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_collapse_substrings():
# AAA|C|GGG
vs_longer = VariantSequence(prefix="AAA",
alt="C",
suffix="GGG",
reads={"1"})
# AAA|C|GG
vs_shorter = VariantSequence(prefix="AAA",
alt="C",
suffix="GG",
reads={"2"})
vs_unrelated = VariantSequence("TAA", alt="C", suffix="GG", reads={"3"})
results = collapse_substrings([vs_longer, vs_shorter, vs_unrelated])
eq_(len(results),
2), "Expected two sequences, got %d: %s" % (len(results), results)
vs_combined = vs_longer.add_reads({"2"})
assert vs_combined in results, "Expected %s to be in %s" % (vs_combined,
results)
assert vs_unrelated in results, "Expected %s to be in %s" % (vs_unrelated,
results)
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)
