def test10():
n = random.randint(50, 400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(10, n - 10)
j = random.randint(10, n - 10)
if i > j:
i, j = j, i
s = s[:i] + "a" + s[j:]
seq[i:j] = 'a'
n2 = random.randint(50, 400)
s2 = randomSeq(n)
seq2 = dnaSeq.dnaSeq(s2)
i2 = random.randint(10, n2 - 10)
j2 = random.randint(10, n2 - 10)
if i2 > j2:
i2, j2 = j2, i2
s2 = s2[:i2] + "aaa" + s2[j2:]
seq2[i2:j2] = 'aaa'
return 0.5 * int(str(seq) == s) + 0.5 * int(str(seq2) == s2)
def test2():
"""Testing constructor exception"""
try:
dnaSeq.dnaSeq(2)
except Exception as e:
return isinstance(e, ValueError)
return False
def test10():
n = random.randint(50,400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(10,n-10)
j = random.randint(10,n-10)
if i > j:
i,j = j,i
s = s[:i] + "a" + s[j:]
seq[i:j] = 'a'
n2 = random.randint(50,400)
s2 = randomSeq(n)
seq2 = dnaSeq.dnaSeq(s2)
i2 = random.randint(10,n2-10)
j2 = random.randint(10,n2-10)
if i2 > j2:
i2,j2 = j2,i2
s2 = s2[:i2] + "aaa" + s2[j2:]
seq2[i2:j2] = 'aaa'
return 0.5*int(str(seq)==s) + 0.5*int(str(seq2)==s2)
def test2():
"""Testing constructor exception"""
try:
dnaSeq.dnaSeq(2)
except Exception as e:
return isinstance(e, ValueError)
return False
def test11():
n = random.randint(50,400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
n2 = random.randint(50,400)
s2 = randomSeq(n2)
seq2 = dnaSeq.dnaSeq(s2)
return 0.8*int(str(seq+seq2) == s+s2) + 0.2*int(isinstance(seq+seq2, dnaSeq.dnaSeq))
def test11():
n = random.randint(50, 400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
n2 = random.randint(50, 400)
s2 = randomSeq(n2)
seq2 = dnaSeq.dnaSeq(s2)
return 0.8 * int(str(seq + seq2) == s + s2) + 0.2 * int(
isinstance(seq + seq2, dnaSeq.dnaSeq))
def test13():
n = random.randint(50, 400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(0, n)
j = random.randint(0, n)
if i > j:
i, j = j, i
return dnaSeq.dnaSeq(s[i:j]) in seq
def test13():
n = random.randint(50,400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(0,n)
j = random.randint(0,n)
if i > j:
i,j = j,i
return dnaSeq.dnaSeq(s[i:j]) in seq
def test6():
n = random.randint(50,400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(0,n-1)
j = -1*random.randint(1,n)
return 0.5*int(seq[i] == s[i]) + 0.5*int(seq[j]==seq[j])
def test19():
"""Test with differnt column width"""
colwidth = random.randint(60, 100)
L = [
dnaSeq_sol.dnaSeq(randomSeq(random.randint(300, 600)))
for i in range(5)
]
for d in L:
d.info = ">" + "".join([random.choice("ABCDEFH ") for i in range(30)])
dnaSeq_sol.writeFA(L, "test1.fa", col_width=colwidth)
L2 = []
for l in L:
d = dnaSeq.dnaSeq(str(l))
d.info = l.info
L2.append(d)
dnaSeq.writeFA(L2, "test2.fa", col_width=colwidth)
## compare files
for l1, l2 in zip(open("test1.fa"), open("test2.fa")):
if l1[0] == '>':
if l1.lstrip('>').strip() != l2.lstrip('>').strip():
return False
else:
if l1 != l2:
return False
return True
def test19():
"""Test with differnt column width"""
colwidth = random.randint(60,100)
L = [dnaSeq_sol.dnaSeq(randomSeq(random.randint(300,600))) for i in range(5)]
for d in L:
d.info = ">" + "".join([random.choice("ABCDEFH ") for i in range(30)])
dnaSeq_sol.writeFA(L, "test1.fa", col_width = colwidth)
L2 = []
for l in L:
d = dnaSeq.dnaSeq(str(l))
d.info = l.info
L2.append(d)
dnaSeq.writeFA(L2, "test2.fa", col_width = colwidth)
## compare files
for l1,l2 in zip(open("test1.fa"), open("test2.fa")):
if l1[0] == '>':
if l1.lstrip('>').strip() != l2.lstrip('>').strip():
return False
else:
if l1 != l2:
return False
return True
def test6():
n = random.randint(50, 400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(0, n - 1)
j = -1 * random.randint(1, n)
return 0.5 * int(seq[i] == s[i]) + 0.5 * int(seq[j] == seq[j])
def test18():
"""Test to make sure it creates a file that is readable"""
L = [dnaSeq.dnaSeq(randomSeq(random.randint(300,600))) for i in range(5)]
for d in L:
d.info = ">" + "".join([random.choice("ABCDEFH ") for i in range(30)])
dnaSeq.writeFA(L, "test1.fa")
L2 = dnaSeq.readFA("test1.fa")
return all([o1.info.lstrip('>').strip()==o2.info.lstrip('>').strip() and str(o1)==str(o2) for o1,o2 in zip(L,L2)])
def test16():
n = random.randint(50, 400)
s = randomSeq(n)
seq1 = dnaSeq.dnaSeq(s)
seq2 = dnaSeq_sol.dnaSeq(s)
seq1.reverse_complement()
seq2.reverse_complement()
return str(seq1) == str(seq2)
def test16():
n = random.randint(50,400)
s = randomSeq(n)
seq1 = dnaSeq.dnaSeq(s)
seq2 = dnaSeq_sol.dnaSeq(s)
seq1.reverse_complement()
seq2.reverse_complement()
return str(seq1)==str(seq2)
def test9():
n = random.randint(50,400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(10,n-10)
s = s[:i] + "a" + s[i+1:]
seq[i] = "a"
return str(seq) == s
def test9():
n = random.randint(50, 400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(10, n - 10)
s = s[:i] + "a" + s[i + 1:]
seq[i] = "a"
return str(seq) == s
def test18():
"""Test to make sure it creates a file that is readable"""
L = [dnaSeq.dnaSeq(randomSeq(random.randint(300, 600))) for i in range(5)]
for d in L:
d.info = ">" + "".join([random.choice("ABCDEFH ") for i in range(30)])
dnaSeq.writeFA(L, "test1.fa")
L2 = dnaSeq.readFA("test1.fa")
return all([
o1.info.lstrip('>').strip() == o2.info.lstrip('>').strip()
and str(o1) == str(o2) for o1, o2 in zip(L, L2)
])
def test7():
n = random.randint(50,400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(0,n//2)
j = random.randint(n//2+1,n)
i2 = -1*random.randint(0,n//2)
j2 = -1*random.randint(n//2+1,n)
i3 = random.randint(0,n//2)
j3 = random.randint(n//2+1,n)
return (1/3.0)*int(str(seq[i:j])==s[i:j]) + (1/3.0)*int(str(seq[i2:j2])==s[i2:j2]) + (1/3.0)*int(str(seq[i3:j3:2])==s[i3:j3:2])
def test7():
n = random.randint(50, 400)
s = randomSeq(n)
seq = dnaSeq.dnaSeq(s)
i = random.randint(0, n // 2)
j = random.randint(n // 2 + 1, n)
i2 = -1 * random.randint(0, n // 2)
j2 = -1 * random.randint(n // 2 + 1, n)
i3 = random.randint(0, n // 2)
j3 = random.randint(n // 2 + 1, n)
return (1 / 3.0) * int(str(seq[i:j]) == s[i:j]) + (1 / 3.0) * int(
str(seq[i2:j2]) == s[i2:j2]) + (1 / 3.0) * int(
str(seq[i3:j3:2]) == s[i3:j3:2])
def test1():
"""Test that the constructor run on a legit sequence withot exceptions"""
s = dnaSeq.dnaSeq("ACGTacgtNn")
return isinstance(s, dnaSeq.dnaSeq)
def test5():
n = random.randint(50, 400)
s = randomSeq(n)
return str(dnaSeq.dnaSeq(s)) == s
def test4():
n = random.randint(50, 150)
s = dnaSeq.dnaSeq(randomSeq(n))
return len(s) == n
def test3():
"""Testing constructor exception"""
try:
dnaSeq.dnaSeq("ABCD")
except Exception as e:
return type(e) == dnaSeq.DNAError
def test3():
"""Testing constructor exception"""
try:
dnaSeq.dnaSeq("ABCD")
except Exception as e:
return type(e) == dnaSeq.DNAError
def setUp(self):
self.seq1 = dnaSeq.dnaSeq("".join(['A' for i in range(80)]))
self.seq1.info = ">ONE"
self.seq2 = dnaSeq.dnaSeq("".join(['C' for i in range(80)]))
self.seq2.info = ">TWO"
self.seqs = [self.seq1, self.seq2]
def test5():
n = random.randint(50,400)
s = randomSeq(n)
return str(dnaSeq.dnaSeq(s)) == s
def test1():
"""Test that the constructor run on a legit sequence withot exceptions"""
s = dnaSeq.dnaSeq("ACGTacgtNn")
return isinstance(s, dnaSeq.dnaSeq)
def test8(): # Make sure index slice returns a sequence
s = dnaSeq.dnaSeq("ACGT")[0:2]
return isinstance(s, dnaSeq.dnaSeq)
def containsTest(self):
self.assertIn(dnaSeq.dnaSeq(self.s[self.i:self.j]), self.seq, "Could not find a substring of bases in the generated dnaSeq")
def baseTest(self):
dna = dnaSeq.dnaSeq("ACGTacgtNn")
self.assertIsInstance(dna, dnaSeq.dnaSeq, "Constructor failed, object is not of type dnaSeq")
def test8(): # Make sure index slice returns a sequence
s = dnaSeq.dnaSeq("ACGT")[0:2]
return isinstance(s, dnaSeq.dnaSeq)
def test4():
n = random.randint(50,150)
s = dnaSeq.dnaSeq(randomSeq(n))
return len(s) == n
def setUp(self):
super(SimpleTwoSeqTestCase, self).setUp()
self.n2 = random.randint(30, 400)
self.s2 = randomSeq(self.n2)
self.seq2 = dnaSeq.dnaSeq(self.s2)
def setUp(self):
super(SimpleSeqTestCase, self).setUp()
self.seq = dnaSeq.dnaSeq(self.s)
