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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import numpy as np
import numpy.testing as npt
from skbio.alignment._path import PairAlignPath, AlignPath, _run_length_encode
from skbio.alignment import TabularMSA
from skbio.sequence import DNA
class TestAlignPath(unittest.TestCase):
def test_init(self):
# test 1-D starts vector
with self.assertRaises(TypeError, msg="`starts` must be a 1-D vector."):
path = AlignPath(lengths=[1, 2, 3], states=[1, 2, 3], starts=[[0], [0]])
# test states and starts matching
with self.assertRaises(ValueError, msg="Sizes of `starts` and `states` do not "
"match."):
path = AlignPath(lengths=[1, 2, 3], states=[1, 2, 3],
starts=[0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
def test_lengths(self):
obs = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0]).lengths
npt.assert_array_equal(obs, np.array([3, 2, 5, 1, 4, 3, 2], dtype=np.int64))
def test_states(self):
obs = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0]).states
npt.assert_array_equal(obs, np.array([[0, 2, 0, 6, 0, 1, 0]], dtype=np.uint8))
def test_starts(self):
obs = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0]).starts
npt.assert_array_equal(obs, np.array([0, 0, 0], dtype=np.int64))
def test_shape(self):
obs = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0]).shape
self.assertEqual(obs.sequence, 3)
self.assertEqual(obs.position, 20)
def test_to_bits(self):
path = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0])
exp = np.array(([0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0]))
obs = path.to_bits()
npt.assert_array_equal(obs, exp)
def test_from_bits(self):
# test 1D base case, less than 8 sequences
bits = np.array(([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]))
exp = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0])
obs = AlignPath.from_bits(bits)
npt.assert_array_equal(obs.lengths, exp.lengths)
npt.assert_array_equal(obs.states, exp.states)
# test starts parameter
starts = [1, 2, 3]
obs = AlignPath.from_bits(bits, starts)
npt.assert_array_equal(obs.lengths, exp.lengths)
npt.assert_array_equal(obs.states, exp.states)
npt.assert_array_equal(obs.starts, starts)
# test 2D base case, more than 8 sequences
rng = np.random.default_rng(seed=42)
bits = rng.choice([0, 1], size=(10, 10), p=[0.85, 0.15])
exp = AlignPath(lengths=[1, 1, 1, 1, 1, 1, 3, 1],
states=[[0, 10, 133, 4, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 2]],
starts=[0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
obs = AlignPath.from_bits(bits)
npt.assert_array_equal(obs.lengths, exp.lengths)
npt.assert_array_equal(obs.states, exp.states)
def test_from_tabular(self):
msa = ('CGGTCGTAACGCGTA---CA',
'CAG--GTAAG-CATACCTCA',
'CGGTCGTCAC-TGTACACTA')
tabular = TabularMSA([DNA(x) for x in msa])
path = AlignPath.from_tabular(tabular)
lengths = [3, 2, 5, 1, 4, 3, 2]
states = [0, 2, 0, 6, 0, 1, 0]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
def test_to_indices(self):
# test gap = -1
path = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0])
exp = np.array([[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1, -1,
15, 16],
[0, 1, 2, -1, -1, 3, 4, 5, 6, 7, -1, 8, 9, 10, 11, 12, 13, 14,
15, 16],
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, -1, 10, 11, 12, 13, 14, 15, 16,
17, 18]])
obs = path.to_indices()
npt.assert_array_equal(obs, exp)
# test gap = 'del'
exp = np.array([[0, 1, 2, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16],
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16],
[0, 1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18]])
obs = path.to_indices(gap='del')
npt.assert_array_equal(obs, exp)
# test gap = 'mask'
exp = np.ma.array(data=[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 14, 14, 14, 15, 16],
[0, 1, 2, 2, 2, 3, 4, 5, 6, 7, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16],
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18]],
mask=[[False, False, False, False, False, False, False,
False, False, False, False, False, False, False,
False, True, True, True, False, False],
[False, False, False, True, True, False, False,
False, False, False, True, False, False, False,
False, False, False, False, False, False],
[False, False, False, False, False, False, False,
False, False, False, True, False, False, False,
False, False, False, False, False, False]],
fill_value=999999)
obs = path.to_indices(gap='mask')
npt.assert_array_equal(obs, exp)
# test with starts as non-zero
path = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[1, 35, 28])
exp = np.array([[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, -1, -1, -1,
16, 17],
[35, 36, 37, -1, -1, 38, 39, 40, 41, 42, -1, 43, 44, 45, 46,
47, 48, 49, 50, 51],
[28, 29, 30, 31, 32, 33, 34, 35, 36, 37, -1, 38, 39, 40, 41,
42, 43, 44, 45, 46]])
obs = path.to_indices()
npt.assert_array_equal(obs, exp)
# test 'del' with non-zero starts
exp = np.array([[1, 2, 3, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17],
[35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51],
[28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46]])
obs = path.to_indices(gap='del')
npt.assert_array_equal(obs, exp)
# test 'mask' with non-zero starts
exp = np.ma.array(data=[[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 15, 15, 15, 16, 17],
[35, 36, 37, 37, 37, 38, 39, 40, 41, 42, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51],
[28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46]],
mask=[[False, False, False, False, False, False, False,
False, False, False, False, False, False, False,
False, True, True, True, False, False],
[False, False, False, True, True, False, False,
False, False, False, True, False, False, False,
False, False, False, False, False, False],
[False, False, False, False, False, False, False,
False, False, False, True, False, False, False,
False, False, False, False, False, False]],
fill_value=999999)
obs = path.to_indices(gap='mask')
npt.assert_array_equal(obs, exp)
# test invalid gap
with self.assertRaises(TypeError,
msg="Gap must be an integer, np.nan, np.inf, 'del', "
"or 'mask'."):
path.to_indices(gap="no")
def test_from_indices(self):
# test no mask
indices = np.array([[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1,
-1, 15, 16],
[0, 1, 2, -1, -1, 3, 4, 5, 6, 7, -1, 8, 9, 10, 11, 12, 13,
14, 15, 16],
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, -1, 10, 11, 12, 13, 14, 15,
16, 17, 18]])
path = AlignPath.from_indices(indices)
lengths = [3, 2, 5, 1, 4, 3, 2]
states = [0, 2, 0, 6, 0, 1, 0]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
# test masked array
masked = np.ma.array(indices, mask=(indices == -1))
path = AlignPath.from_indices(masked, gap="mask")
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
# test non-zero indices
indices = np.array([[25, 26, -1, -1, 27, 28, 29, 30],
[-1, 79, 80, 81, 82, 83, 84, -1]])
path = AlignPath.from_indices(indices)
lengths = [1, 1, 2, 3, 1]
states = [2, 0, 1, 0, 2]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
npt.assert_array_equal(path.starts, [25, 79])
# test masked array and non-zero indices
# TODO
# test indices all gaps
indices = np.array([[25, 26, -1, -1, 27, 28, 29, 30],
[-1, -1, -1, -1, -1, -1, -1, -1]])
path = AlignPath.from_indices(indices)
lengths = [2, 2, 4]
states = [2, 3, 2]
starts = [25, -1]
npt.assert_array_equal(path.lengths, lengths)
npt.assert_array_equal(np.squeeze(path.states), states)
npt.assert_array_equal(path.starts, starts)
def test_to_coordinates(self):
# test base case
exp = np.array([[0, 3, 5, 10, 11, 15, 15, 17],
[0, 3, 3, 8, 8, 12, 15, 17],
[0, 3, 5, 10, 10, 14, 17, 19]])
path = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[0, 0, 0])
obs = path.to_coordinates()
npt.assert_array_equal(obs, exp)
# test non-zero starts
exp = np.array([[2, 5, 7, 12, 13, 17, 17, 19],
[512, 515, 515, 520, 520, 524, 527, 529],
[28, 31, 33, 38, 38, 42, 45, 47]])
path = AlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 6, 0, 1, 0],
starts=[2, 512, 28])
obs = path.to_coordinates()
npt.assert_array_equal(obs, exp)
def test_from_coordinates(self):
# test base case
coords = np.array([[0, 3, 5, 10, 11, 15, 15, 17],
[0, 3, 3, 8, 8, 12, 15, 17],
[0, 3, 5, 10, 10, 14, 17, 19]])
path = AlignPath.from_coordinates(coords)
lengths = [3, 2, 5, 1, 4, 3, 2]
states = [0, 2, 0, 6, 0, 1, 0]
starts = [0, 0, 0]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
npt.assert_array_equal(starts, path.starts)
# test non-zero starts
coords = np.array([[2, 5, 7, 12, 13, 17, 17, 19],
[512, 515, 515, 520, 520, 524, 527, 529],
[28, 31, 33, 38, 38, 42, 45, 47]])
path = AlignPath.from_coordinates(coords)
lengths = [3, 2, 5, 1, 4, 3, 2]
states = [0, 2, 0, 6, 0, 1, 0]
starts = [2, 512, 28]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
npt.assert_array_equal(starts, path.starts)
class TestPairAlignPath(unittest.TestCase):
def test_from_cigar(self):
# test valid cigar with no = or X
cigar = "3M42I270M32D"
path = PairAlignPath.from_cigar(cigar)
lengths = [3, 42, 270, 32]
states = [0, 1, 0, 2]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
# test valid cigar with = or X
cigar = "3M42I270M23X663=32D24X43="
path = PairAlignPath.from_cigar(cigar)
lengths = [3, 42, 956, 32, 67]
states = [0, 1, 0, 2, 0]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
# test empty cigar string
with self.assertRaises(ValueError, msg="CIGAR string must not be empty."):
PairAlignPath.from_cigar("")
# test invalid cigar string
with self.assertRaises(ValueError, msg="Invalid characters in CIGAR string."):
PairAlignPath.from_cigar("23M45B13X")
# test valid cigar with no 1's
cigar = "MID12MI"
path = PairAlignPath.from_cigar(cigar)
lengths = [1, 1, 1, 12, 1]
states = [0, 1, 2, 0, 1]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
# test cigar with all possible valid codes
cigar = "1M2I3D4P5=6X7N8S9H"
path = PairAlignPath.from_cigar(cigar)
lengths = [1, 2, 3, 4, 11, 7, 8, 9]
states = [0, 1, 2, 3, 0, 2, 1, 3]
npt.assert_array_equal(lengths, path.lengths)
npt.assert_array_equal(states, np.squeeze(path.states))
def test_to_cigar(self):
# test base case
lengths = [1, 2, 3, 4, 50, 234]
gaps = [1, 0, 2, 1, 0, 1]
ExamplePairAlignPath = PairAlignPath(lengths=lengths,
states=gaps,
starts=[0, 0])
obs = ExamplePairAlignPath.to_cigar()
exp = "1I2M3D4I50M234I"
self.assertEqual(obs, exp)
# test if seqs are provided
seq1 = "-AATCT----" + "C"*50 + "-"*234
seq2 = "TAC---GGCC" + "C"*20 + "A"*264
seqs = [DNA(seq1), DNA(seq2)]
obs = ExamplePairAlignPath.to_cigar(seqs=seqs)
exp = "1I2X3D4I5X18=27X234I"
self.assertEqual(obs, exp)
# test if alignment has two gaps in same position
lengths = [1, 2, 3, 4, 1]
gaps = [1, 0, 2, 1, 3]
path = PairAlignPath(lengths=lengths, states=gaps, starts=[0, 0])
obs = path.to_cigar()
exp = "1I2M3D4I1P"
self.assertEqual(obs, exp)
# two gaps with seqs provided
seq1 = '-ATCGC-----'
seq2 = 'GTA---ATTA-'
seqs = [DNA(seq1), DNA(seq2)]
obs = path.to_cigar(seqs=seqs)
exp = "1I1X1=3D4I1P"
self.assertEqual(obs, exp)
# test sequences as strings
seq1 = '-ATCGC-----'
seq2 = 'GTA---ATTA-'
seqs = [seq1, seq2]
obs = path.to_cigar(seqs=seqs)
exp = "1I1X1=3D4I1P"
self.assertEqual(obs, exp)
# test invalid sequence input
seq1 = 1
seq2 = 'GTA---ATTA-'
seqs = [seq1, seq2]
with self.assertRaises(TypeError,
msg="`seqs` must be of type string or Sequence object."):
obs = path.to_cigar(seqs=seqs)
def test_from_bits(self):
# test base case
bits = np.array(([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]))
exp = PairAlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 2, 0, 1, 0],
starts=[0, 0])
obs = PairAlignPath.from_bits(bits)
npt.assert_array_equal(obs.lengths, exp.lengths)
npt.assert_array_equal(obs.states, exp.states)
# test empty bit array
bits = np.array(([], []))
with self.assertRaises(TypeError,
msg="Input 'bits' must be a non-empty 2D numpy array."):
PairAlignPath.from_bits(bits)
# test 1D bit array
bits = np.array([0, 0, 1])
with self.assertRaises(TypeError,
msg="Input 'bits' must be a non-empty 2D numpy array."):
PairAlignPath.from_bits(bits)
# test array with invalid values
bits = np.array(([1, 2, 3], [0, 5, 1]))
with self.assertRaises(ValueError,
msg="Input 'bits' must contain only zeros and ones."):
PairAlignPath.from_bits(bits)
# test non numpy array input
bits = [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
exp = PairAlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 2, 0, 1, 0],
starts=[0, 0, 0])
obs = PairAlignPath.from_bits(bits)
npt.assert_array_equal(obs.lengths, exp.lengths)
npt.assert_array_equal(obs.states, exp.states)
def test_to_bits(self):
# test input with invalid values
with self.assertRaises(ValueError,
msg="For pairwise alignment, `states` must only "
"contain zeros, ones, twos, or threes."):
PairAlignPath(lengths=[1, 2, 3], states=[1, 2, 4], starts=[0, 0]).to_bits()
# test base case
path = PairAlignPath(lengths=[3, 2, 5, 1, 4, 3, 2],
states=[0, 2, 0, 2, 0, 1, 0],
starts=[0, 0])
exp = np.array(([0, 0, 0, 0, 0, 1, 0], [0, 1, 0, 1, 0, 0, 0]))
obs = path.to_bits()
npt.assert_array_equal(np.squeeze(obs), exp)
def test_run_length_encode(self):
obs = _run_length_encode("ABBCCCDDDD")
exp = "1A2B3C4D"
self.assertEqual(obs, exp)
if __name__ == "__main__":
unittest.main()
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