def test_read_variants_large_mode(self):
pipeline = test_pipeline.TestPipeline()
all_patterns = [testdata_util.get_full_file_path('valid-4.0.vcf')]
variants = pipeline_common.read_variants(pipeline, all_patterns,
PipelineModes.LARGE, False)
assert_that(variants, asserts.count_equals_to(5))
pipeline.run()
def test_read_variants_use_1_based_coordinate(self):
pipeline = test_pipeline.TestPipeline()
all_patterns = [testdata_util.get_full_file_path('valid-4.0.vcf')]
variants = pipeline_common.read_variants(pipeline,
all_patterns,
PipelineModes.SMALL,
False,
use_1_based_coordinate=True)
assert_that(variants, asserts.count_equals_to(5))
pipeline.run()
def test_pipeline_read_all_multiple_files_large(self):
pipeline = TestPipeline()
pcoll = (pipeline
| 'Create' >> beam.Create(
[testdata_util.get_full_file_path('valid-4.0.vcf'),
testdata_util.get_full_file_path('valid-4.1-large.vcf'),
testdata_util.get_full_file_path('valid-4.2.vcf')])
| 'Read' >> ReadAllFromVcf())
assert_that(pcoll, asserts.count_equals_to(9900))
pipeline.run()
def test_pipeline_read_all_multiple_files(self):
with TempDir() as tempdir:
file_name_1 = self._create_temp_vcf_file(
_SAMPLE_HEADER_LINES + _SAMPLE_TEXT_LINES, tempdir)
file_name_2 = self._create_temp_vcf_file(
_SAMPLE_HEADER_LINES + _SAMPLE_TEXT_LINES, tempdir)
pipeline = TestPipeline()
pcoll = (pipeline
| 'Create' >> beam.Create([file_name_1, file_name_2])
| 'Read' >> ReadAllFromVcf())
assert_that(pcoll, asserts.count_equals_to(2 * len(_SAMPLE_TEXT_LINES)))
pipeline.run()
def _assert_pipeline_read_files_record_count_equal(
self, input_pattern, expected_count, use_read_all=False):
"""Helper method for verifying total records read.
Args:
input_pattern (str): Input file pattern to read.
expected_count (int): Expected number of reacords that was read.
use_read_all (bool): Whether to use the scalable ReadAllFromVcf transform
instead of ReadFromVcf.
"""
pipeline = TestPipeline()
if use_read_all:
pcoll = (pipeline
| 'Create' >> beam.Create([input_pattern])
| 'Read' >> ReadAllFromVcf())
else:
pcoll = pipeline | 'Read' >> ReadFromVcf(input_pattern)
assert_that(pcoll, asserts.count_equals_to(expected_count))
pipeline.run()