tests package

Submodules

tests.test_core module

This script executes testing of core INDIGOpy functions.

class tests.test_core.TestClassify

Bases: object

classes = ('S', 'N', 'A')

scores = [-2, 1.5, 0.5, -0.1, 1]

test_classify_classes()

Make sure that classify works with the classes parameter.

test_classify_default()

Make sure that classify works with required inputs only.

test_classify_thresholds()

Make sure that classify works with the thresholds parameter.

thresholds = (-1, 1)

class tests.test_core.TestFeaturize

Bases: object

binarize = False

entropy = True

feature_names = ['G1', 'G2', 'G3']

interactions = [['A', 'B'], ['A', 'C'], ['B', 'C'], ['A', 'B', 'C']]

key = [('A', 'Drug_A'), ('B', 'Drug_B'), ('C', 'Drug_C')]

na_handle = 0

norm_method = 'minmax'

normalize = True

orthology_map = {'IAI1': ['G1'], 'MC1400': ['G1', 'G3'], 'MG1655': ['G1', 'G2']}

profiles = {'A': [1, nan, 1], 'B': [-2, 1.5, -0.5], 'C': [1, 2, 3]}

profiles_alt = {'Drug_A': [1, nan, 1], 'Drug_B': [-2, 1.5, -0.5], 'Drug_C': [1, 2, 3]}

remove_zero_rows = True

silent = False

strains = ['MG1655', 'MG1655', 'MC1400', 'IAI1']

test_featurize_binarize()

Make sure that featurize works with the binarize parameter.

test_featurize_default()

Make sure that featurize works with required inputs only.

test_featurize_entropy()

Make sure that featurize works with the entropy parameter.

test_featurize_feature_names()

Make sure that featurize works with the feature_names parameter.

test_featurize_key_and_silent()

Make sure that featurize works with the key parameter provided mismatching interactions and profiles. Also check that a warning is raised.

test_featurize_na_handle()

Make sure that featurize works with the na_handle parameter.

test_featurize_normalize_and_norm_method()

Make sure that featurize works with normalize and norm_method parameters.

test_featurize_remove_zero_rows()

Make sure that featurize works with the remove_zero_rows parameter.

test_featurize_strains_and_orthology_map()

Make sure that featurize works with strains and orthology_map parameters.

test_featurize_thresholds()

Make sure that featurize works with the thresholds parameter.

test_featurize_time_and_time_values()

Make sure that featurize works with time and time_values parameters.

thresholds = (-1, 1)

time = True

time_values = [[0, 0], [1, 1], [1, 2], [1, 2, 3]]

class tests.test_core.TestLoadSample

Bases: object

input1 = 'ecoli'

input2 = 'mtb'

input3 = 'saureus'

input4 = 'abaumannii'

test_load_sample_abaumannii()

Make sure that load_sample works for A. baumannii data.

test_load_sample_ecoli()

Make sure that load_sample works for E. coli data.

test_load_sample_mtb()

Make sure that load_sample works for M. tuberculosis data.

test_load_sample_saureus()

Make sure that load_sample works for S. aureus data.

Module contents