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())
def __init__(self, input_path, num_fields=0):
"""Initializes a NativeBedReader.
Args:
input_path: string. A path to a resource containing BED records.
num_fields: int. The number of fields to read in the BED. If unset or set
to zero, all fields in the input are read.
"""
super(NativeBedReader, self).__init__()
bed_path = input_path.encode('utf8')
if bed_path.endswith('.gz'):
options = bed_pb2.BedReaderOptions(
compression_type=bed_pb2.BedReaderOptions.GZIP,
num_fields=num_fields)
else:
options = bed_pb2.BedReaderOptions(num_fields=num_fields)
self._reader = bed_reader.BedReader.from_file(bed_path, options)
self.header = self._reader.header
def setUp(self):
self.bed = test_utils.genomics_core_testdata('test_regions.bed')
self.zipped_bed = test_utils.genomics_core_testdata(
'test_regions.bed.gz')
self.options = bed_pb2.BedReaderOptions()
self.first = bed_pb2.BedRecord(reference_name='chr1',
start=10,
end=20,
name='first',
score=100,
strand=bed_pb2.BedRecord.FORWARD_STRAND,
thick_start=12,
thick_end=18,
item_rgb='255,124,1',
block_count=3,
block_sizes='2,6,2',
block_starts='10,12,18')
def test_bed_iterate(self):
with bed_reader.BedReader.from_file(self.bed, self.options) as reader:
self.assertEqual(reader.header.num_fields, 12)
iterable = reader.iterate()
self.assertIsInstance(iterable, clif_postproc.WrappedCppIterable)
actual = list(iterable)
self.assertLen(actual, 2)
self.assertEqual(actual[0], self.first)
zreader = bed_reader.BedReader.from_file(self.zipped_bed,
bed_pb2.BedReaderOptions())
self.assertEqual(zreader.header.num_fields, 12)
with zreader:
ziterable = zreader.iterate()
self.assertIsInstance(ziterable, clif_postproc.WrappedCppIterable)
zactual = list(ziterable)
self.assertLen(zactual, 2)
self.assertEqual(zactual[0], self.first)