def test_pipeline_read_file_pattern(self):
with temp_dir.TempDir() as tempdir:
headers_1 = [self.lines[1], self.lines[-1]]
headers_2 = [self.lines[2], self.lines[3], self.lines[-1]]
headers_3 = [self.lines[4], self.lines[-1]]
file_name_1 = tempdir.create_temp_file(suffix='.vcf',
lines=headers_1)
file_name_2 = tempdir.create_temp_file(suffix='.vcf',
lines=headers_2)
file_name_3 = tempdir.create_temp_file(suffix='.vcf',
lines=headers_3)
pipeline = TestPipeline()
pcoll = pipeline | 'ReadHeaders' >> ReadVcfHeaders(
os.path.join(tempdir.get_path(), '*.vcf'))
expected = [
_get_vcf_header_from_lines(h, file_name=file_name)
for h, file_name in [(
headers_1,
file_name_1), (headers_2,
file_name_2), (headers_3, file_name_3)]
]
assert_that(pcoll, asserts.header_vars_equal(expected))
pipeline.run()
def test_pipeline_read_file_headers(self):
headers = self.lines
self.lines = testdata_util.get_sample_vcf_file_lines()
with temp_dir.TempDir() as tempdir:
filename = tempdir.create_temp_file(suffix='.vcf', lines=self.lines)
pipeline = TestPipeline()
pcoll = pipeline | 'ReadHeaders' >> ReadVcfHeaders(filename)
assert_that(pcoll, equal_to([_get_vcf_header_from_lines(headers)]))
pipeline.run()