def test_scores(self):
""" Test the scores function. """
obio = OboIO()
terms = obio.get_graph(GOFILE2)
gsgo = GsesameGO(terms)
output = 0.8259052924791086
self.assertEqual(output, gsgo.scores('0043229','0043231'))
def test_scores_article(self):
""" Test the scores function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
gsgo = GsesameGO(terms)
output = 0.7727272727272726
self.assertEqual(output, gsgo.scores('0043229','0043231'))
def test_semantic_value(self):
""" Test the semantic_value function. """
obio = OboIO()
terms = obio.get_graph(GOFILE2)
gsgo = GsesameGO(terms)
output = 4.7440000000000015
self.assertEqual(output, gsgo.semantic_value('0043229'))
output = 5.5952
self.assertEqual(output, gsgo.semantic_value('0043231'))
def test_semantic_value_article(self):
""" Test the semantic_value function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
gsgo = GsesameGO(terms)
output = 3.4000000000000004
self.assertEqual(output, gsgo.semantic_value('0043229'))
output = 4.520000000000001
self.assertEqual(output, gsgo.semantic_value('0043231'))
def test_scores(self):
""" Test the scores function. """
obio = OboIO()
terms = obio.get_graph(GOFILE2)
sesamegene = GsesameGene(terms)
gene1 = ['0043229', '0044424']
gene2 = ['0043231', '0043227']
output = 0.6743128041470686
self.assertEqual(output, sesamegene.scores(gene1, gene2))
def test_scores(self):
""" Test the scores function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
gdc = GoDistanceCounter(terms)
self.assertEqual((5, 5), gdc.scores('11', '0'))
self.assertEqual((4, 4), gdc.scores('11', '1'))
self.assertEqual((6, 0), gdc.scores('9', '5'))
self.assertEqual((5, 1), gdc.scores('7', '5'))
self.assertEqual((6, 0), gdc.scores('8', '5'))
def test_scores(self):
""" Test the scores function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
gdc = GoDistanceCounter(terms)
self.assertEqual((5, 5), gdc.scores('11', '0'))
self.assertEqual((4, 4), gdc.scores('11', '1'))
self.assertEqual((6, 0), gdc.scores('9', '5'))
self.assertEqual((5, 1), gdc.scores('7', '5'))
self.assertEqual((6, 0), gdc.scores('8', '5'))
def test_alt_id(self):
""" Test that a GO term with an alt_id is added to the list. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
gdc = GoDistanceCounter(terms)
term = terms['12']
self.assertEqual('7', term['id'])
term = terms['13']
self.assertEqual('8', term['id'])
gdc = GoDistanceCounter(terms)
self.assertEqual((5, 1), gdc.scores('12', '5'))
self.assertEqual((6, 0), gdc.scores('13', '5'))
def test_alt_id(self):
""" Test that a GO term with an alt_id is added to the list. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
gdc = GoDistanceCounter(terms)
term = terms['12']
self.assertEqual('7', term['id'])
term = terms['13']
self.assertEqual('8', term['id'])
gdc = GoDistanceCounter(terms)
self.assertEqual((5, 1), gdc.scores('12', '5'))
self.assertEqual((6, 0), gdc.scores('13', '5'))
def test_get_path(self):
""" Test the get_path function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
golib = PyGoLib(terms)
term = terms['4']
print term['id']
output = ['4,2,1,0']
self.assertEqual(output,
golib.get_path(term, pred=term['id'], paths=[], verbose=True))
self.assertEqual(output,
golib.get_path(term, pred=term['id'], paths=[]))
output = ['2,1,0']
self.assertEqual(output,
golib.get_path(term, paths=[]))
def test_get_path(self):
""" Test the get_path function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
golib = PyGoLib(terms)
term = terms['4']
print term['id']
output = ['4,2,1,0']
self.assertEqual(
output,
golib.get_path(term, pred=term['id'], paths=[], verbose=True))
self.assertEqual(output, golib.get_path(term,
pred=term['id'],
paths=[]))
output = ['2,1,0']
self.assertEqual(output, golib.get_path(term, paths=[]))
def test_get_go_terms(self):
""" Test the get_go_terms function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
def test_get_go_terms(self):
""" Test the get_go_terms function. """
obio = OboIO()
terms = obio.get_graph(GOFILE)
