def test_messy_graph():
reference = "GCATATTTT"
variants = VcfVariants([
VcfVariant(1, 2, "CAT", "C", type="DELETION"),
VcfVariant(1, 3, "A", "G", type="SNP"),
VcfVariant(1, 4, "TA", "T", type="DELETION"),
VcfVariant(1, 5, "A", "AT", type="INSERTION"),
])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
print(graph)
print(constructor.get_graph_with_dummy_nodes())
ref, var = graph.get_variant_nodes(variants[2])
assert ref == 5
assert var == 10
ref, var = graph.get_variant_nodes(variants[0])
assert ref == 3
assert var == 9
ref, var = graph.get_variant_nodes(variants[1])
assert ref == 3
assert var == 2
ref, var = graph.get_variant_nodes(variants[3])
assert ref == 11
assert var == 6
assert list(graph.get_edges(10)) == [6, 11]
assert list(graph.get_edges(11)) == [7]
assert list(graph.get_edges(9)) == [5, 10]
def test_deletion_with_snp_at_end():
reference = "TCTGTCTAGG"
variants = VcfVariants([
VcfVariant(1, 4, "GTCTA", "G", type="DELETION"),
VcfVariant(1, 8, "A", "T", type="SNP")
])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
print(graph)
def test_insertion_with_snp_right_before_and_right_after():
reference = "AAAAAA"
variants = VcfVariants([
VcfVariant(1, 2, "A", "T", type="SNP"),
VcfVariant(1, 2, "A", "AC", type="INSERTION"),
VcfVariant(1, 3, "A", "C", type="SNP")
])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
print(graph)
def test_single_insertion():
reference = "AATTGG"
variants = VcfVariants([VcfVariant(1, 2, "A", "AAA", type="INSERTION")])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph_with_dummy_nodes()
print(graph)
assert list(graph.get_edges(1)) == [2, 5]
assert list(graph.get_edges(5)) == [3]
assert list(graph.get_edges(3)) == []
def test_deletion_with_snp_right_before_and_right_after():
reference = "AAAAAA"
variants = VcfVariants([
VcfVariant(1, 2, "A", "T", type="SNP"),
VcfVariant(1, 2, "AA", "A", type="DELETION"),
VcfVariant(1, 3, "A", "C", type="SNP")
])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
graph_with_dummy_nodes = constructor.get_graph_with_dummy_nodes()
print(graph)
print(graph_with_dummy_nodes)
def test_double_deletion_with_snp_inside_first_deletion():
reference = "ACTGATAAAG"
variants = VcfVariants([
VcfVariant(1, 4, "GAT", "G", type="DELETION"),
VcfVariant(1, 6, "T", "C", type="SNP"),
VcfVariant(1, 6, "TAAA", "T", type="DELETION")
])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
print(graph.get_node_at_ref_offset(0))
print(graph.get_node_at_ref_offset(1))
graph_with_dummy_nodes = constructor.get_graph_with_dummy_nodes()
print(graph_with_dummy_nodes)
def test_single_deletion():
logging.info("\n\nTest single deletion")
reference = "AATTGG"
variants = VcfVariants([VcfVariant(1, 2, "ATT", "A", type="DELETION")])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
print(graph)
assert list(graph.get_edges(1)) == [2, 5]
assert list(graph.get_edges(2)) == [3]
assert graph.get_node_sequence(5) == ""
assert graph.get_node_sequence(2) == "TT"
assert graph.get_node_sequence(1) == "AA"
assert graph.get_node_sequence(3) == "GG"
assert graph.linear_ref_nodes() == set([1, 2, 3])
def test_insertion_with_snp_right_before():
reference = "AAAAAA"
variants = VcfVariants([
VcfVariant(1, 2, "A", "T", type="SNP"),
VcfVariant(1, 2, "A", "AC", type="INSERTION")
])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph_with_dummy_nodes()
assert list(graph.get_edges(1)) == [2, 3]
assert list(graph.get_edges(2)) == [4, 7]
assert list(graph.get_edges(3)) == [4, 7]
assert list(graph.get_edges(4)) == [5]
assert list(graph.get_edges(5)) == []
assert list(graph.get_edges(7)) == [5]
assert graph.get_node_sequence(5) == "AAAA"
assert graph.get_node_sequence(7) == ""
assert graph.get_node_sequence(4) == "C"
assert graph.get_node_sequence(2) == "T"
assert graph.linear_ref_nodes() == set([1, 3, 5])
def test_single_snp():
reference = "ACTGGG"
variants = VcfVariants([VcfVariant(1, 2, "C", "T", type="SNP")])
constructor = GraphConstructor(reference, variants)
graph = constructor.get_graph()
assert list(graph.get_edges(1)) == [2, 3], graph.get_edges(1)
assert list(graph.get_edges(2)) == [4], graph.get_edges(2)
assert list(graph.get_edges(3)) == [4], graph.get_edges(3)
assert list(graph.get_edges(4)) == [], graph.get_edges(4)
assert graph.get_node_size(1) == 1
assert graph.get_node_size(2) == 1
assert graph.get_node_size(3) == 1
assert graph.get_node_size(4) == 4
assert graph.get_node_sequence(1) == "A"
assert graph.get_node_sequence(2) == "T"
assert graph.get_node_sequence(3) == "C"
assert graph.get_node_sequence(4) == "TGGG"
assert graph.linear_ref_nodes() == set([1, 3, 4])