def set_up_IPT(self):
self.gs = IPTDataDict(enumerate([
[RC(('H1', 'H2')), RC(('H1', 'H3'))],
[RC(('H1', 'H4'))],
[RC(('H1', 'H2'))],
[RC(('H1', 'H2')), RC(('H2', 'H3'))],
[RC(('H2', 'H3'))],
[RC(('H2', 'H3')), RC(('H1', 'H2'))],
[RC(('H2', 'H3')), RC(('F3', 'H2'))],
[RC(('W1', 'H3'))],
]))
self.results = IPTDataDict(enumerate([
[RC(('M1', 'M2'), 1), RC(('F3', 'M1'), 2)], # 1:1
[RC(('M1', 'M4'), 1)], # 0:0
[RC(('H2', 'M1'), 1)], # partial
[RC(('H2', 'W1'), 1)], # 1:n
[RC(('M2', 'W1'), 1), RC(('M2', 'F3'), 2)], # n:1
[
RC(('W2', 'W3'), 2), RC(('F1', 'W2'), 2),
RC(('M2', 'W1'), 3)
], # n:m
[RC(('F3', 'M2')), RC(('H2', 'H3'))], # 1:0
[RC(('W1', 'W3'))], # organism filter test
]))
self.expected_ho_results = enumerate([
[('H1', 'H2'), ('H1', 'H3')],
[('M1', 'M4')],
[('H1', 'H2')],
[('H2', 'H3'), ('H1', 'H2')],
[('H2', 'H3'), ('M2', 'F3')],
[('W2', 'W3'), ('H1', 'H2'), ('H2', 'H3')],
[('F3', 'H2'), ('H2', 'H3')],
[('W1', 'W3')],
])
self.expected_of_results = enumerate([
[('H1', 'H2'), ('H1', 'H3')],
[],
[('H1', 'H2')],
[('H2', 'H3'), ('H1', 'H2')],
[('H2', 'H3')],
[('H1', 'H2'), ('H2', 'H3')],
[('F3', 'H2'), ('H2', 'H3')],
[('W1', 'W3')],
])
def set_up_INT(self):
self.gs = INTDataDict(enumerate([
[RC('H1'), RC('H2')],
[RC('H4')],
[RC('H1'), RC('H3')],
[RC('H3')],
[RC('H3'), RC('H1')],
[RC('H3'), RC('F3')],
[RC('H3'), RC('F3')],
]))
self.results = INTDataDict(enumerate([
[RC('M1', 1), RC('M2', 2), RC('M3', 3)], # 1:1
[RC('M4', 1)], # 0:0
[RC('W1', 3)], # 1:n
[RC('F3', 1), RC('W1', 2)], # n:1
[RC('W2', 2), RC('F1', 2), RC('W1', 3)], # n:m
[RC('F3', 1), RC('H3', 2)], # 1:0
[RC('F3', 1)], # 1:0
]))
self.expected_ho_results = enumerate([
['H1', 'H2', 'M3'],
['M4'],
['H3', 'H1'],
['H3'],
['W2', 'H1', 'H3'],
['F3', 'H3'],
['F3'],
])
self.expected_of_results = enumerate([
['H1', 'H2'],
[],
['H3', 'H1'],
['H3'],
['H1', 'H3'],
['F3', 'H3'],
['F3'],
])
class MapFilterTests(unittest.TestCase):
def setUp(self):
self.ho_map = {
'H1': ['M1', 'F1', 'W1'],
'H2': ['M2', 'W2'],
'H3': ['F3', 'W1'],
'F3': ['H3'], # NB: creates the circularity problem
}
self.tax_map = {
'H1': 'H', 'H2': 'H', 'H3': 'H', 'H4': 'H',
'M1': 'M', 'M2': 'M', 'M3': 'M', 'M4': 'M',
'F1': 'F', 'F2': 'F', 'F3': 'F', 'F4': 'F',
'W1': 'W', 'W2': 'W', 'W3': 'W', 'W4': 'W',
}
def set_up_INT(self):
self.gs = INTDataDict(enumerate([
[RC('H1'), RC('H2')],
[RC('H4')],
[RC('H1'), RC('H3')],
[RC('H3')],
[RC('H3'), RC('H1')],
[RC('H3'), RC('F3')],
[RC('H3'), RC('F3')],
]))
self.results = INTDataDict(enumerate([
[RC('M1', 1), RC('M2', 2), RC('M3', 3)], # 1:1
[RC('M4', 1)], # 0:0
[RC('W1', 3)], # 1:n
[RC('F3', 1), RC('W1', 2)], # n:1
[RC('W2', 2), RC('F1', 2), RC('W1', 3)], # n:m
[RC('F3', 1), RC('H3', 2)], # 1:0
[RC('F3', 1)], # 1:0
]))
self.expected_ho_results = enumerate([
['H1', 'H2', 'M3'],
['M4'],
['H3', 'H1'],
['H3'],
['W2', 'H1', 'H3'],
['F3', 'H3'],
['F3'],
])
self.expected_of_results = enumerate([
['H1', 'H2'],
[],
['H3', 'H1'],
['H3'],
['H1', 'H3'],
['F3', 'H3'],
['F3'],
])
def test_int_homonym_ortholog_mapping(self):
self.set_up_INT()
self.results.map_homonym_orthologs(self.ho_map, self.gs)
self.assert_results(self.expected_ho_results)
def test_int_organism_filtering(self):
self.set_up_INT()
self.results.map_homonym_orthologs(self.ho_map, self.gs)
self.results.filter_organisms(self.tax_map, self.gs)
self.assert_results(self.expected_of_results)
def set_up_IPT(self):
self.gs = IPTDataDict(enumerate([
[RC(('H1', 'H2')), RC(('H1', 'H3'))],
[RC(('H1', 'H4'))],
[RC(('H1', 'H2'))],
[RC(('H1', 'H2')), RC(('H2', 'H3'))],
[RC(('H2', 'H3'))],
[RC(('H2', 'H3')), RC(('H1', 'H2'))],
[RC(('H2', 'H3')), RC(('F3', 'H2'))],
[RC(('W1', 'H3'))],
]))
self.results = IPTDataDict(enumerate([
[RC(('M1', 'M2'), 1), RC(('F3', 'M1'), 2)], # 1:1
[RC(('M1', 'M4'), 1)], # 0:0
[RC(('H2', 'M1'), 1)], # partial
[RC(('H2', 'W1'), 1)], # 1:n
[RC(('M2', 'W1'), 1), RC(('M2', 'F3'), 2)], # n:1
[
RC(('W2', 'W3'), 2), RC(('F1', 'W2'), 2),
RC(('M2', 'W1'), 3)
], # n:m
[RC(('F3', 'M2')), RC(('H2', 'H3'))], # 1:0
[RC(('W1', 'W3'))], # organism filter test
]))
self.expected_ho_results = enumerate([
[('H1', 'H2'), ('H1', 'H3')],
[('M1', 'M4')],
[('H1', 'H2')],
[('H2', 'H3'), ('H1', 'H2')],
[('H2', 'H3'), ('M2', 'F3')],
[('W2', 'W3'), ('H1', 'H2'), ('H2', 'H3')],
[('F3', 'H2'), ('H2', 'H3')],
[('W1', 'W3')],
])
self.expected_of_results = enumerate([
[('H1', 'H2'), ('H1', 'H3')],
[],
[('H1', 'H2')],
[('H2', 'H3'), ('H1', 'H2')],
[('H2', 'H3')],
[('H1', 'H2'), ('H2', 'H3')],
[('F3', 'H2'), ('H2', 'H3')],
[('W1', 'W3')],
])
def test_ipt_homonym_ortholog_mapping(self):
self.set_up_IPT()
self.results.map_homonym_orthologs(self.ho_map, self.gs)
self.assert_results(self.expected_ho_results)
def test_ipt_organism_filtering(self):
self.set_up_IPT()
self.results.map_homonym_orthologs(self.ho_map, self.gs)
self.results.filter_organisms(self.tax_map, self.gs)
self.assert_results(self.expected_of_results)
def assert_results(self, expected_results):
for doi, expected in expected_results:
items = [rc.item for rc in self.results[doi]]
self.assertEqual(items, expected, "failed on DOI %i: %s != %s" % (
doi, str(items), str(expected)
))
