def test_bulk_re_search_variants(self):
sorted_queries = [
CoordinateQuery('7', 140453136, 140453136),
CoordinateQuery('7', 140453136, 140453137)
]
search_results = civic.bulk_search_variants_by_coordinates(
sorted_queries, search_mode='record_encompassing')
assert len(search_results[sorted_queries[0]]) == 19
assert len(search_results[sorted_queries[1]]) == 16
def test_bulk_any_search_variants(self):
sorted_queries = [
CoordinateQuery('7', 140453136, 140453136, 'T'),
CoordinateQuery('7', 140453136, 140453137, 'TT')
]
search_results = civic.bulk_search_variants_by_coordinates(
sorted_queries, search_mode='any')
assert len(search_results[sorted_queries[0]]) == 19
assert len(search_results[sorted_queries[1]]) >= 19
def test_bulk_exact_search_variants(self):
sorted_queries = [
CoordinateQuery('7', 140453136, 140453136, 'T', '*'),
CoordinateQuery('7', 140453136, 140453137, 'TT', '*'),
CoordinateQuery('7', 140453136, 140453136, 'T', 'A'),
CoordinateQuery('7', 140453136, 140453137, 'TT', 'AC'),
]
search_results = civic.bulk_search_variants_by_coordinates(
sorted_queries, search_mode='exact')
assert len(search_results[sorted_queries[0]]) == 1
assert len(search_results[sorted_queries[1]]) == 1
assert len(search_results[sorted_queries[2]]) == 1
assert len(search_results[sorted_queries[3]]) == 1
def test_errors(self):
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, 'T', 'A')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='wrong_mode')
assert "unexpected search mode" in str(context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140753336, 140753336, '*', 'A',
'GRCh38')
search_results = civic.search_variants_by_coordinates(
query, search_mode='exact')
assert "Can't use wildcard when searching for non-GRCh37 coordinates" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140753336, 140753336, None, None,
'GRCh38')
search_results = civic.search_variants_by_coordinates(
query, search_mode='exact')
assert "alt or ref required for non-GRCh37 coordinate queries" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140753336, 140753336, 'T', 'A',
'GRCh38')
search_results = civic.search_variants_by_coordinates(
query, search_mode='any')
assert "Only exact search mode is supported for non-GRCh37 coordinate queries" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, '-', 'A')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
assert "Unexpected alt `-` in coordinate query. Did you mean `None`?" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, 'T', '-')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
assert "Unexpected ref `-` in coordinate query. Did you mean `None`?" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, '-', 'A',
'GRCh38')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
assert "Unexpected alt `-` in coordinate query. Did you mean `None`?" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, 'T', '-',
'GRCh38')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
assert "Unexpected ref `-` in coordinate query. Did you mean `None`?" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, '-', 'A')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert "Unexpected alt `-` in coordinate query. Did you mean `None`?" in str(
context.value)
with pytest.raises(ValueError) as context:
query = CoordinateQuery('7', 140453136, 140453136, 'T', '-')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert "Unexpected ref `-` in coordinate query. Did you mean `None`?" in str(
context.value)
def test_single_and_bulk_exact_return_same_variants(self):
query = CoordinateQuery('7', 140453136, 140453136, 'T', '*')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 1
assert len(variants_bulk[query]) == 1
assert hash(variants_single[0]) == variants_bulk[query][0].v_hash
query = CoordinateQuery('7', 140453136, 140453136, 'T', 'A')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 1
assert len(variants_bulk[query]) == 1
assert hash(variants_single[0]) == variants_bulk[query][0].v_hash
query = CoordinateQuery('7', 140453136, 140453136, 'T', None)
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 0
assert len(variants_bulk) == 0
query = CoordinateQuery('7', 140453136, 140453137, 'TT', '*')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 1
assert len(variants_bulk[query]) == 1
assert hash(variants_single[0]) == variants_bulk[query][0].v_hash
query = CoordinateQuery('7', 140453136, 140453137, 'TT', 'AC')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 1
assert len(variants_bulk[query]) == 1
assert hash(variants_single[0]) == variants_bulk[query][0].v_hash
query = CoordinateQuery('7', 140453136, 140453137, 'TT', None)
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 0
assert len(variants_bulk) == 0
query = CoordinateQuery('3', 10183706, 10183706, None, 'C')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 1
assert len(variants_bulk[query]) == 1
assert hash(variants_single[0]) == variants_bulk[query][0].v_hash
query = CoordinateQuery('3', 10183706, 10183706, 'T', 'C')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
assert len(variants_single) == 1
assert len(variants_bulk[query]) == 1
assert hash(variants_single[0]) == variants_bulk[query][0].v_hash
query = CoordinateQuery('3', 10183706, 10183706, '*', 'C')
variants_single = civic.search_variants_by_coordinates(
query, search_mode='exact')
variants_bulk = civic.bulk_search_variants_by_coordinates(
[query], search_mode='exact')
variants_single = list(map(lambda v: hash(v), variants_single))
variants_bulk = list(map(lambda v: v.v_hash, variants_bulk[query]))
assert len(variants_single) == 2
assert len(variants_bulk) == 2
assert sorted(variants_single) == sorted(variants_bulk)
assert sorted(variants_single) == sorted(variants_bulk)