def test_sum_counts_by_consensus(self):
"""should sum otu counts by consensus"""
#otu_table = parse_otu_table(self.otu_table)
#otu_table = parse_biom_table(self.otu_table)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 3)
exp_result = {
('Root', 'Bacteria', 'Actinobacteria'): array([1, 0, 2, 4]),
('Root', 'Bacteria', 'Firmicutes'): array([1, 3, 1, 1]),
('Root', 'Bacteria', 'Other'): array([1, 2, 1, 0])
}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 2)
exp_result = {('Root', 'Bacteria'): array([3, 5, 4, 5])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 4)
exp_result = {
('Root', 'Bacteria', 'Actinobacteria', 'Actinobacteria'):
array([1, 0, 2, 4]),
('Root', 'Bacteria', 'Firmicutes', '"Clostridia"'):
array([1, 3, 1, 1]),
('Root', 'Bacteria', 'Other', 'Other'):
array([1, 2, 1, 0])
}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
def test_sum_counts_by_consensus(self):
"""should sum otu counts by consensus"""
#otu_table = parse_otu_table(self.otu_table)
#otu_table = parse_biom_table(self.otu_table)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 3)
exp_result = {(
'Root', 'Bacteria', 'Actinobacteria'): array([1, 0, 2, 4]),
('Root', 'Bacteria', 'Firmicutes'): array([1, 3, 1, 1]),
('Root', 'Bacteria', 'Other'): array([1, 2, 1, 0])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertItemsEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 2)
exp_result = {('Root', 'Bacteria'): array([3, 5, 4, 5])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertItemsEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 4)
exp_result = {('Root', 'Bacteria', 'Actinobacteria', 'Actinobacteria'):
array([1, 0, 2, 4]),
('Root', 'Bacteria', 'Firmicutes', '"Clostridia"'):
array([1, 3, 1, 1]),
('Root', 'Bacteria', 'Other', 'Other'): array([1, 2, 1, 0])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertItemsEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)