def test___get_query_name_to_best_record___one_query_name_with_several_records___several_covers_allele___difference_does_not_exceed_threshold___returns_empty_dict(
self, *mocks):
mapq_sam_records_filter = MAPQSamRecordsFilter(
[], mapping_quality_threshold=10)
actual = mapq_sam_records_filter._get_query_name_to_best_record(
[mapping_quality_50_mock, mapping_quality_60_mock])
assert actual == {}
def test___get_first_and_second_records_with_highest_mapping_qualities_that_covers_the_allele___several_records_covers_the_allele(
self, *mocks):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
actual = mapq_sam_records_filter._get_first_and_second_records_with_highest_mapping_qualities_that_covers_the_allele(
[])
expected = (mapping_quality_60_mock, mapping_quality_51_mock)
assert actual == expected
def test___get_query_name_to_best_record___one_query_name_with_several_records___one_covers_allele(
self, *mocks):
mapq_sam_records_filter = MAPQSamRecordsFilter(
[], mapping_quality_threshold=10)
actual = mapq_sam_records_filter._get_query_name_to_best_record(
[mapping_quality_49_mock, mapping_quality_40_mock])
assert actual == {"query_name_1": mapping_quality_40_mock}
def test___get_query_name_to_best_record___one_query_name_with_one_record___returns_the_only_record(
self):
mapq_sam_records_filter = MAPQSamRecordsFilter(
[], mapping_quality_threshold=10)
actual = mapq_sam_records_filter._get_query_name_to_best_record(
[mapping_quality_49_mock])
assert actual == {"query_name_1": mapping_quality_49_mock}
def test____get_only_records_that_cover_the_allele_core___no_classifications___returns_empty_list(
self):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
classifications = []
actual = mapq_sam_records_filter._get_only_records_that_cover_the_allele_core(
classifications)
expected = []
assert actual == expected
def test___get_record_with_highest_mapping_quality___several_records(self):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
record_with_highest_mapping_quality = mapq_sam_records_filter._get_record_with_highest_mapping_quality(
[
mapping_quality_49_mock, mapping_quality_50_mock,
mapping_quality_51_mock, mapping_quality_49_mock,
mapping_quality_49_mock, mapping_quality_51_mock,
mapping_quality_60_mock
])
assert record_with_highest_mapping_quality == mapping_quality_60_mock
def test___get_query_name_to_best_record___several_query_names_with_several_records(
self,
get_first_and_second_records_with_highest_mapping_qualities_that_covers_the_allele_mock
):
query_name_2_mapping_quality_60_mock = Mock(query_name="query_name_2",
mapping_quality=60)
query_name_2_mapping_quality_51_mock = Mock(query_name="query_name_2",
mapping_quality=51)
query_name_3_mapping_quality_30_mock = Mock(query_name="query_name_3",
mapping_quality=30)
query_name_3_mapping_quality_0_mock = Mock(query_name="query_name_3",
mapping_quality=0)
query_name_4_mapping_quality_32_mock = Mock(query_name="query_name_4",
mapping_quality=32)
query_name_4_mapping_quality_35_mock = Mock(query_name="query_name_4",
mapping_quality=35)
def return_mock_function(records):
if records[0].query_name == "query_name_1":
# query_name_1 - exceeds threshold
return (mapping_quality_60_mock, mapping_quality_49_mock)
elif records[0].query_name == "query_name_2":
# query_name_2 - does not exceed threshold
return (query_name_2_mapping_quality_60_mock,
query_name_2_mapping_quality_51_mock)
elif records[0].query_name == "query_name_3":
# query_name_3 - only one record covers the allele
return (query_name_3_mapping_quality_30_mock, None)
elif records[0].query_name == "query_name_4":
# query_name_4 - no record covers the allele
return (None, None)
get_first_and_second_records_with_highest_mapping_qualities_that_covers_the_allele_mock.side_effect = return_mock_function
mapq_sam_records_filter = MAPQSamRecordsFilter(
[], mapping_quality_threshold=10)
actual = mapq_sam_records_filter._get_query_name_to_best_record([
mapping_quality_49_mock,
mapping_quality_40_mock,
mapping_quality_60_mock,
mapping_quality_40_mock,
mapping_quality_40_mock,
query_name_2_mapping_quality_51_mock,
query_name_2_mapping_quality_60_mock,
query_name_3_mapping_quality_0_mock,
query_name_3_mapping_quality_30_mock,
query_name_4_mapping_quality_32_mock,
query_name_4_mapping_quality_35_mock,
])
assert actual == {
"query_name_1": mapping_quality_60_mock,
"query_name_3": query_name_3_mapping_quality_30_mock,
"query_name_4": query_name_4_mapping_quality_32_mock
}
def test____get_only_records_that_cover_the_allele_core___several_classifications_only_two_cover_allele___returns_two_records(
self):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
records = [
record_do_not_cover_allele_mock, record_do_not_cover_allele_mock,
record_cover_allele_mock_1, record_do_not_cover_allele_mock,
record_do_not_cover_allele_mock, record_cover_allele_mock_2
]
actual = mapq_sam_records_filter._get_only_records_that_cover_the_allele_core(
records)
expected = ["record_1", "record_2"]
assert actual == expected
def test___constructor___one_sam_record___records_to_keep_has_sam_record(
self, get_query_name_to_best_record_mock):
records_mock = Mock()
mapq_sam_records_filter = MAPQSamRecordsFilter(records_mock)
assert mapq_sam_records_filter.records_to_keep == {"best_record_1"}
assert get_query_name_to_best_record_mock.called_once_with(
records_mock)
def test___constructor___no_sam_records___records_to_keep_is_empty(
self, get_query_name_to_best_record_mock):
records_mock = Mock()
mapq_sam_records_filter = MAPQSamRecordsFilter(records_mock)
assert mapq_sam_records_filter.records_to_keep == set()
assert get_query_name_to_best_record_mock.called_once_with(
records_mock)
# setup
sam_filepath = snakemake.input.variant_call_probeset_mapped_to_ref
sample_id = snakemake.wildcards.sample_id
tool = snakemake.wildcards.tool
mask_filepath = snakemake.input.mask
variant_call_precision_report = snakemake.output.variant_call_precision_report
nb_of_records_removed_with_mapq_sam_records_filter_filepath = snakemake.output.nb_of_records_removed_with_mapq_sam_records_filter_filepath
# API usage
with pysam.AlignmentFile(sam_filepath) as sam:
records = [record for record in sam]
logging.info(f"Applying MAPQ SAM records filter")
nb_of_records_before_mapq_sam_records_filter = len(records)
mapq_sam_records_filter = MAPQSamRecordsFilter(records)
records = mapq_sam_records_filter.filter_records(records)
nb_of_records_after_mapq_sam_records_filter = len(records)
nb_of_records_removed_with_mapq_sam_records_filter = nb_of_records_before_mapq_sam_records_filter - nb_of_records_after_mapq_sam_records_filter
nb_of_records_removed_with_mapq_sam_records_filter_proportion = nb_of_records_removed_with_mapq_sam_records_filter / nb_of_records_before_mapq_sam_records_filter if nb_of_records_before_mapq_sam_records_filter > 0 else 0
nb_of_records_removed_with_mapq_sam_records_filter_df = pd.DataFrame({
"tool": [tool],
"nb_of_records_before_mapq_sam_records_filter":
[nb_of_records_before_mapq_sam_records_filter],
"nb_of_records_after_mapq_sam_records_filter":
[nb_of_records_after_mapq_sam_records_filter],
"nb_of_records_removed_with_mapq_sam_records_filter":
[nb_of_records_removed_with_mapq_sam_records_filter],
"nb_of_records_removed_with_mapq_sam_records_filter_proportion":
[nb_of_records_removed_with_mapq_sam_records_filter_proportion]
def test___get_record_with_highest_mapping_quality___no_records___returns_None(
self):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
record_with_highest_mapping_quality = mapq_sam_records_filter._get_record_with_highest_mapping_quality(
[])
assert record_with_highest_mapping_quality is None
def test___record_should_be_filtered_out___record_is_NOT_in_records_to_keep___should_be_filtered_out(
self, *mocks):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
assert mapq_sam_records_filter.record_should_be_filtered_out(
mapping_quality_50_mock)
def test___get_query_name_to_best_record___no_records___return_empty_dict(
self):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
actual = mapq_sam_records_filter._get_query_name_to_best_record([])
assert actual == {}
def test___get_record_with_highest_mapping_quality___one_record___returns_given_record(
self):
mapq_sam_records_filter = MAPQSamRecordsFilter([])
record_with_highest_mapping_quality = mapq_sam_records_filter._get_record_with_highest_mapping_quality(
[mapping_quality_49_mock])
assert record_with_highest_mapping_quality == mapping_quality_49_mock
