def test_compute_structured_pathway_abundance_or_coverage_test_coverage_missing_optional_reaction(
self):
"""
Test the compute_structured_pathway_abundance_or_coverage function for a simple structure with coverage
Test the PathwaysDatabase add and get pathway structure along with key reactions
Test with an optional reaction missing
"""
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
structure_string = " A -B C "
pathways_database_store.add_pathway_structure("pathway1",
structure_string)
reaction_scores = {"A": 1, "B": 0, "C": 3}
structure = pathways_database_store.get_structure_for_pathway(
"pathway1")
key_reactions = pathways_database_store.get_key_reactions_for_pathway(
"pathway1")
median = 1
# Compute the coverage
coverage = modules.compute_structured_pathway_abundance_or_coverage(
structure, key_reactions, reaction_scores, True, median)
# Compute the expected coverage which is the harmonic mean of the chi2cdf for the required reactions
del reaction_scores["B"]
expected_coverage = modules.harmonic_mean(
[chi2cdf.chi2cdf(v, median) for v in reaction_scores.values()])
self.assertEqual(coverage, expected_coverage)
def test_harmonic_mean_one_zero(self):
"""
Test the harmonmic mean function with a set of values with on zero
"""
result = modules.harmonic_mean([1, 2, 3, 0, 4])
expect_result = 0
self.assertEqual(result, expect_result)
def test_harmonic_mean_empty_list(self):
"""
Test the harmonmic mean function with an empty list
"""
result = modules.harmonic_mean([])
expect_result = 0
self.assertEqual(result, expect_result)
def test_harmonic_mean(self):
"""
Test the harmonmic mean function
"""
values = [1, 2, 3, 4]
result = modules.harmonic_mean(values)
expect_result = len(values) / sum(1.0 / v for v in values)
self.assertEqual(result, expect_result)