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from unittest import TestCase
from numpy import all as alltrue
from numpy import array, transpose
from numpy.testing import assert_equal
from cogent3.core.alignment import Alignment, ArrayAlignment
from cogent3.core.moltype import RNA
from cogent3.core.sequence import ArraySequence, RnaSequence
class AllTests(TestCase):
def setUp(self):
"""setUp method for all tests"""
# named sequences
self.rna1 = RnaSequence("UCAGGG", name="rna1")
self.rna2 = RnaSequence("YCU-RG", name="rna2")
self.rna3 = RnaSequence("CAA-NR", name="rna3")
self.model1 = ArraySequence(
"UCAGGG", name="rna1", alphabet=RNA.alphabets.degen_gapped
)
self.model2 = ArraySequence(
"YCU-RG", name="rna2", alphabet=RNA.alphabets.degen_gapped
)
self.model3 = ArraySequence(
"CAA-NR", name="rna3", alphabet=RNA.alphabets.degen_gapped
)
self.aln = Alignment([self.rna1, self.rna2, self.rna3], moltype=RNA)
self.da = ArrayAlignment(
[self.model1, self.model2, self.model3],
moltype=RNA,
)
# seqs no name
self.nn_rna1 = RnaSequence("UCAGGG")
self.nn_rna2 = RnaSequence("YCU-RG")
self.nn_rna3 = RnaSequence("CAA-NR")
self.nn_model1 = ArraySequence("UCAGGG", alphabet=RNA.alphabets.degen_gapped)
self.nn_model2 = ArraySequence("YCU-RG", alphabet=RNA.alphabets.degen_gapped)
self.nn_model3 = ArraySequence("CAA-NR", alphabet=RNA.alphabets.degen_gapped)
self.nn_aln = Alignment([self.nn_rna1, self.nn_rna2, self.nn_rna3], moltype=RNA)
self.nn_da = ArrayAlignment(
[self.nn_model1, self.nn_model2, self.nn_model3],
moltype=RNA,
)
def test_printing_named_seqs(self):
"""Printing named seqs should work the same on Aln and DenseAln"""
# Note: the newline trailing each sequence is intentional, because
# we want each FASTA-format record to be separated.
exp_lines_general = [">rna1", "UCAGGG", ">rna2", "YCU-RG", ">rna3", "CAA-NR"]
self.assertEqual(str(self.aln), "\n".join(exp_lines_general) + "\n")
self.assertEqual(str(self.da), "\n".join(exp_lines_general) + "\n")
def test_printing_unnamed_seqs(self):
"""Printing unnamed sequences should work the same on Aln and DenseAln"""
exp_lines_gen = [">seq_0", "UCAGGG", ">seq_1", "YCU-RG", ">seq_2", "CAA-NR\n"]
self.assertEqual(str(self.nn_aln), "\n".join(exp_lines_gen))
self.assertEqual(str(self.nn_da), "\n".join(exp_lines_gen))
def test_ArrayAlignment_without_moltype(self):
"""Expect MolType to be picked up from the sequences."""
m1 = ArraySequence("UCAG", alphabet=RNA.alphabets.degen_gapped, name="rna1")
m2 = ArraySequence("CCCR", alphabet=RNA.alphabets.degen_gapped, name="rna2")
da = ArrayAlignment([m1, m2])
exp_lines = [">rna1", "UCAG", ">rna2", "CCCR"]
self.assertEqual(str(da), "\n".join(exp_lines) + "\n")
def test_names(self):
# Should both alignments handle names the same way?
self.assertEqual(self.aln.names, ["rna1", "rna2", "rna3"])
self.assertEqual(self.da.names, ["rna1", "rna2", "rna3"])
# On unnamed sequences the behavior is now the same.
self.assertEqual(self.nn_aln.names, ["seq_0", "seq_1", "seq_2"])
self.assertEqual(self.nn_da.names, ["seq_0", "seq_1", "seq_2"])
def test_seqFreqs(self):
"""seqFreqs should work the same on Alignment and ArrayAlignment"""
RNA.alphabets.degen_gapped.index
# 'UCAGGG'
# 'YCU-RG'
# 'CAA-NR'
expected_counts = {
0: {"U": 1, "C": 1, "A": 1, "G": 3},
1: {"Y": 1, "C": 1, "U": 1, "-": 1, "R": 1, "G": 1},
2: {"C": 1, "A": 2, "-": 1, "N": 1, "R": 1},
}
got1 = self.da.counts_per_seq(allow_gap=True, include_ambiguity=True)
got2 = self.aln.counts_per_seq(allow_gap=True, include_ambiguity=True)
for pos, counts in expected_counts.items():
for char in counts:
self.assertEqual(got1[pos, char], expected_counts[pos][char])
self.assertEqual(got2[pos, char], expected_counts[pos][char])
def test_subset_positions_ArrayAlignment(self):
# because dict order volatile, need to grab the
# the index for ambig characters from the object
# The full data comes from these seqs
# 'UCAGGG'
# 'YCU-RG'
# 'CAA-NR'
get_index = RNA.alphabets.degen_gapped.index
G = get_index("-")
N = get_index("N")
R = get_index("R")
Y = get_index("Y")
full_data = array([[0, 1, 2, 3, 3, 3], [Y, 1, 0, G, R, 3], [1, 2, 2, G, N, R]])
model1 = ArraySequence("UCG", name="rna1", alphabet=RNA.alphabets.degen_gapped)
model2 = ArraySequence("YCG", name="rna2", alphabet=RNA.alphabets.degen_gapped)
model3 = ArraySequence("CAR", name="rna3", alphabet=RNA.alphabets.degen_gapped)
sub_da = ArrayAlignment(
[model1, model2, model3],
moltype=RNA,
)
sub_data = array([[0, 1, 3], [Y, 1, 3], [1, 2, R]])
# First check some data
assert_equal(self.da.array_seqs, full_data)
assert_equal(self.da.array_positions, transpose(full_data))
assert_equal(sub_da.array_seqs, sub_data)
assert_equal(sub_da.array_positions, transpose(sub_data))
obs_sub_da_TP = self.da.take_positions([0, 1, 5])
obs_sub_da_SA = self.da.get_sub_alignment(pos=[0, 1, 5])
# When using the get_sub_alignment method the data is right
self.assertEqual(obs_sub_da_SA, sub_da)
self.assertNotEqual(obs_sub_da_SA, self.da)
assert_equal(obs_sub_da_SA.array_seqs, sub_data)
assert_equal(obs_sub_da_SA.array_positions, transpose(sub_data))
# For the take_positions method: Why does this work
self.assertEqual(obs_sub_da_TP, sub_da)
self.assertNotEqual(obs_sub_da_TP, self.da)
# If the data doesn't match?
assert_equal(obs_sub_da_TP.array_seqs, sub_data)
assert_equal(obs_sub_da_TP.array_positions, transpose(sub_data))
# Shouldn't the __eq__ method check the data at least?
def test_subset_positions_Alignment(self):
rna1 = RnaSequence("UCG", name="rna1")
rna2 = RnaSequence("YCG", name="rna2")
rna3 = RnaSequence("CAR", name="rna3")
sub_aln = Alignment([rna1, rna2, rna3], moltype=RNA)
obs_sub_aln = self.aln.take_positions([0, 1, 5])
self.assertEqual(obs_sub_aln, sub_aln)
self.assertNotEqual(obs_sub_aln, self.aln)
# string representations should be the same. This fails right
# now, because sequence order is not maintained. See separate test.
self.assertEqual(str(obs_sub_aln), str(sub_aln))
def test_take_positions_sequence_order(self):
"""Alignment take_positions should maintain seq order"""
# This works
self.assertEqual(self.da.names, ["rna1", "rna2", "rna3"])
sub_da = self.da.get_sub_alignment(pos=[0, 1, 5])
self.assertEqual(sub_da.names, ["rna1", "rna2", "rna3"])
# seq order not maintained in Alignment
self.assertEqual(self.aln.names, ["rna1", "rna2", "rna3"])
sub_aln = self.aln.take_positions([0, 1, 5])
self.assertEqual(sub_aln.names, ["rna1", "rna2", "rna3"])
def test_subset_seqs_Alignment(self):
rna1 = RnaSequence("UCG", name="rna1")
rna2 = RnaSequence("YCG", name="rna2")
rna3 = RnaSequence("CAR", name="rna3")
sub_aln = Alignment([rna2, rna3], moltype=RNA)
aln = Alignment([rna1, rna2, rna3], moltype=RNA)
obs_sub_aln = aln.take_seqs(["rna2", "rna3"])
self.assertEqual(obs_sub_aln, sub_aln)
self.assertEqual(str(obs_sub_aln), str(sub_aln))
# Selected sequences should be in specified order?
obs_sub_aln_1 = self.aln.take_seqs(["rna3", "rna2"])
obs_sub_aln_2 = self.aln.take_seqs(["rna2", "rna3"])
self.assertNotEqual(str(obs_sub_aln_1), str(obs_sub_aln_2))
def test_subset_seqs_ArrayAlignment(self):
model1 = ArraySequence("UCG", name="rna1", alphabet=RNA.alphabets.degen_gapped)
model2 = ArraySequence("YCG", name="rna2", alphabet=RNA.alphabets.degen_gapped)
model3 = ArraySequence("CAR", name="rna3", alphabet=RNA.alphabets.degen_gapped)
sub_da = ArrayAlignment(
[model1, model2, model3],
moltype=RNA,
)
# take_seqs by name should have the same effect as
# get_sub_alignment by seq idx?
obs_sub_da_TS = self.da.take_seqs(["rna1"])
obs_sub_da_SA = self.da.get_sub_alignment(seqs=[0])
# These two are now the same. Fixed mapping of key to char array.
self.assertEqual(obs_sub_da_TS, obs_sub_da_SA)
self.assertEqual(str(obs_sub_da_TS), str(obs_sub_da_SA))
def test_aln_equality(self):
# When does something compare equal?
self.assertEqual(self.da == self.da, True)
# one sequence less
other_da1 = ArrayAlignment(
[self.model1, self.model2],
moltype=RNA,
)
self.assertEqual(self.da == other_da1, False)
# seqs in different order -- doesn't matter
other_da2 = ArrayAlignment(
[self.model1, self.model3, self.model2],
moltype=RNA,
)
self.assertEqual(self.da == other_da2, True)
# seqs in different encoding -- doesn't matter, only looks at data
other_da3 = ArrayAlignment([self.model1, self.model2, self.model3])
# Should this compare False even though the data is exactly the same?
# The moltype is different...
self.assertEqual(self.da == other_da3, True)
assert alltrue(list(map(alltrue, self.da.array_seqs == other_da3.array_seqs)))
def test_seq_equality(self):
model1 = ArraySequence("UCG", name="rna1", alphabet=RNA.alphabets.degen_gapped)
model2 = ArraySequence("UCG", name="rna1", alphabet=RNA.alphabets.degen_gapped)
# Shouldn't the above two sequences be equal?
self.assertEqual(model1, model2)
# string comparison is True
self.assertEqual(str(model1), str(model2))
def test_seq_ungapping(self):
rna1 = RnaSequence("U-C-A-G-", name="rna1")
model1 = ArraySequence(
"U-C-A-G-", name="rna1", alphabet=RNA.alphabets.degen_gapped
)
self.assertEqual(rna1, "U-C-A-G-")
self.assertEqual(rna1.degap(), "UCAG")
# check is produces the right string from the beginning
self.assertEqual(str(model1), "U-C-A-G-")
assert_equal(model1._data, [0, 4, 1, 4, 2, 4, 3, 4])
# ArraySequence should maybe have the same degap method as normal seq
self.assertEqual(str(model1.degap()), "UCAG")
def test_the_rest_of_ModelSequence(self):
"""The class ArraySequence has 14 methods, but only 2 unittests.
You might want to add some tests there..."""
# note: mostly these are tested in derived classes, for convenience.
pass
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