def test_reverse_complement(self):
s = dna("GGGGaaaaaaaatttatatat")
rc = s.reverse_complement()
self.assertEqual(rc, dna("atatataaattttttttCCCC"))
self.assertEqual(
dna("ACGTRYSWKMBDHVN").reverse_complement(),
dna("NBDHVKMWSRYACGT"))
self.assertRaises(ValueError, protein("G").reverse_complement)
def test_reverse_complement(self):
s = dna('GGGGaaaaaaaatttatatat')
rc = s.reverse_complement()
self.assertEqual(rc, dna('atatataaattttttttCCCC'))
self.assertEqual(
dna('ACGTRYSWKMBDHVN').reverse_complement(),
dna('NBDHVKMWSRYACGT'))
self.assertRaises(ValueError, protein('G').reverse_complement)
def test_shortcuts(self):
protein('gGGGGG-PPPPP')
dna('ACGTRYSWKMBDHVN')
dna('t')
dna('actgta')
dna('acgtrysw-kmb-dhvn')
rna('ACUUUUU')
def test_shortcuts(self):
protein("gGGGGG-PPPPP")
dna("ACGTRYSWKMBDHVN")
dna("t")
dna("actgta")
dna("acgtrysw-kmb-dhvn")
rna("ACUUUUU")
def test_bad_mask():
with pytest.raises(ValueError):
dna('AAaaaaAAA').mask(mask='ABC')
def test_slice(self):
s1 = dna('ACGTRYSWKMBDHVN')
s2 = s1[4:6]
assert s2 == dna('RY')
def test_casechange(self):
s1 = dna('ACGTRYSWKMBDHVN')
s2 = s1.lower().upper()
self.assertEqual(s1, s2)
def test_mask(self):
s = dna('AAaaaaAAA').mask()
self.assertEqual(str(s), 'AAXXXXAAA')
def test_translate(self):
s = dna('GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA')
p = s.translate()
self.assertEqual(str(p), 'AIVMGR*KGAR')
p.back_translate()
def test_bad_mask():
with pytest.raises(ValueError):
dna("AAaaaaAAA").mask(mask="ABC")
def test_slice(self):
s1 = dna("ACGTRYSWKMBDHVN")
s2 = s1[4:6]
assert s2 == dna("RY")
def test_mask(self):
s = dna("AAaaaaAAA").mask()
self.assertEqual(str(s), "AAXXXXAAA")