class StarTestCases(unittest.TestCase):
def setUp(self):
self.star_PAM250 = Star(PAM250())
self.star_Blosum62 = Star(Blosum62())
def test_most_frequent_A_with_BLOSUM62(self):
# setup
sequences = ['AA', 'AC', 'AC']
# results
result = self.star_Blosum62.compute(sequences)
expected = 30
# check
self.assertEqual(expected, result)
def test_most_frequent_with_PAM250(self):
# setup
sequences = ['AA', 'AC', 'AC']
# results
result = self.star_PAM250.compute(sequences)
expected = 28
# check
self.assertEqual(expected, result)
def test_most_frequent_gaps_with_PAM250(self):
# setup
sequences = ['AA', 'A-', 'AC']
# results
result = self.star_PAM250.compute(sequences)
expected = -2
# check
self.assertEqual(expected, result)
def test_most_frequent_gaps_with_BLOSUM62(self):
# setup
sequences = ['AA', 'A-', 'AC']
# results
result = self.star_Blosum62.compute(sequences)
expected = 8
# check
self.assertEqual(expected, result)
def test_should_print_class_name(self):
# setup
sumofpairs = SumOfPairs().get_name()
star = Star().get_name()
entropy = Entropy().get_name()
# check
self.assertEqual("SumOfPairs", sumofpairs)
self.assertEqual("Star", star)
self.assertEqual("Entropy", entropy)
def test_most_frequent_A_with_BLOSUM62(self):
# setup
sequences = MSA(['AA', 'AC', 'AC'])
# results
result = Star(sequences, Blosum62()).compute()
expected = 30
# check
self.assertEqual(expected, result)
def test_most_frequent_gaps_with_PAM250(self):
# setup
sequences = MSA(['AA', 'A-', 'AC'])
# results
result = Star(sequences, PAM250()).compute()
expected = -2
# check
self.assertEqual(expected, result)
def run_all_scores(msa: list) -> None:
align_sequences = list(pair[1] for pair in msa)
sequences_id = list(pair[0] for pair in msa)
# Percentage of non-gaps and totally conserved columns
non_gaps = PercentageOfNonGaps()
totally_conserved_columns = PercentageOfTotallyConservedColumns()
percentage = non_gaps.compute(align_sequences)
conserved = totally_conserved_columns.compute(align_sequences)
print("Percentage of non-gaps: {0} %".format(percentage))
print("Percentage of totally conserved columns: {0}".format(conserved))
# Entropy
value = Entropy().compute(align_sequences=align_sequences)
print("Entropy score: {0}".format(value))
# Sum of pairs
value = SumOfPairs(Blosum62()).compute(align_sequences=align_sequences)
print("SumOfPairs score (Blosum62): {0}".format(value))
value = SumOfPairs(PAM250()).compute(align_sequences=align_sequences)
print("SumOfPairs score (PAM250): {0}".format(value))
value = SumOfPairs(FileMatrix('PAM380.txt')).compute(align_sequences=align_sequences)
print("SumOfPairs score (PAM380): {0}".format(value))
# Star
value = Star(Blosum62()).compute(align_sequences=align_sequences)
print("Star score (Blosum62): {0}".format(value))
value = Star(PAM250()).compute(align_sequences=align_sequences)
print("Star score (PAM250): {0}".format(value))
# STRIKE
value = Strike().compute(align_sequences=align_sequences,
sequences_id=sequences_id,
chains=['A', 'E', 'A', 'A'])
print("STRIKE score: {0}".format(value))
def setUp(self):
self.star_PAM250 = Star(PAM250())
self.star_Blosum62 = Star(Blosum62())