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"""Tests for third_party.nucleus.io.bed."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from absl.testing import absltest
from absl.testing import parameterized
from third_party.nucleus.io import bed
from third_party.nucleus.io.python import bed_reader
from third_party.nucleus.protos import bed_pb2
from third_party.nucleus.testing import test_utils
_VALID_NUM_BED_FIELDS = [3, 4, 5, 6, 8, 9, 12]
class BedReaderTests(parameterized.TestCase):
@parameterized.parameters(['5col.bed'])
def test_bed_reader_on_5_columns_because_mistaken_as_fai(self, bed_filename):
bed_path = test_utils.genomics_core_testdata(bed_filename)
with self.assertRaisesRegex(ValueError,
'Could not open .*5col.bed. The file might not '
'exist, or the format detected by htslib might '
'be incorrect.'):
_ = bed_reader.BedReader.from_file(bed_path, bed_pb2.BedReaderOptions())
@parameterized.parameters('test_regions.bed', 'test_regions.bed.gz',
'test_regions.bed.tfrecord',
'test_regions.bed.tfrecord.gz')
def test_iterate_bed_reader(self, bed_filename):
bed_path = test_utils.genomics_core_testdata(bed_filename)
expected = [('chr1', 10, 20), ('chr1', 100, 200)]
with bed.BedReader(bed_path) as reader:
records = list(reader.iterate())
self.assertLen(records, 2)
self.assertEqual([(r.reference_name, r.start, r.end) for r in records],
expected)
@parameterized.parameters('test_regions.bed', 'test_regions.bed.gz')
def test_native_bed_header(self, bed_filename):
bed_path = test_utils.genomics_core_testdata(bed_filename)
with bed.BedReader(bed_path) as reader:
self.assertEqual(reader.header.num_fields, 12)
with bed.NativeBedReader(bed_path) as native_reader:
self.assertEqual(native_reader.header.num_fields, 12)
@parameterized.parameters(1, 2, 7, 10, 11, 13)
def test_invalid_num_fields(self, invalid_num_fields):
bed_path = test_utils.genomics_core_testdata('test_regions.bed')
with self.assertRaisesRegexp(ValueError, 'Invalid requested number of fie'):
_ = bed.BedReader(bed_path, num_fields=invalid_num_fields)
class BedWriterTests(parameterized.TestCase):
"""Tests for BedWriter."""
def setUp(self):
self.records = [
bed_pb2.BedRecord(
reference_name='chr1', start=30, end=40, name='first', score=55.5),
bed_pb2.BedRecord(
reference_name='chr2', start=32, end=38, name='second', score=0),
bed_pb2.BedRecord(
reference_name='chr3', start=40, end=50, name='third', score=99),
]
self.tokens = [
[
'chr1', '30', '40', 'first', '55.5', '+', '35', '38', '128,242,16',
'2', '5,3', '30,37'
],
[
'chr2', '32', '38', 'second', '0', '.', '32', '38', '128,128,128',
'1', '6', '32'
],
[
'chr3', '40', '50', 'third', '99', '-', '40', '44', '0,0,0', '3',
'40,43,48', '3,2,2'
],
]
@parameterized.parameters('test_raw.bed', 'test_zipped.bed.gz',
'test_raw.tfrecord', 'test_zipped.tfrecord.gz')
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)
@parameterized.parameters(3, 4, 5, 6, 8, 9, 12)
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)
if __name__ == '__main__':
absltest.main()
