def test_variant_sequence_add_reads():
vs = VariantSequence(prefix="A", alt="C", suffix="G", reads={"1"})
# adding reads '2' and '3', sometimes multiple times
vs_result = vs.add_reads("2").add_reads("1").add_reads("2").add_reads("3")
expected = VariantSequence(prefix="A",
alt="C",
suffix="G",
reads={"1", "2", "3"})
eq_(vs_result, expected)
def test_variant_sequence_min_coverage():
# 1: AA|C|TT
# 2: AA|C|T
# 3: A|C|TT
reads = [
AlleleRead(prefix="AA", allele="C", suffix="TT", name="1"),
AlleleRead(prefix="AA", allele="C", suffix="T", name="2"),
AlleleRead(prefix="A", allele="C", suffix="TT", name="3")
]
vs = VariantSequence(prefix="AA", alt="C", suffix="TT", reads=reads)
eq_(vs.min_coverage(), 2)
def test_variant_sequence_mean_coverage():
# 1: AA|C|TT
# 2: AA|C|T
# 3: A|C|TT
reads = [
AlleleRead(prefix="AA", allele="C", suffix="TT", name="1"),
AlleleRead(prefix="AA", allele="C", suffix="T", name="2"),
AlleleRead(prefix="A", allele="C", suffix="TT", name="3")
]
vs = VariantSequence(prefix="AA", alt="C", suffix="TT", reads=reads)
# count the number of times a nucleotide in the sequences above
# is contained in a read
expected_mean_coverage = (2 + 3 + 3 + 3 + 2) / 5
eq_(vs.mean_coverage(), expected_mean_coverage)
def test_variant_sequence_trim_by_coverage():
reads = [
AlleleRead(prefix="AA", allele="C", suffix="T", name="1"),
AlleleRead(prefix="A", allele="C", suffix="T", name="2")
]
vs = VariantSequence(prefix="AA", alt="C", suffix="T", reads=reads)
# every nucleotide is spanned by one read
eq_(vs.trim_by_coverage(1), vs)
vs_expected_trim_by_2 = VariantSequence(prefix="A",
alt="C",
suffix="T",
reads=reads)
eq_(vs.trim_by_coverage(2), vs_expected_trim_by_2)
def test_variant_sequence_len():
vs = VariantSequence(
prefix="AA",
alt="C",
suffix="TT",
reads=[])
eq_(len(vs), 5)
def test_variant_sequence_overlaps():
# AAA|GG|TT
vs_3A = VariantSequence(
prefix="AAA",
alt="GG",
suffix="TT",
reads=[
AlleleRead(
prefix="AAA", allele="GG", suffix="TT", name="1")])
# AA|GG|TT
vs_2A = VariantSequence(
prefix="AA",
alt="GG",
suffix="TT",
reads=[
AlleleRead(
prefix="AA", allele="GG", suffix="TT", name="1")])
for min_overlap_size in [1, 2, 3, 4, 5, 6]:
assert vs_3A.left_overlaps(vs_2A, min_overlap_size=min_overlap_size), \
"Expected %s to overlap %s from left (min overlap size=%d)" % (
vs_3A, vs_2A, min_overlap_size)
assert not vs_2A.left_overlaps(vs_3A, min_overlap_size=min_overlap_size), \
"Expected %s to not overlap %s from left (min overlap size=%d)" % (
vs_2A, vs_3A, min_overlap_size)
assert not vs_3A.left_overlaps(vs_2A, min_overlap_size=7), \
"Unexpected overlap between %s and %s for min_overlap_size=7" % (
vs_3A, vs_2A)
def test_variant_sequence_read_names():
vs = VariantSequence(
prefix="A",
alt="C",
suffix="T",
reads=[
AlleleRead(prefix="A", allele="C", suffix="T", name="1"),
AlleleRead(prefix="A", allele="C", suffix="T", name="2")])
eq_(vs.read_names, {"1", "2"})
def test_variant_sequence_combine():
vs1 = VariantSequence(prefix="A", alt="C", suffix="GG", reads={"1"})
vs2 = VariantSequence(prefix="AA", alt="C", suffix="GG", reads={"2"})
vs_result_1_to_2 = vs1.combine(vs2)
expected = VariantSequence(prefix="AA", alt="C", suffix="GG", reads={"1", "2"})
eq_(vs_result_1_to_2, expected)
# shouldn't matter which sequence is first as an argument to the combine
# function
vs_result_2_to_1 = vs2.combine(vs1)
eq_(vs_result_2_to_1, expected)
def test_variant_sequence_contains():
# AA|C|T
vs_longer_prefix = VariantSequence(
prefix="AA",
alt="C",
suffix="T",
reads=[
AlleleRead(
prefix="AA", allele="C", suffix="T", name="longer_prefix")])
# A|C|TT
vs_longer_suffix = VariantSequence(
prefix="A",
alt="C",
suffix="TT",
reads=[
AlleleRead(
prefix="A", allele="C", suffix="TT", name="longer_suffix")])
# A|C|T
vs_short = VariantSequence(
prefix="A",
alt="C",
suffix="T",
reads=[
AlleleRead(
prefix="A", allele="C", suffix="T", name="short")])
# two longer sequences contain the shorter subsequence
assert vs_longer_prefix.contains(vs_short), \
"Expected %s to contain %s" % (vs_longer_prefix, vs_short)
assert vs_longer_suffix.contains(vs_short), \
"Expected %s to contain %s" % (vs_longer_suffix, vs_short)
# other pairs do not contain each other
assert not vs_longer_prefix.contains(vs_longer_suffix), \
"Expected %s to not contain %s" % (vs_longer_prefix, vs_longer_suffix)
assert not vs_longer_suffix.contains(vs_longer_prefix), \
"Expected %s to not contain %s" % (vs_longer_suffix, vs_longer_prefix)
assert not vs_short.contains(vs_longer_prefix), \
"Expected %s to not contain %s" % (vs_short, vs_longer_prefix)
assert not vs_short.contains(vs_longer_suffix), \
"Expected %s to not contain %s" % (vs_short, vs_longer_suffix)
# Sequences above has 'C' allele whereas this one has 'G'
# A|G|T
vs_different_allele = VariantSequence(
prefix="A",
alt="G",
suffix="T",
reads=[
AlleleRead(
prefix="A", allele="G", suffix="T", name="short")])
for vs in [vs_longer_suffix, vs_longer_prefix, vs_short]:
assert not vs.contains(vs_different_allele), \
"Expected %s to not contain %s" % (vs, vs_different_allele)
assert not vs_different_allele.contains(vs), \
"Expected %s to not contain %s" % (vs_different_allele, vs)