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.insert_at(0, "A", dna_seq)
dna_seq2 = dna.substitution(dna_seq, 0, "T")
print(dna_seq2.value == "T", end=" ")
dna_seq = linked_code.insert_at(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.insert_at(2, "G", dna_seq)
dna_seq = linked_code.insert_at(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.insert_at(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.insert_at(0, "A", dna_seq1)
print(dna.is_match(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insert_at(1, "T", dna_seq1)
dna_seq1 = linked_code.insert_at(2, "G", dna_seq1)
dna_seq1 = linked_code.insert_at(3, "C", dna_seq1)
dna_seq2 = linked_code.insert_at(1, "T", dna_seq2)
dna_seq2 = linked_code.insert_at(2, "G", dna_seq2)
print(dna.is_match(dna_seq1, dna_seq2) == False, end=" ")
dna_seq2 = linked_code.insert_at(3, "C", dna_seq2)
print(dna.is_match(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insert_at(2, "A", dna_seq1)
dna_seq2 = linked_code.insert_at(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.insert_at(0, "A", dna_seq)
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insert_at(0, "T", dna_seq)
print(dna.is_palindrome(dna_seq) == False, end=" ")
dna_seq = linked_code.remove_at(0, dna_seq)
dna_seq = linked_code.insert_at(0, "A", dna_seq)
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insert_at(1, "G", dna_seq)
print(dna.is_palindrome(dna_seq) == True, end=" ")
dna_seq = linked_code.insert_at(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.insert_at(0, "A", dna_seq1)
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 0)
print(dna_seq3.value == "A" \
and linked_code.length_rec(dna_seq3) == 1, end=" ")
dna_seq3 = dna.insertion(dna_seq1, dna_seq2, 1)
print(dna_seq3.value == "A" \
and linked_code.length_rec(dna_seq3) == 1, end=" ")
dna_seq2 = linked_code.insert_at(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.length_rec(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.length_rec(dna_seq3) == 2, end=" ")
dna_seq1 = linked_code.insert_at(0, "T", dna_seq1) # now TA
dna_seq2 = linked_code.insert_at(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.length_rec(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.length_rec(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.length_rec(dna_seq3) == 4)
def substitution(dna_seq, index, base):
"""
This function takes the input of the DNA sequence, index at which the base has to be replaced and the base by which the original sequence will be replaced
"""
if linked_code.length_rec(dna_seq) < index:
raise IndexError("Invalid Insertion Index")
else:
return linked_code.insert_at(index, base,
linked_code.remove_at(index, dna_seq))
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.insert_at(0, "C", dna_seq)
dna_str2 = dna.convert_to_string(dna_seq)
print(dna_str2 == "C", end=" ")
dna_seq = None
dna_seq = linked_code.insert_at(0, 'T', dna_seq)
dna_seq = linked_code.insert_at(1, 'A', dna_seq)
dna_seq = linked_code.insert_at(2, 'G', dna_seq)
dna_str3 = dna.convert_to_string(dna_seq)
print(dna_str3 == "TAG")
def duplication(dna_seq, idx, segment_size):
"""
This function takes the dna_seq, index a and the segment size that has to be copied and added after that
"""
if segment_size != 0:
a = segment_size
while (segment_size > 0):
v = linked_code.value_at(dna_seq, idx)
dna_seq = linked_code.insert_at(idx + a, v, dna_seq)
idx += 1
segment_size -= 1
return dna_seq
else:
return dna_seq
def duplication(DNA, idx, size):
"""
Insert duplicate segment of specific size at index of idx + size
:param DNA: dna sequence
:param idx: index where dna sequence starts to be copied
:param size: size of segment copied
:return: new linked-node with duplicate segment of specific size inserted at index of idx + size
"""
if size == 0:
return DNA
elif DNA is None:
raise IndexError("Out of Bounds")
lnk = None
for i in range(size):
val = linked_code.value_at(DNA, i + idx)
lnk = linked_code.insert_at(i, val, lnk)
new_link = insertion(DNA, lnk, idx + size)
return new_link
def substitution(dna_seq1, idx, base):
"""
This function substitutes a value in a linked list with another value.
Pre: dna_seq must be a linked list, idx must be an integer.
Post: a new linked list is returned with the substituted value.
:param dna_seq1: a linked list
:param idx: index at which substitution occurs
:param base: value that will replace the one already at the chosen index.
:return: a linked list with correctly substituted value
"""
if dna_seq1.value == None:
return False
else:
if idx < 0:
raise IndexError('Index out of range')
elif idx == 0:
dna_seq1 = linked_code.remove_at(idx, dna_seq1)
dna_seq1 = linked_code.insert_at(idx, base, dna_seq1)
return dna_seq1
else:
return LinkNode(dna_seq1.value,
substitution(dna_seq1.rest, idx - 1, base))
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.insert_at(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.insert_at(0, "T", dna_seq1)
print(dna.is_pairing(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insert_at(1, "T", dna_seq1)
dna_seq1 = linked_code.insert_at(2, "G", dna_seq1)
dna_seq1 = linked_code.insert_at(3, "C", dna_seq1)
dna_seq2 = linked_code.insert_at(1, "A", dna_seq2)
dna_seq2 = linked_code.insert_at(2, "C", dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == False, end=" ")
dna_seq2 = linked_code.insert_at(3, "G", dna_seq2)
print(dna.is_pairing(dna_seq1, dna_seq2) == True, end=" ")
dna_seq1 = linked_code.insert_at(2, "A", dna_seq1)
dna_seq2 = linked_code.insert_at(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.remove_at(2, dna_seq1)
dna_seq2 = linked_code.remove_at(2, dna_seq2)
dna_seq1 = linked_code.insert_at(2, test_str1[idx], dna_seq1)
dna_seq2 = linked_code.insert_at(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.insert_at(0, "A", dna_seq1)
dna_seq2 = dna.duplication(dna_seq1, 2, 0)
print(dna_seq2.value == "A" and \
linked_code.length_rec(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.length_rec(dna_seq2) == 2, end=" ")
dna_seq1 = linked_code.insert_at(1, "T", dna_seq1)
dna_seq1 = linked_code.insert_at(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.length_rec(dna_seq2) == 4, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 1, 1)
print(dna_seq2.value == "A" and \
dna_seq2.rest.value == "T" and \
dna_seq2.rest.rest.value == "T" and \
linked_code.length_rec(dna_seq2) == 4, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 2, 1)
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.length_rec(dna_seq2) == 4, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 0, 2)
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.length_rec(dna_seq2) == 5, end=" ")
dna_seq2 = dna.duplication(dna_seq1, 1, 2)
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.length_rec(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()
