def test_gap_fill_greater_than_threshold(self):
"""
Test the gap fill function, with a set of scores where the gaps are
greater than threshold to apply gap filling
"""
key_reactions = ["A", "B", "C", "D", "E", "G"]
reaction_scores = {"A": 1, "B": 2, "C": 2, "D": 1}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
self.assertDictEqual(gap_filled_reaction_scores, reaction_scores)
def test_gap_fill_all_required_two_lowest_scores(self):
"""
Test the gap fill function, with a set of scores of all required reactions
Test the lowest score is boosted
Test the two lowest scores are unchanged
"""
key_reactions = ["A", "B", "C", "D", "E"]
reaction_scores = {"A": 1, "B": 2, "C": 2, "D": 0.1, "E": 0.1}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
self.assertDictEqual(gap_filled_reaction_scores, reaction_scores)
def test_gap_fill_equal_threshold(self):
"""
Test the gap fill function, with a set of scores where the gaps equal the
threshold to apply gap filling
"""
key_reactions = ["A", "B", "C", "D", "E"]
reaction_scores = {"A": 1, "B": 2, "C": 2, "D": 1}
expected_result = {"A": 1, "B": 2, "C": 2, "D": 1, "E": 1}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
self.assertDictEqual(gap_filled_reaction_scores, expected_result)
def test_gap_fill_zero_gaps(self):
"""
Test the gap fill function, with a set of scores that do not have gaps
Test for boost of lowest score
"""
key_reactions = ["A", "B"]
reaction_scores = {"A": 1, "B": 2}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
expected_gap_filled_reaction_scores = {"A": 2, "B": 2}
self.assertDictEqual(gap_filled_reaction_scores,
expected_gap_filled_reaction_scores)
def test_gap_fill_optional_reactions_greater_than_threshold(self):
"""
Test the gap fill function, with a set of scores that include optional reactions
where just considering the required reactions the gaps are greater than the threshold
for gap filling
Test with a minimum score lower for all reactions that the required reactions
"""
key_reactions = ["A", "B", "C", "D", "E", "G"]
reaction_scores = {"A": 1, "B": 2, "C": 2, "D": 1, "F": 0.1}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
self.assertDictEqual(gap_filled_reaction_scores, reaction_scores)
def test_gap_fill_optional_reactions_zero_gaps(self):
"""
Test the gap fill function, with a set of scores that include optional reactions
where just considering the required reactions it does not require gap filling
Test boost lowest abundance score of key reactions
"""
key_reactions = ["A", "B"]
reaction_scores = {"A": 1, "B": 2, "E": 0.1}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
expected_gap_filled_reaction_scores = {"A": 2, "B": 2, "E": 0.1}
self.assertDictEqual(gap_filled_reaction_scores,
expected_gap_filled_reaction_scores)
def test_gap_fill_all_required_reactions_one_optional(self):
"""
Test the gap fill function, with a set of scores of all required reactions
Test the lowest score is boosted
Test the optional reaction is not boosted
"""
key_reactions = ["A", "B", "C", "D", "E"]
reaction_scores = {"A": 1, "B": 2, "C": 2, "D": 1, "E": 0.1, "F": 0.1}
gap_filled_reaction_scores = modules.gap_fill(key_reactions,
reaction_scores)
expected_reaction_scores = {
"A": 1,
"B": 2,
"C": 2,
"D": 1,
"E": 1,
"F": 0.1
}
self.assertDictEqual(gap_filled_reaction_scores,
expected_reaction_scores)