def test_roundtrip_writer(self, filename):
output_path = test_utils.test_tmpfile(filename)
with bed.BedWriter(output_path,
header=bed_pb2.BedHeader(num_fields=5)) as writer:
for record in self.records:
writer.write(record)
with bed.BedReader(output_path) as reader:
v2_records = list(reader.iterate())
self.assertEqual(self.records, v2_records)
def test_roundtrip_num_fields(self, num_fields):
all_num_fields_in_file = [
n for n in _VALID_NUM_BED_FIELDS if n >= num_fields
]
for num_fields_in_file in all_num_fields_in_file:
lines = ['\t'.join(line[:num_fields_in_file]) for line in self.tokens]
contents = '{}\n'.format('\n'.join(lines))
input_path = test_utils.test_tmpfile('test_field.bed', contents=contents)
with bed.BedReader(input_path, num_fields=num_fields) as reader:
records = list(reader.iterate())
output_path = test_utils.test_tmpfile('test_field2.bed')
with bed.BedWriter(output_path, header=reader.header) as writer:
for record in records:
writer.write(record)
with bed.BedReader(output_path) as reader2:
v2_records = list(reader2.iterate())
self.assertLen(records, 3)
self.assertEqual(records, v2_records)