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from unittest import TestCase
import numpy
from cogent3 import DNA, make_unaligned_seqs
from cogent3.core.alignment import Aligned, ArrayAlignment
from cogent3.core.location import IndelMap
from cogent3.draw.dotplot import Dotplot, _convert_input, get_align_coords
class TestUtilFunctions(TestCase):
def test_len_seq(self):
"""returns length of sequence minus gaps"""
m, seq = DNA.make_seq("ACGGT--A").parse_out_gaps()
self.assertEqual(m.parent_length, 6)
def test_convert_input(self):
"""converts data for dotplotting"""
m, seq = DNA.make_seq("ACGGT--A").parse_out_gaps()
aligned_seq = Aligned(m, seq)
mapped_gap, new_seq = _convert_input(aligned_seq, None)
self.assertIs(new_seq.moltype, DNA)
self.assertIs(mapped_gap, m)
self.assertIs(new_seq, seq)
mapped_gap, new_seq = _convert_input("ACGGT--A", DNA)
self.assertEqual(str(mapped_gap), str(m))
self.assertEqual(str(new_seq), str(seq))
def test_get_align_coords(self):
"""correctly returns the alignment coordinates"""
# 01234 5
# ACGGT--A
# 012345
# --GGTTTA
m1, seq1 = DNA.make_seq("ACGGT--A").parse_out_gaps()
m2, seq2 = DNA.make_seq("--GGTTTA").parse_out_gaps()
path = get_align_coords(m1, m2)
expect = [2, 4, None, 5, 5], [0, 2, None, 5, 5]
self.assertEqual(path.get_coords(), expect)
# we have no gaps, so coords will be None
m1, s1 = seq1.parse_out_gaps()
m2, s2 = seq2.parse_out_gaps()
path = get_align_coords(m1, m2)
self.assertEqual(path.get_coords(), ([], []))
# unless we indicate the seqs came from an Alignment
m1, seq1 = DNA.make_seq("ACGGTTTA").parse_out_gaps()
m2, seq2 = DNA.make_seq("GGGGTTTA").parse_out_gaps()
paths = get_align_coords(m1, m2, aligned=True)
# display ranges are inclusive, thus length - 1
self.assertEqual(paths.get_coords(), ([0, len(seq1) - 1], [0, len(seq1) - 1]))
# raises an exception if the Aligned seqs are different lengths
m1, seq1 = DNA.make_seq("ACGGTTTA").parse_out_gaps()
m2, seq2 = DNA.make_seq("GGGGTT").parse_out_gaps()
with self.assertRaises(AssertionError):
get_align_coords(m1, m2, aligned=True)
def test_display2d(self):
"""correctly constructs a Display2d"""
# 111111
# 0123456789012345
# 11111
# 012345678901234
# -TGATGTAAGGTAGTT
# CTGG---AAG---GGT
# 0123 456 789
# check alignment coords are correct
dp = Dotplot("-TGATGTAAGGTAGTT", "CTGG---AAG---GGT", is_aligned=True, window=5)
expect = [0, 2, None, 6, 8, None, 12, 14], [1, 3, None, 4, 6, None, 7, 9]
self.assertEqual(dp._aligned_coords.get_coords(), expect)
dp._build_fig()
traces = dp.traces
self.assertEqual(len(traces), 2) # no rev complement
# we nudge alignment coordinates by 0.2 on x-axis
expect = [0.2, 2.2, None, 6.2, 8.2, None, 12.2, 14.2]
self.assertEqual(traces[-1].x, expect)
self.assertEqual(traces[-1].name, "Alignment")
self.assertEqual(traces[0].name, "+ strand")
# check + strand has integers/float/None
expect = {int, float, type(None), numpy.int64, numpy.int32}
for trace in traces:
for axis in "xy":
got = {type(v) for v in trace[axis]}
self.assertTrue(got <= expect, trace[axis])
def test_display2d_rc(self):
"""correctly constructs a Display2d with rc"""
# fail if specify rc but incompatible moltype
seqs = make_unaligned_seqs(
{"a": "-TGATGTAAGGTAGTT", "b": "CTGG---AAG---GGT"}, moltype="text"
)
with self.assertRaises(TypeError):
Dotplot(*seqs.seqs, is_aligned=True, window=5, rc=True)
seqs = make_unaligned_seqs(
{"a": "-TGATGTAAGGTAGTT", "b": "CTGG---AAG---GGT"}, moltype="dna"
)
dp = Dotplot(*seqs.seqs, is_aligned=True, window=5, rc=True)
dp._build_fig()
traces = dp.traces
self.assertEqual(len(traces), 3)
self.assertEqual(traces[1].name, "- strand")
def test_align_without_gaps(self):
"""dotplot has alignment coordinates if no gaps"""
aln = ArrayAlignment(
{"seq1": "ACGG", "seq2": "CGCA", "seq3": "CCG-"}, moltype="dna"
)
aln_plot = aln.dotplot("seq1")
self.assertNotEqual(aln_plot._aligned_coords, None)
def test_dotplot_seqcoll(self):
"""dotplot sequence collection, gaps are removed"""
seqs = make_unaligned_seqs(
{"seq1": "ACGG", "seq2": "CGCA", "seq3": "CCG-"}, moltype="dna"
)
dp = seqs.dotplot("seq1", "seq3")
self.assertNotEqual(dp._aligned_coords, None)
self.assertEqual(len(dp.seq1), 4)
self.assertEqual(len(dp.seq2), 3)
def test_dotplot_single(self):
"""dotplot with single sequence should not fail"""
seqs = make_unaligned_seqs({"seq1": "CACACCACTGCAGTCGGATAGACC"}, moltype="dna")
dp = seqs.dotplot(window=4, threshold=4, rc=True)
self.assertEqual(dp.seq1, dp.seq2)
def test_dotplot_missing(self):
"""fail if a sequence name not present"""
seqs = make_unaligned_seqs(
{"seq1": "ACGG", "seq2": "CGCA", "seq3": "CCG-"}, moltype="dna"
)
with self.assertRaises(ValueError):
_ = seqs.dotplot("seq1", "seq5")
with self.assertRaises(ValueError):
_ = seqs.dotplot("seq5", "seq1")
with self.assertRaises(ValueError):
_ = seqs.dotplot("seq5", "seq6")
def test_dotplot_title(self):
"""setting empty string title works"""
seqs = make_unaligned_seqs(
{"seq1": "ACGG", "seq2": "CGCA", "seq3": "CCG-"}, moltype="dna"
)
dp = seqs.dotplot("seq1", "seq3", title="")
self.assertEqual(dp.figure.layout.title, "")
def test_aligned_path():
imap1 = IndelMap(
gap_pos=numpy.array([4, 5, 6, 8, 10]),
cum_gap_lengths=numpy.array([6, 10, 12, 14, 15]),
parent_length=10,
)
imap2 = IndelMap(
gap_pos=numpy.array([], dtype=int),
cum_gap_lengths=numpy.array([], dtype=int),
parent_length=25,
)
coords = get_align_coords(imap1, imap2)
assert coords.get_coords() == (
[0, 3, None, 4, 4, None, 5, 5, None, 6, 7, None, 8, 9],
[0, 3, None, 10, 10, None, 15, 15, None, 18, 19, None, 22, 23],
)
def test_dotplot_unaligned():
seqs = make_unaligned_seqs(dict(a="ACGGT", b="CGTT"), moltype="dna")
dp = seqs.dotplot(window=3, k=2)
assert dp
# trigger building traces
_ = dp.figure
assert len(dp.traces[0].x)
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