def test_one_empty(self):
"""Checks if everything is fine with one empty sequence."""
nw = needleman_wunsch.NeedlemanWunsch()
result = nw.run("../T_INPUT/empty_test.fasta", "../T_INPUT/5test_seq2.fasta", "../T_INPUT/3eva.txt", -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == ""
assert id_seq2 == "Seq2"
assert seq1 == ""
assert seq2 == "TCCGA"
assert score == -5
assert alignments == [["-----", "TCCGA"]] # order of elements is random!
def test_2(self):
"""Long sequence test. Test taken from Bioinformatics exercise sheet."""
nw = needleman_wunsch.NeedlemanWunsch()
result = nw.run("../T_INPUT/2test_seq1.fasta", "../T_INPUT/2test_seq2.fasta", "../T_INPUT/2eva.txt", -2, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "Seq1"
assert id_seq2 == "Seq2"
assert seq1 == "CCCCGCGACUCGGGUUCAAGGG"
assert seq2 == "GGGUGAGACCCCAGUUCAACCC"
assert score == 33
assert alignments == [["CCCCGCGACUCGGGUUCAAGGG", "GGGUGAGACCCCAGUUCAACCC"]] # order of elements is random!
def test_3(self):
"""Another sequence test. Test taken from Bioinformatics exercise sheet."""
nw = needleman_wunsch.NeedlemanWunsch()
result = nw.run("../T_INPUT/3test_seq1.fasta", "../T_INPUT/3test_seq2.fasta", "../T_INPUT/3eva.txt", -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "animal| seq1"
assert id_seq2 == "plant| seq2"
assert seq1 == "TCCGA"
assert seq2 == "TACGCGC"
assert score == 2
assert alignments == [["T-C-CGA", "TACGCGC"]] # order of elements is random!
def test_1(self):
"""Short sequence test."""
nw = needleman_wunsch.NeedlemanWunsch()
result = nw.run("../T_INPUT/1test_seq1.fasta", "../T_INPUT/1test_seq2.fasta", "../T_INPUT/1eva.txt", -2, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "Seq1"
assert id_seq2 == "Seq2"
assert seq1 == "AGTC"
assert seq2 == "ATC"
assert score == 1
assert alignments == [["AGTC", "A-TC"]] # order of elements is random!
def test_instance(self):
"""Check inheritance."""
assert issubclass(needleman_wunsch.NeedlemanWunsch, NeedlemanWunschBase)
assert isinstance(needleman_wunsch.NeedlemanWunsch(), NeedlemanWunschBase)