def test_init(self):
"""JointEnumeration init should work as expected"""
#should work for alphabet object
a = JointEnumeration([DnaBases, RnaBases])
self.assertEqual(len(a), 16)
self.assertEqual(a.Shape, (4,4))
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
self.assertEqual(a._sub_enum_factors, array([[4],[1]]))
#should work for arbitrary sequences
a = JointEnumeration(['TCAG', 'UCAG'])
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
self.assertEqual(a._sub_enum_factors, array([[4],[1]]))
#should work for different length sequences
a = JointEnumeration(['TCA', 'UCAG'])
self.assertEqual(a.Shape, (3,4))
self.assertEqual(len(a), 12)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('A','G'))
self.assertEqual(a._sub_enum_factors, \
array([[4],[1]])) #note: _not_ [3,1]
def test_init(self):
"""JointEnumeration init should work as expected"""
#should work for alphabet object
a = JointEnumeration([DnaBases, RnaBases])
self.assertEqual(len(a), 16)
self.assertEqual(a.Shape, (4,4))
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
self.assertEqual(a._sub_enum_factors, array([[4],[1]]))
#should work for arbitrary sequences
a = JointEnumeration(['TCAG', 'UCAG'])
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
self.assertEqual(a._sub_enum_factors, array([[4],[1]]))
#should work for different length sequences
a = JointEnumeration(['TCA', 'UCAG'])
self.assertEqual(a.Shape, (3,4))
self.assertEqual(len(a), 12)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('A','G'))
self.assertEqual(a._sub_enum_factors, \
array([[4],[1]])) #note: _not_ [3,1]
def test_toString(self):
"""CharAlphabet toString should convert an input array to string"""
r = CharAlphabet('UCAG')
self.assertEqual(r.toString(array([[0,0,1],[0,3,2]], 'B')), 'UUC\nUGA')
#should work with single seq
self.assertEqual(r.toString(array([[0,0,1,0,3,2]], 'B')), 'UUCUGA')
#should work with single seq
self.assertEqual(r.toString(array([0,0,1,0,3,2], 'B')), 'UUCUGA')
#should work with empty seq
self.assertEqual(r.toString(array([], 'B')), '')
def test_toString(self):
"""CharAlphabet toString should convert an input array to string"""
r = CharAlphabet('UCAG')
self.assertEqual(r.toString(array([[0,0,1],[0,3,2]], 'B')), 'UUC\nUGA')
#should work with single seq
self.assertEqual(r.toString(array([[0,0,1,0,3,2]], 'B')), 'UUCUGA')
#should work with single seq
self.assertEqual(r.toString(array([0,0,1,0,3,2], 'B')), 'UUCUGA')
#should work with empty seq
self.assertEqual(r.toString(array([], 'B')), '')
def test_init(self):
"""CharAlphabet init should make correct translation tables"""
r = CharAlphabet('UCAG')
i2c, c2i = r._indices_to_chars, r._chars_to_indices
s = array([0,0,1,0,3,2], 'b').tostring()
self.assertEqual(s.translate(i2c), 'UUCUGA')
self.assertEqual('UUCUGA'.translate(c2i), '\000\000\001\000\003\002')
def test_init(self):
"""CharAlphabet init should make correct translation tables"""
r = CharAlphabet('UCAG')
i2c, c2i = r._indices_to_chars, r._chars_to_indices
s = array([0,0,1,0,3,2], 'b').tostring()
self.assertEqual(s.translate(i2c), 'UUCUGA')
self.assertEqual('UUCUGA'.translate(c2i), '\000\000\001\000\003\002')
def test_unpackArrays(self):
"""JointEnumeration unpackArrays should return correct arrays."""
a = JointEnumeration(['xyz', 'abcd', 'ef'])
v = [7, 15, 18, 0]
result = a.unpackArrays(v)
self.assertEqual(result,
array([[0, 1, 2, 0], [3, 3, 1, 0], [1, 1, 0, 0]]))
def test_unpackArrays(self):
"""JointEnumeration unpackArrays should return correct arrays."""
a = JointEnumeration(['xyz', 'abcd', 'ef'])
v = [7,15,18,0]
result = a.unpackArrays(v)
self.assertEqual(result, array([[0,1,2,0],[3,3,1,0], [1,1,0,0]]))
def test_toChars(self):
"""CharAlphabet toChars should convert an input array to chars"""
r = CharAlphabet('UCAG')
c = r.toChars(array([[0,0,1],[0,3,2]], 'B'))
self.assertEqual(c, \
array(['UUC','UGA'], 'c'))
def test_fromArray(self):
"""CharAlphabet fromArray should return correct array"""
r = CharAlphabet('UCAG')
self.assertEqual(r.fromArray(array(['UUC','UGA'], 'c')), \
array([[0,0,1],[0,3,2]], 'B'))
def test_fromString(self):
"""CharAlphabet fromString should return correct array"""
r = CharAlphabet('UCAG')
self.assertEqual(r.fromString('UUCUGA'), array([0,0,1,0,3,2],'B'))
def test_counts(self):
"""Enumeration counts should count freqs in array"""
a = DnaBases
f = array([[0,0,1,0,0,3]])
self.assertEqual(a.counts(f), array([4,1,0,1]))
#check that it works with byte array
f = array([[0,0,1,0,0,3]], 'B')
self.assertEqual(a.counts(f), array([4,1,0,1]))
#should ignore out-of-bounds items
g = [0,4]
self.assertEqual(a.counts(g), array([1,0,0,0]))
#make sure it works for long sequences, i.e. no wraparound at 255
h = [0, 3] * 70000
self.assertEqual(a.counts(h), array([70000,0,0,70000]))
h2 = array(h).astype('B')
self.assertEqual(a.counts(h2), array([70000,0,0,70000]))
i = array([0,3] * 75000)
self.assertEqual(a.counts(i), array([75000,0,0,75000]))
#make sure it works for long _binary_ sequences, e.g. the results
#of array comparisons.
a = array([0,1,2,3]*10000)
b = array([0,0,0,0]*10000)
same = (a==b)
def test_toChars(self):
"""CharAlphabet toChars should convert an input array to chars"""
r = CharAlphabet('UCAG')
c = r.toChars(array([[0,0,1],[0,3,2]], 'B'))
self.assertEqual(c, \
array(['UUC','UGA'], 'c'))
def test_fromArray(self):
"""CharAlphabet fromArray should return correct array"""
r = CharAlphabet('UCAG')
self.assertEqual(r.fromArray(array(['UUC','UGA'], 'c')), \
array([[0,0,1],[0,3,2]], 'B'))
def test_fromString(self):
"""CharAlphabet fromString should return correct array"""
r = CharAlphabet('UCAG')
self.assertEqual(r.fromString('UUCUGA'), array([0,0,1,0,3,2],'B'))
def test_counts(self):
"""Enumeration counts should count freqs in array"""
a = DnaBases
f = array([[0,0,1,0,0,3]])
self.assertEqual(a.counts(f), array([4,1,0,1]))
#check that it works with byte array
f = array([[0,0,1,0,0,3]], 'B')
self.assertEqual(a.counts(f), array([4,1,0,1]))
#should ignore out-of-bounds items
g = [0,4]
self.assertEqual(a.counts(g), array([1,0,0,0]))
#make sure it works for long sequences, i.e. no wraparound at 255
h = [0, 3] * 70000
self.assertEqual(a.counts(h), array([70000,0,0,70000]))
h2 = array(h).astype('B')
self.assertEqual(a.counts(h2), array([70000,0,0,70000]))
i = array([0,3] * 75000)
self.assertEqual(a.counts(i), array([75000,0,0,75000]))
#make sure it works for long _binary_ sequences, e.g. the results
#of array comparisons.
a = array([0,1,2,3]*10000)
b = array([0,0,0,0]*10000)
same = (a==b)