def test6():
"""
Tests substitution function.
:return: None
"""
print("Test6: testing substitution")
dna_seq = None
try:
dna_seq = dna.substitution(dna_seq, 0, "A")
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
dna_seq = linked_code.insertAt(0, "A", dna_seq)
dna_seq2 = dna.substitution(dna_seq, 0, "T")
print(dna_seq2.value == "T", end=" ")
dna_seq = linked_code.insertAt(1, "T", dna_seq)
dna_seq2 = dna.substitution(dna_seq, 1, "G")
print(dna_seq2.value == "A" and dna_seq2.rest.value == "G", end=" ")
dna_seq = linked_code.insertAt(2, "G", dna_seq)
dna_seq = linked_code.insertAt(3, "C", dna_seq)
try:
dna_seq2 = dna.substitution(dna_seq, 4, "A")
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
dna_seq2 = dna.substitution(dna_seq, 2, "A")
print(dna_seq2.value == "A" and dna_seq2.rest.value == "T" \
and dna_seq2.rest.rest.value == "A")
def test3():
"""
Tests is_match function.
:return: None
"""
print("Test3: testing is_match")
dna_seq1 = None
dna_seq2 = None
print(dna.is_match(dna_seq1, dna_seq2) == True, end=" ")
dna_seq2 = linked_code.insertAt(0, "A", dna_seq2)
print(dna.is_match(dna_seq1, dna_seq2) == False, end=" ")
print(dna.is_match(dna_seq2, dna_seq1) == False, end=" ")
dna_seq1 = linked_code.insertAt(0, "A", dna_seq1)
print(dna.is_match(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insertAt(1, "T", dna_seq1)
dna_seq1 = linked_code.insertAt(2, "G", dna_seq1)
dna_seq1 = linked_code.insertAt(3, "C", dna_seq1)
dna_seq2 = linked_code.insertAt(1, "T", dna_seq2)
dna_seq2 = linked_code.insertAt(2, "G", dna_seq2)
print(dna.is_match(dna_seq1, dna_seq2) == False, end=" ")
dna_seq2 = linked_code.insertAt(3, "C", dna_seq2)
print(dna.is_match(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insertAt(2, "A", dna_seq1)
dna_seq2 = linked_code.insertAt(2, "G", dna_seq2)
print(dna.is_match(dna_seq1, dna_seq2) == False)
def test5():
"""
Tests is_palindrome function.
:return: None
"""
print("Test5: testing is_palindrome")
dna_seq = None
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insertAt(0, "A", dna_seq)
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insertAt(0, "T", dna_seq)
print(dna.is_palindrome(dna_seq) == False, end=" ")
dna_seq = linked_code.removeAt(0, dna_seq)
dna_seq = linked_code.insertAt(0, "A", dna_seq)
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insertAt(1, "G", dna_seq)
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insertAt(2, "T", dna_seq)
print(dna.is_palindrome(dna_seq) == False)
def test7():
"""
Tests insertion function.
:return: None
"""
print("Test7: testing insertion")
dna_seq1 = None
dna_seq2 = None
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 0)
print(dna_seq3 == None, end=" ")
try:
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 1)
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
dna_seq1 = linked_code.insertAt(0, "A", dna_seq1)
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 0)
print(dna_seq3.value == "A" \
and linked_code.lengthRec(dna_seq3) == 1, end=" ")
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 1)
print(dna_seq3.value == "A" \
and linked_code.lengthRec(dna_seq3) == 1, end=" ")
dna_seq2 = linked_code.insertAt(0, "C", dna_seq2)
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 0)
print(dna_seq3.value == "C" and dna_seq3.rest.value == "A" \
and linked_code.lengthRec(dna_seq3) == 2, end=" ")
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 1)
print(dna_seq3.value == "A" and dna_seq3.rest.value == "C" \
and linked_code.lengthRec(dna_seq3) == 2, end=" ")
dna_seq1 = linked_code.insertAt(0, "T", dna_seq1) # now TA
dna_seq2 = linked_code.insertAt(0, "G", dna_seq2) # now GC
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 0)
print(dna_seq3.value == "G" and dna_seq3.rest.value == "C" \
and dna_seq3.rest.rest.value == "T" \
and dna_seq3.rest.rest.rest.value == "A"
and linked_code.lengthRec(dna_seq3) == 4, end=" ")
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 1)
print(dna_seq3.value == "T" and dna_seq3.rest.value == "G" \
and dna_seq3.rest.rest.value == "C" \
and dna_seq3.rest.rest.rest.value == "A"
and linked_code.lengthRec(dna_seq3) == 4, end=" ")
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 2)
print(dna_seq3.value == "T" and dna_seq3.rest.value == "A" \
and dna_seq3.rest.rest.value == "G" \
and dna_seq3.rest.rest.rest.value == "C"
and linked_code.lengthRec(dna_seq3) == 4)
def test2():
"""
Tests function to convert a DNA linked Node
structure into a string.
:return:
"""
print("Test2: testing convert_to_string")
dna_str1 = dna.convert_to_string(None)
print(dna_str1 == "", end=" ")
dna_seq = None
dna_seq = linked_code.insertAt(0, "C", dna_seq)
dna_str2 = dna.convert_to_string(dna_seq)
print(dna_str2 == "C", end=" ")
dna_seq = None
dna_seq = linked_code.insertAt(0, 'T', dna_seq)
dna_seq = linked_code.insertAt(1, 'A', dna_seq)
dna_seq = linked_code.insertAt(2, 'G', dna_seq)
dna_str3 = dna.convert_to_string(dna_seq)
print(dna_str3 == "TAG")
def test4():
"""
Tests is_pairing function.
:return: None
"""
print("Test4: testing is_pairing")
dna_seq1 = None
dna_seq2 = None
print(dna.is_pairing(dna_seq1, dna_seq2) == True, end=" ")
dna_seq2 = linked_code.insertAt(0, "A", dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == False, end=" ")
print(dna.is_pairing(dna_seq2, dna_seq1) == False, end=" ")
dna_seq1 = linked_code.insertAt(0, "T", dna_seq1)
print(dna.is_pairing(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insertAt(1, "T", dna_seq1)
dna_seq1 = linked_code.insertAt(2, "G", dna_seq1)
dna_seq1 = linked_code.insertAt(3, "C", dna_seq1)
dna_seq2 = linked_code.insertAt(1, "A", dna_seq2)
dna_seq2 = linked_code.insertAt(2, "C", dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == False, end=" ")
dna_seq2 = linked_code.insertAt(3, "G", dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insertAt(2, "A", dna_seq1)
dna_seq2 = linked_code.insertAt(2, "A", dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == False, end=" ")
test_str1 = "AATTTGC"
test_str2 = "GCGCTGC"
for idx in range(len(test_str1)):
dna_seq1 = linked_code.removeAt(2, dna_seq1)
dna_seq2 = linked_code.removeAt(2, dna_seq2)
dna_seq1 = linked_code.insertAt(2, test_str1[idx], dna_seq1)
dna_seq2 = linked_code.insertAt(2, test_str2[idx], dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == False, end=" ")
print()
def test9():
"""
Tests duplication function.
:return: None
"""
print("Test9: testing duplication")
dna_seq1 = None
dna_seq2 = dna.duplication(dna_seq1, 0, 0)
print(dna_seq2 == None, end=" ")
try:
dna_seq2 = dna.duplication(dna_seq1, 0, 1)
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
dna_seq1 = linked_code.insertAt(0, "A", dna_seq1)
dna_seq2 = dna.duplication(dna_seq1, 2, 0)
print(dna_seq2.value == "A" and \
linked_code.lengthRec(dna_seq2) == 1, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 0, 1)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "A" and \
linked_code.lengthRec(dna_seq2) == 2, end=" ")
dna_seq1 = linked_code.insertAt(1, "T", dna_seq1)
dna_seq1 = linked_code.insertAt(2, "C", dna_seq1)
dna_seq2 = dna.duplication(dna_seq1, 0, 1)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "A" and \
linked_code.lengthRec(dna_seq2) == 4, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 1, 1)
value = dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "T" and \
linked_code.lengthRec(dna_seq2) == 4
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "T" and \
linked_code.lengthRec(dna_seq2) == 4, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 2, 1)
value = dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "C" and \
dna_seq2.rest.rest.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 4
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "C" and \
dna_seq2.rest.rest.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 4, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 0, 2)
value = dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "A" and \
dna_seq2.rest.rest.rest.value == "T" and \
dna_seq2.rest.rest.rest.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 5
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "A" and \
dna_seq2.rest.rest.rest.value == "T" and \
dna_seq2.rest.rest.rest.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 5, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 1, 2)
value = dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "C" and \
dna_seq2.rest.rest.rest.value == "T" and \
dna_seq2.rest.rest.rest.rest.value == "C"
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "C" and \
dna_seq2.rest.rest.rest.value == "T" and \
dna_seq2.rest.rest.rest.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 5, end=" ")
try:
dna_seq2 = dna.duplication(dna_seq1, 2, 2)
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
print()
def test8():
"""
Tests deletion function.
:return: None
"""
print("Test8: testing deletion")
dna_seq1 = None
dna_seq2 = dna.deletion(dna_seq1, 0, 0)
print(dna_seq2 == None, end=" ")
try:
dna_seq2 = dna.deletion(dna_seq1, 0, 1)
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
dna_seq1 = linked_code.insertAt(0, "A", dna_seq1)
dna_seq2 = dna.deletion(dna_seq1, 2, 0)
print(dna_seq2.value == "A" and \
linked_code.lengthRec(dna_seq2) == 1, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 0, 1)
print(dna_seq2 == None, end=" ")
dna_seq1 = linked_code.insertAt(1, "T", dna_seq1)
dna_seq1 = linked_code.insertAt(2, "G", dna_seq1)
dna_seq1 = linked_code.insertAt(3, "C", dna_seq1)
dna_seq2 = dna.deletion(dna_seq1, 0, 1)
print(dna_seq2.value == "T" and \
linked_code.lengthRec(dna_seq2) == 3, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 1, 1)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "G" and \
linked_code.lengthRec(dna_seq2) == 3, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 2, 1)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 3, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 3, 1)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "G" and \
linked_code.lengthRec(dna_seq2) == 3, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 0, 2)
print(dna_seq2.value == "G" and \
dna_seq2.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 2, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 1, 2)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "C" and \
linked_code.lengthRec(dna_seq2) == 2, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 2, 2)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
linked_code.lengthRec(dna_seq2) == 2, end=" ")
try:
dna_seq2 = dna.deletion(dna_seq1, 3, 2)
print("False", end=" ") # failed to catch exception
except:
print("True", end=" ")
dna_seq2 = dna.deletion(dna_seq1, 0, 3)
print(dna_seq2.value == "C" and \
linked_code.lengthRec(dna_seq2) == 1, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 1, 3)
print(dna_seq2.value == "A" and \
linked_code.lengthRec(dna_seq2) == 1, end=" ")
dna_seq2 = dna.deletion(dna_seq1, 0, 4)
print(dna_seq2 == None)