def test_configure2(self):
ref_domains = ('D1', 'D2', 'DX')
ref_relations = ('A', 'B', 'C')
go = GOManager()
# configure with custom values
go.configure(domains=ref_domains, recognized_relations=ref_relations)
self.assertTrue(go.configured)
self.assertEquals(ref_domains, go.domains)
self.assertEquals(ref_relations, go.recognizedRelations)
self.assertItemsEqual(ref_relations, go.termsRelationsHierarchy.keys())
def test_configure1(self):
go = GOManager()
# configure with default values
go.configure()
self.assertTrue(go.configured)
self.assertEquals(tuple(GO_DS), go.domains)
self.assertEqual(GO_DEF_RECOGNIZED_RELATIONS, go.recognizedRelations)
self.assertIsInstance(go.domain2concepts, SetBDMap)
self.assertIsInstance(go.synonyms, SetBDMap)
self.assertIsInstance(go.terms, dict)
self.assertFalse(hasattr(go, 'domain2validTerms'))
self.assertItemsEqual(GO_DEF_RECOGNIZED_RELATIONS,
go.termsRelationsHierarchy.keys())
def setUp(self):
self.sample_data_root = TEST_INVARIANTS['test_data_root']
self.sample_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample.obo-xml'))
with open(self.sample_obo_xml, 'rb') as f:
self.go = GOManager()
self.go.configure()
self.go.load(f)
self.sample_xml_fh1 = open(self.sample_obo_xml, 'rb')
self.sample_recognized_relations = [
'is_a', 'part_of', 'regulates', 'positively_regulates',
'negatively_regulates'
]
self.recognized_relations_1 = ['is_a']
self.notpresent_fwd_1 = ['GO:0000019', 'GO:0000022']
self.notpresent_bwd_1 = ['GO:0006310', 'GO:0006312', 'GO:0007052']
self.recognized_relations_2 = [
'positively_regulates', 'negatively_regulates'
]
self.present_fwd_2 = list()
self.present_bwd_2 = list()
self.recognized_relations_x = ['AAA', 'BBB']
self.present_fwd_x = list()
self.present_bwd_x = list()
def test_hierarchy3(self):
go1 = GOManager()
go1.configure(recognized_relations=self.recognized_relations_x)
go1.load(self.sample_xml_fh1)
# recognize 'AAA', 'BBB'
self.assertItemsEqual(self.recognized_relations_x,
go1.termsRelationsHierarchy.keys())
# compare plain hierarchy maps
mfwd2 = set(self.go.termsPlainHierarchy.dumpFwdMap().keys())
mbwd2 = set(self.go.termsPlainHierarchy.dumpBwdMap().keys())
cfwd2 = set(go1.termsPlainHierarchy.dumpFwdMap().keys())
cbwd2 = set(go1.termsPlainHierarchy.dumpBwdMap().keys())
self.assertNotEqual(mfwd2, cfwd2)
self.assertEqual(set(self.present_fwd_x), cfwd2)
self.assertNotEqual(mbwd2, cbwd2)
self.assertEqual(set(self.present_bwd_x), cbwd2)
def test_hierarchy2(self):
go1 = GOManager()
go1.configure(recognized_relations=self.recognized_relations_2)
go1.load(self.sample_xml_fh1)
# recognize only 'positively_regulates', 'negatively_regulates'
self.assertItemsEqual(self.recognized_relations_2,
go1.termsRelationsHierarchy.keys())
# compare plain hierarchy maps
mfwd2 = set(self.go.termsPlainHierarchy.dumpFwdMap().keys())
mbwd2 = set(self.go.termsPlainHierarchy.dumpBwdMap().keys())
cfwd2 = set(go1.termsPlainHierarchy.dumpFwdMap().keys())
cbwd2 = set(go1.termsPlainHierarchy.dumpBwdMap().keys())
self.assertNotEqual(mfwd2, cfwd2)
self.assertEqual(set(self.present_fwd_2), cfwd2)
self.assertNotEqual(mbwd2, cbwd2)
self.assertEqual(set(self.present_bwd_2), cbwd2)
def test_hierarchy1(self):
go1 = GOManager()
go1.configure(recognized_relations=self.recognized_relations_1)
go1.load(self.sample_xml_fh1)
# recognize only 'is_a'
self.assertItemsEqual(self.recognized_relations_1,
go1.termsRelationsHierarchy.keys())
# compare detailed hierarchy maps for 'is_a'
mfwd1 = self.go.termsRelationsHierarchy['is_a'].dumpFwdMap()
mbwd1 = self.go.termsRelationsHierarchy['is_a'].dumpBwdMap()
cfwd1 = go1.termsRelationsHierarchy['is_a'].dumpFwdMap()
cbwd1 = go1.termsRelationsHierarchy['is_a'].dumpBwdMap()
self.assertEqual(mfwd1, cfwd1)
self.assertEqual(mbwd1, cbwd1)
# compare plain hierarchy maps
mfwd2 = set(self.go.termsPlainHierarchy.dumpFwdMap().keys())
mbwd2 = set(self.go.termsPlainHierarchy.dumpBwdMap().keys())
cfwd2 = set(go1.termsPlainHierarchy.dumpFwdMap().keys())
cbwd2 = set(go1.termsPlainHierarchy.dumpBwdMap().keys())
self.assertNotEqual(mfwd2, cfwd2)
self.assertEqual(set(self.notpresent_fwd_1), mfwd2 - cfwd2)
self.assertNotEqual(mbwd2, cbwd2)
self.assertEqual(set(self.notpresent_bwd_1), mbwd2 - cbwd2)
def setUp(self):
self.sample_data_root = TEST_INVARIANTS['test_data_root']
self.sample_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample.obo-xml'))
self.sample_err_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample-err.obo-xml'))
self.sample_xml_fh = open(self.sample_obo_xml, 'rb')
self.sample_err_xml_fh = open(self.sample_err_obo_xml, 'rb')
self.sample_format = '1.2'
self.sample_release_date = datetime.datetime(2012, 02, 21, 15, 03)
self.sample_root_tag = 'obo'
self.sample_recognized_relations = [
'is_a', 'part_of', 'regulates', 'positively_regulates',
'negatively_regulates'
]
self.sample_terms = set([
'GO:0000001', 'GO:0000002', 'GO:0000003', 'GO:0000005',
'GO:0000006', 'GO:0000007', 'GO:0000008', 'GO:0000009',
'GO:0000010', 'GO:0000011', 'GO:0000012', 'GO:0000014',
'GO:0000015', 'GO:0000016', 'GO:0000017', 'GO:0000018',
'GO:0000019', 'GO:0000020', 'GO:0000022'
])
self.sample_obsolete_terms = set(
['GO:0000005', 'GO:0000008', 'GO:0000020'])
self.sample_valid_terms = self.sample_terms - self.sample_obsolete_terms
self.sample_t19 = {
'obsolete':
False,
'name':
'regulation of mitotic recombination',
'desc':
'Any process that modulates the frequency, rate or '
'extent of DNA recombination during mitosis.'
}
self.sample_t16 = {
'obsolete':
False,
'name':
'lactase activity',
'desc':
'Catalysis of the reaction: lactose + H2O = '
'D-glucose + D-galactose.'
}
self.pkc_t16 = {
'additionalInfo': {
'obsolete': False
},
'conceptID': 'GO:0000016',
'domainID': ('molecular_function', ),
'description': 'Catalysis of the reaction: lactose + H2O = '
'D-glucose + D-galactose.',
'conceptName': 'lactase activity'
}
self.pkc_t19 = {
'additionalInfo': {
'obsolete': False
},
'conceptID': 'GO:0000019',
'domainID': ('biological_process', ),
'description': 'Any process that modulates the frequency, '
'rate or extent of DNA recombination during mitosis.',
'conceptName': 'regulation of mitotic recombination'
}
self.samples = {
'GO:0000016': self.sample_t16,
'GO:0000019': self.sample_t19
}
self.root_tag_x = 'AAA'
self.d2c_fwd = {
'molecular_function':
set([
'GO:0000006', 'GO:0000007', 'GO:0000005', 'GO:0000010',
'GO:0000014', 'GO:0000008', 'GO:0000009', 'GO:0000016'
]),
'cellular_component':
set(['GO:0000015']),
'biological_process':
set([
'GO:0000017', 'GO:0000011', 'GO:0000003', 'GO:0000012',
'GO:0000001', 'GO:0000019', 'GO:0000018', 'GO:0000020',
'GO:0000002', 'GO:0000022'
])
}
self.d2c_bwd = {
'GO:0000015': set(['cellular_component']),
'GO:0000014': set(['molecular_function']),
'GO:0000016': set(['molecular_function']),
'GO:0000020': set(['biological_process']),
'GO:0000011': set(['biological_process']),
'GO:0000022': set(['biological_process']),
'GO:0000010': set(['molecular_function']),
'GO:0000006': set(['molecular_function']),
'GO:0000007': set(['molecular_function']),
'GO:0000017': set(['biological_process']),
'GO:0000005': set(['molecular_function']),
'GO:0000002': set(['biological_process']),
'GO:0000003': set(['biological_process']),
'GO:0000001': set(['biological_process']),
'GO:0000012': set(['biological_process']),
'GO:0000019': set(['biological_process']),
'GO:0000018': set(['biological_process']),
'GO:0000008': set(['molecular_function']),
'GO:0000009': set(['molecular_function'])
}
self.go = GOManager()
self.go.configure()
class TestGOManager2(unittest.TestCase):
def setUp(self):
self.sample_data_root = TEST_INVARIANTS['test_data_root']
self.sample_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample.obo-xml'))
self.sample_err_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample-err.obo-xml'))
self.sample_xml_fh = open(self.sample_obo_xml, 'rb')
self.sample_err_xml_fh = open(self.sample_err_obo_xml, 'rb')
self.sample_format = '1.2'
self.sample_release_date = datetime.datetime(2012, 02, 21, 15, 03)
self.sample_root_tag = 'obo'
self.sample_recognized_relations = [
'is_a', 'part_of', 'regulates', 'positively_regulates',
'negatively_regulates'
]
self.sample_terms = set([
'GO:0000001', 'GO:0000002', 'GO:0000003', 'GO:0000005',
'GO:0000006', 'GO:0000007', 'GO:0000008', 'GO:0000009',
'GO:0000010', 'GO:0000011', 'GO:0000012', 'GO:0000014',
'GO:0000015', 'GO:0000016', 'GO:0000017', 'GO:0000018',
'GO:0000019', 'GO:0000020', 'GO:0000022'
])
self.sample_obsolete_terms = set(
['GO:0000005', 'GO:0000008', 'GO:0000020'])
self.sample_valid_terms = self.sample_terms - self.sample_obsolete_terms
self.sample_t19 = {
'obsolete':
False,
'name':
'regulation of mitotic recombination',
'desc':
'Any process that modulates the frequency, rate or '
'extent of DNA recombination during mitosis.'
}
self.sample_t16 = {
'obsolete':
False,
'name':
'lactase activity',
'desc':
'Catalysis of the reaction: lactose + H2O = '
'D-glucose + D-galactose.'
}
self.pkc_t16 = {
'additionalInfo': {
'obsolete': False
},
'conceptID': 'GO:0000016',
'domainID': ('molecular_function', ),
'description': 'Catalysis of the reaction: lactose + H2O = '
'D-glucose + D-galactose.',
'conceptName': 'lactase activity'
}
self.pkc_t19 = {
'additionalInfo': {
'obsolete': False
},
'conceptID': 'GO:0000019',
'domainID': ('biological_process', ),
'description': 'Any process that modulates the frequency, '
'rate or extent of DNA recombination during mitosis.',
'conceptName': 'regulation of mitotic recombination'
}
self.samples = {
'GO:0000016': self.sample_t16,
'GO:0000019': self.sample_t19
}
self.root_tag_x = 'AAA'
self.d2c_fwd = {
'molecular_function':
set([
'GO:0000006', 'GO:0000007', 'GO:0000005', 'GO:0000010',
'GO:0000014', 'GO:0000008', 'GO:0000009', 'GO:0000016'
]),
'cellular_component':
set(['GO:0000015']),
'biological_process':
set([
'GO:0000017', 'GO:0000011', 'GO:0000003', 'GO:0000012',
'GO:0000001', 'GO:0000019', 'GO:0000018', 'GO:0000020',
'GO:0000002', 'GO:0000022'
])
}
self.d2c_bwd = {
'GO:0000015': set(['cellular_component']),
'GO:0000014': set(['molecular_function']),
'GO:0000016': set(['molecular_function']),
'GO:0000020': set(['biological_process']),
'GO:0000011': set(['biological_process']),
'GO:0000022': set(['biological_process']),
'GO:0000010': set(['molecular_function']),
'GO:0000006': set(['molecular_function']),
'GO:0000007': set(['molecular_function']),
'GO:0000017': set(['biological_process']),
'GO:0000005': set(['molecular_function']),
'GO:0000002': set(['biological_process']),
'GO:0000003': set(['biological_process']),
'GO:0000001': set(['biological_process']),
'GO:0000012': set(['biological_process']),
'GO:0000019': set(['biological_process']),
'GO:0000018': set(['biological_process']),
'GO:0000008': set(['molecular_function']),
'GO:0000009': set(['molecular_function'])
}
self.go = GOManager()
self.go.configure()
def tearDown(self):
self.sample_xml_fh.close()
self.sample_err_xml_fh.close()
def test_load1(self):
with self.assertRaises(Error):
self.go.load(self.sample_xml_fh, self.root_tag_x)
def test_load2(self):
with self.assertRaises(Error):
self.go.load(self.sample_err_xml_fh)
def test_load3(self):
self.go.load(self.sample_xml_fh)
self.assertEqual(self.sample_format, self.go._format)
self.assertEqual(self.sample_release_date, self.go._release_date)
self.assertEqual(self.sample_root_tag, self.go.root_tag)
self.assertEqual(self.sample_recognized_relations,
self.go.recognizedRelations)
self.assertNotEqual(dict(), self.go.terms)
self.assertEqual(self.sample_terms, set(self.go.terms.keys()))
self.assertEqual(self.sample_obsolete_terms,
set(self.go.obsolete_terms))
self.assertEqual(self.sample_valid_terms, set(self.go.valid_terms))
for t, td in self.samples.iteritems():
self.assertEqual(td, self.go.terms[t])
self.assertItemsEqual(self.sample_recognized_relations,
self.go.termsRelationsHierarchy.keys())
d2c_fwd = self.go.domain2concepts.dumpFwdMap()
d2c_bwd = self.go.domain2concepts.dumpBwdMap()
self.assertEqual(self.d2c_fwd, d2c_fwd)
self.assertEqual(self.d2c_bwd, d2c_bwd)
def test_getPKC1(self):
self.go.load(self.sample_xml_fh)
pkc_t16 = self.go.getPKC('GO:0000016')
self.assertEqual(self.pkc_t16, pkc_t16._pkc)
for det_key in PKC_DETAIL_ELEMENTS:
self.assertEqual(self.pkc_t16[det_key], pkc_t16[det_key])
pkc_t19 = self.go.getPKC('GO:0000019')
self.assertEqual(self.pkc_t19, pkc_t19._pkc)
for det_key in PKC_DETAIL_ELEMENTS:
self.assertEqual(self.pkc_t19[det_key], pkc_t19[det_key])
def test_getPKC2(self):
self.go.load(self.sample_xml_fh)
pkc = self.go.getPKC('GO:XXXXXXX')
self.assertIsNone(pkc)
def setUp(self):
self.sample_data_root = TEST_INVARIANTS['test_data_root']
self.sample_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample.obo-xml'))
with open(self.sample_obo_xml, 'rb') as f:
self.go = GOManager()
self.go.configure()
self.go.load(f)
self.sample_xml_fh1 = open(self.sample_obo_xml, 'rb')
self.sample_recognized_relations = [
'is_a', 'part_of', 'regulates', 'positively_regulates',
'negatively_regulates'
]
self.sample_descendants_nodepth = {
'GO:0000019': set(['GO:0006312']),
'GO:0000018': set(['GO:0006310', 'GO:0006312', 'GO:0000019']),
'GO:0000022': set(['GO:0007052'])
}
self.sample_descendants_depth = {
'GO:0000019':
set([('GO:0006312', 1)]),
'GO:0000018':
set([('GO:0006310', 1), ('GO:0000019', 1), ('GO:0006312', 2)]),
'GO:0000022':
set(set([('GO:0007052', 1)]))
}
self.sample_ancestors_nodepth = {
'GO:0000006': set(['GO:0005385']),
'GO:0000007': set(['GO:0005385']),
'GO:0000017': set(['GO:0042946']),
'GO:0000002': set(['GO:0007005']),
'GO:0000003': set(['GO:0008150']),
'GO:0000001': set(['GO:0048308', 'GO:0048311']),
'GO:0000015': set(['GO:0043234', 'GO:0044445']),
'GO:0000012': set(['GO:0006281']),
'GO:0000019': set(['GO:0000018', 'GO:0051052']),
'GO:0000018': set(['GO:0051052']),
'GO:0000009': set(['GO:0000030']),
'GO:0000016': set(['GO:0004553']),
'GO:0000014': set(['GO:0004520']),
'GO:0000011': set(['GO:0048308', 'GO:0007033']),
'GO:0000022': set(['GO:0051231']),
'GO:0000010': set(['GO:0016765'])
}
self.sample_ancestors_depth = {
'GO:0000006': set([('GO:0005385', -1)]),
'GO:0000007': set([('GO:0005385', -1)]),
'GO:0000017': set([('GO:0042946', -1)]),
'GO:0000002': set([('GO:0007005', -1)]),
'GO:0000003': set([('GO:0008150', -1)]),
'GO:0000001': set([('GO:0048308', -1), ('GO:0048311', -1)]),
'GO:0000015': set([('GO:0043234', -1), ('GO:0044445', -1)]),
'GO:0000012': set([('GO:0006281', -1)]),
'GO:0000019': set([('GO:0000018', -1), ('GO:0051052', -2)]),
'GO:0000018': set([('GO:0051052', -1)]),
'GO:0000009': set([('GO:0000030', -1)]),
'GO:0000016': set([('GO:0004553', -1)]),
'GO:0000014': set([('GO:0004520', -1)]),
'GO:0000011': set([('GO:0048308', -1), ('GO:0007033', -1)]),
'GO:0000022': set([('GO:0051231', -1)]),
'GO:0000010': set([('GO:0016765', -1)])
}
self.sample_synonyms = {
'GO:0000003': set(['GO:0050876', 'GO:0019952'])
}
class TestGOManager4(unittest.TestCase):
def setUp(self):
self.sample_data_root = TEST_INVARIANTS['test_data_root']
self.sample_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample.obo-xml'))
with open(self.sample_obo_xml, 'rb') as f:
self.go = GOManager()
self.go.configure()
self.go.load(f)
self.sample_xml_fh1 = open(self.sample_obo_xml, 'rb')
self.sample_recognized_relations = [
'is_a', 'part_of', 'regulates', 'positively_regulates',
'negatively_regulates'
]
self.sample_descendants_nodepth = {
'GO:0000019': set(['GO:0006312']),
'GO:0000018': set(['GO:0006310', 'GO:0006312', 'GO:0000019']),
'GO:0000022': set(['GO:0007052'])
}
self.sample_descendants_depth = {
'GO:0000019':
set([('GO:0006312', 1)]),
'GO:0000018':
set([('GO:0006310', 1), ('GO:0000019', 1), ('GO:0006312', 2)]),
'GO:0000022':
set(set([('GO:0007052', 1)]))
}
self.sample_ancestors_nodepth = {
'GO:0000006': set(['GO:0005385']),
'GO:0000007': set(['GO:0005385']),
'GO:0000017': set(['GO:0042946']),
'GO:0000002': set(['GO:0007005']),
'GO:0000003': set(['GO:0008150']),
'GO:0000001': set(['GO:0048308', 'GO:0048311']),
'GO:0000015': set(['GO:0043234', 'GO:0044445']),
'GO:0000012': set(['GO:0006281']),
'GO:0000019': set(['GO:0000018', 'GO:0051052']),
'GO:0000018': set(['GO:0051052']),
'GO:0000009': set(['GO:0000030']),
'GO:0000016': set(['GO:0004553']),
'GO:0000014': set(['GO:0004520']),
'GO:0000011': set(['GO:0048308', 'GO:0007033']),
'GO:0000022': set(['GO:0051231']),
'GO:0000010': set(['GO:0016765'])
}
self.sample_ancestors_depth = {
'GO:0000006': set([('GO:0005385', -1)]),
'GO:0000007': set([('GO:0005385', -1)]),
'GO:0000017': set([('GO:0042946', -1)]),
'GO:0000002': set([('GO:0007005', -1)]),
'GO:0000003': set([('GO:0008150', -1)]),
'GO:0000001': set([('GO:0048308', -1), ('GO:0048311', -1)]),
'GO:0000015': set([('GO:0043234', -1), ('GO:0044445', -1)]),
'GO:0000012': set([('GO:0006281', -1)]),
'GO:0000019': set([('GO:0000018', -1), ('GO:0051052', -2)]),
'GO:0000018': set([('GO:0051052', -1)]),
'GO:0000009': set([('GO:0000030', -1)]),
'GO:0000016': set([('GO:0004553', -1)]),
'GO:0000014': set([('GO:0004520', -1)]),
'GO:0000011': set([('GO:0048308', -1), ('GO:0007033', -1)]),
'GO:0000022': set([('GO:0051231', -1)]),
'GO:0000010': set([('GO:0016765', -1)])
}
self.sample_synonyms = {
'GO:0000003': set(['GO:0050876', 'GO:0019952'])
}
def tearDown(self):
self.sample_xml_fh1.close()
def test_getDescendants1(self):
descendants = dict()
for term in self.go.valid_terms:
desc = self.go.getDescendants(term, depth=False)
if len(desc) > 0:
descendants[term] = desc
self.assertEqual(self.sample_descendants_nodepth, descendants)
def test_getDescendants2(self):
descendants = dict()
for term in self.go.valid_terms:
desc = self.go.getDescendants(term, depth=True)
if len(desc) > 0:
descendants[term] = desc
self.assertEqual(self.sample_descendants_depth, descendants)
def test_getAncestors1(self):
ancestors = dict()
for term in self.go.valid_terms:
ancs = self.go.getAncestors(term, depth=False)
if len(ancs) > 0:
ancestors[term] = ancs
self.assertEqual(self.sample_ancestors_nodepth, ancestors)
def test_getAncestors2(self):
ancestors = dict()
for term in self.go.valid_terms:
ancs = self.go.getAncestors(term, depth=True)
if len(ancs) > 0:
ancestors[term] = ancs
self.assertEqual(self.sample_ancestors_depth, ancestors)
def test_getSynonyms(self):
synonyms = dict()
for term in self.go.terms:
syn = self.go.getSynonyms(term)
if syn is not None:
synonyms[term] = syn
self.assertEqual(self.sample_synonyms, synonyms)
def test_init1(self):
go = GOManager()
self.assertFalse(go.configured)
class TestGOManager3(unittest.TestCase):
def setUp(self):
self.sample_data_root = TEST_INVARIANTS['test_data_root']
self.sample_obo_xml = os.path.abspath(
os.path.join(self.sample_data_root, 'sample.obo-xml'))
with open(self.sample_obo_xml, 'rb') as f:
self.go = GOManager()
self.go.configure()
self.go.load(f)
self.sample_xml_fh1 = open(self.sample_obo_xml, 'rb')
self.sample_recognized_relations = [
'is_a', 'part_of', 'regulates', 'positively_regulates',
'negatively_regulates'
]
self.recognized_relations_1 = ['is_a']
self.notpresent_fwd_1 = ['GO:0000019', 'GO:0000022']
self.notpresent_bwd_1 = ['GO:0006310', 'GO:0006312', 'GO:0007052']
self.recognized_relations_2 = [
'positively_regulates', 'negatively_regulates'
]
self.present_fwd_2 = list()
self.present_bwd_2 = list()
self.recognized_relations_x = ['AAA', 'BBB']
self.present_fwd_x = list()
self.present_bwd_x = list()
def tearDown(self):
self.sample_xml_fh1.close()
def test_hierarchy1(self):
go1 = GOManager()
go1.configure(recognized_relations=self.recognized_relations_1)
go1.load(self.sample_xml_fh1)
# recognize only 'is_a'
self.assertItemsEqual(self.recognized_relations_1,
go1.termsRelationsHierarchy.keys())
# compare detailed hierarchy maps for 'is_a'
mfwd1 = self.go.termsRelationsHierarchy['is_a'].dumpFwdMap()
mbwd1 = self.go.termsRelationsHierarchy['is_a'].dumpBwdMap()
cfwd1 = go1.termsRelationsHierarchy['is_a'].dumpFwdMap()
cbwd1 = go1.termsRelationsHierarchy['is_a'].dumpBwdMap()
self.assertEqual(mfwd1, cfwd1)
self.assertEqual(mbwd1, cbwd1)
# compare plain hierarchy maps
mfwd2 = set(self.go.termsPlainHierarchy.dumpFwdMap().keys())
mbwd2 = set(self.go.termsPlainHierarchy.dumpBwdMap().keys())
cfwd2 = set(go1.termsPlainHierarchy.dumpFwdMap().keys())
cbwd2 = set(go1.termsPlainHierarchy.dumpBwdMap().keys())
self.assertNotEqual(mfwd2, cfwd2)
self.assertEqual(set(self.notpresent_fwd_1), mfwd2 - cfwd2)
self.assertNotEqual(mbwd2, cbwd2)
self.assertEqual(set(self.notpresent_bwd_1), mbwd2 - cbwd2)
def test_hierarchy2(self):
go1 = GOManager()
go1.configure(recognized_relations=self.recognized_relations_2)
go1.load(self.sample_xml_fh1)
# recognize only 'positively_regulates', 'negatively_regulates'
self.assertItemsEqual(self.recognized_relations_2,
go1.termsRelationsHierarchy.keys())
# compare plain hierarchy maps
mfwd2 = set(self.go.termsPlainHierarchy.dumpFwdMap().keys())
mbwd2 = set(self.go.termsPlainHierarchy.dumpBwdMap().keys())
cfwd2 = set(go1.termsPlainHierarchy.dumpFwdMap().keys())
cbwd2 = set(go1.termsPlainHierarchy.dumpBwdMap().keys())
self.assertNotEqual(mfwd2, cfwd2)
self.assertEqual(set(self.present_fwd_2), cfwd2)
self.assertNotEqual(mbwd2, cbwd2)
self.assertEqual(set(self.present_bwd_2), cbwd2)
def test_hierarchy3(self):
go1 = GOManager()
go1.configure(recognized_relations=self.recognized_relations_x)
go1.load(self.sample_xml_fh1)
# recognize 'AAA', 'BBB'
self.assertItemsEqual(self.recognized_relations_x,
go1.termsRelationsHierarchy.keys())
# compare plain hierarchy maps
mfwd2 = set(self.go.termsPlainHierarchy.dumpFwdMap().keys())
mbwd2 = set(self.go.termsPlainHierarchy.dumpBwdMap().keys())
cfwd2 = set(go1.termsPlainHierarchy.dumpFwdMap().keys())
cbwd2 = set(go1.termsPlainHierarchy.dumpBwdMap().keys())
self.assertNotEqual(mfwd2, cfwd2)
self.assertEqual(set(self.present_fwd_x), cfwd2)
self.assertNotEqual(mbwd2, cbwd2)
self.assertEqual(set(self.present_bwd_x), cbwd2)