def test_many(self):
"""Checks if everything is fine with a sequence of not matching characters."""
nussinov = nussinov_alg.Nussinov()
result = nussinov.run("../T_INPUT/multi_not_matching_test.fasta")
(id_seq, seq, dot_bracket_notation) = result
assert id_seq == "RNA_many"
assert seq == "ACACACCAC"
assert dot_bracket_notation == "........."
def test_very_short(self):
"""Checks if everything is fine with a sequence of lenght one."""
nussinov = nussinov_alg.Nussinov()
result = nussinov.run("../T_INPUT/very_short_test.fasta")
(id_seq, seq, dot_bracket_notation) = result
assert id_seq == "RNA_one"
assert seq == "A"
assert dot_bracket_notation == "."
def test_empty(self):
"""Checks if everything is fine with an empty sequence."""
nussinov = nussinov_alg.Nussinov()
result = nussinov.run("../T_INPUT/empty_test.fasta")
(id_seq, seq, dot_bracket_notation) = result
assert id_seq == ""
assert seq == ""
assert dot_bracket_notation == ""
def test_10(self):
"""Short sequence test. Test taken from my presentation."""
nussinov = nussinov_alg.Nussinov()
result = nussinov.run("../T_INPUT/10test_seq.fasta")
(id_seq, seq, dot_bracket_notation) = result
assert id_seq == "RNA_Seq"
assert seq == "GAUC"
assert dot_bracket_notation == "(())"
def test_9(self):
"""Short sequence test. Test taken from my report."""
nussinov = nussinov_alg.Nussinov()
result = nussinov.run("../T_INPUT/9test_seq.fasta")
(id_seq, seq, dot_bracket_notation) = result
assert id_seq == "RNA_Seq"
assert seq == "CGAAU"
assert dot_bracket_notation == "()(.)"
def test_8(self):
"""Short sequence test. Test taken from Bioinformatics exercise sheet."""
nussinov = nussinov_alg.Nussinov()
result = nussinov.run("../T_INPUT/8test_seq.fasta")
(id_seq, seq, dot_bracket_notation) = result
assert id_seq == "RNA1"
assert seq == "CCUGUAAG"
assert dot_bracket_notation == "((.)().)"
def test_instance(self):
"""Check inheritance."""
assert issubclass(nussinov_alg.Nussinov, NussinovBase)
assert isinstance(nussinov_alg.Nussinov(), NussinovBase)