C00532" => "L-Arabitol",
"C00312" => "L-Xylulose",
"C00181" => "D-Xylose",
"C00379" => "Xylitol",
"C00259" => "L-Arabinose"
}
assert_equal(expected, @obj.compounds_as_hash)
end
def test_compounds
expected = {
"C00231" => "D-Xylulose 5-phosphate",
"C00474" => "Ribitol",
"C00309" => "D-Ribulose",
"C00199" => "D-Ribulose 5-phosphate",
"C01101" => "L-Ribulose 5-phosphate",
"C00310" => "D-Xylulose",
"C00508" => "L-Ribulose",
"C00532" => "L-Arabitol",
"C00312" => "L-Xylulose",
"C00181" => "D-Xylose",
"C00379" => "Xylitol",
"C00259" => "L-Arabinose"
}
assert_equal(expected, @obj.compounds)
end
end
end
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