def test_average_flowgrams(self):
"""_average_flowgrams computes an averaged flowgram for each cluster."""
fc = FlowgramCollection({"a": "1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8", "b": "1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0"})
# return the centroid unmodified if sample_mapping = 1
actual = list(_average_flowgrams({"a": "b"}, fc, {"a": ["a"]}))
self.assertEqual(actual, [(fc.getFlow("a"), "a")])
actual = list(_average_flowgrams({"a": "b"}, fc, {"a": ["a", "b"]}))
self.assertEqual(actual, [(Flowgram(["1.1 0.5 0.0 0.9 1.1 1.8 1.1 0.4"]), "a")])
def test_average_flowgrams(self):
"""_average_flowgrams computes an averaged flowgram for each cluster."""
fc = FlowgramCollection({'a': '1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8',
'b': '1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0'})
# return the centroid unmodified if sample_mapping = 1
actual = list(_average_flowgrams({'a': 'b'}, fc, {'a': ['a']}))
self.assertEqual(actual, [(fc.getFlow('a'), 'a')])
actual = list(_average_flowgrams({'a': 'b'}, fc, {'a': ['a', 'b']}))
self.assertEqual(
actual, [(Flowgram(['1.1 0.5 0.0 0.9 1.1 1.8 1.1 0.4']), 'a')])
def test_average_flowgrams(self):
"""_average_flowgrams computes an averaged flowgram for each cluster."""
fc = FlowgramCollection({'a': '1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8',
'b': '1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0'})
# return the centroid unmodified if sample_mapping = 1
actual = list(_average_flowgrams({'a': 'b'}, fc, {'a': ['a']}))
self.assertEqual(actual, [(fc.getFlow('a'), 'a')])
actual = list(_average_flowgrams({'a': 'b'}, fc, {'a': ['a', 'b']}))
self.assertEqual(
actual, [(Flowgram(['1.1 0.5 0.0 0.9 1.1 1.8 1.1 0.4']), 'a')])
def test_container(self):
"""FlowgramContainerArray works as expectected"""
fc = FlowgramCollection({'a': '1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8',
'b': '1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0'})
f_container = FlowgramContainerArray(header)
for f in fc:
f_container.add(f)
for f_obs, f_exp in zip(f_container, fc):
self.assertEqual(str(f_obs), str(f_exp))
def test_prefix_filter_flowgrams(self):
"""prefix_filter_flowgrams maps all flowgrams which are exact prefixe."""
fc = FlowgramCollection({'a': '1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8',
'b': '1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0',
'c': '2.0 0.0 0.0 1.0',
'd': '1.1 0.3 0.0 1.1'})
expected_squeeze_map = {'a': ['c', 'd'], 'b': []}
expected_map = {'a': ['d'], 'b': [], 'c': []}
obs = prefix_filter_flowgrams(fc)
self.assertEqual(obs, (3, 4, expected_map))
obs = prefix_filter_flowgrams(fc, squeeze=True)
self.assertEqual(obs, (2, 4, expected_squeeze_map))
def test_container(self):
"""FlowgramContainerFile works as expected"""
fc = FlowgramCollection({'a': '1.0 0.0 0.0 1.0 1.0 1.2 1.2 0.8',
'b': '1.2 1.0 0.0 0.8 1.2 2.4 1.0 0.0'})
f_container = FlowgramContainerFile(header)
for f in fc:
f_container.add(f)
for f_obs, f_exp in zip(f_container, fc):
self.assertEqual(str(f_obs), str(f_exp))
# adding after iter started raises errror
self.assertRaises(ValueError, f_container.add, f_obs)