def __init__(self, input_path):
"""Initializes a NativeFastqReader.
Args:
input_path: str. A path to a resource containing FASTQ records.
"""
super(NativeFastqReader, self).__init__()
fastq_path = input_path.encode('utf8')
options = fastq_pb2.FastqReaderOptions()
self._reader = fastq_reader.FastqReader.from_file(fastq_path, options)
self.header = None
def test_fastq_iterate(self):
with fastq_reader.FastqReader.from_file(self.fastq,
self.options) as reader:
iterable = reader.iterate()
self.assertIsInstance(iterable, clif_postproc.WrappedCppIterable)
self.assertEqual(test_utils.iterable_len(iterable), 3)
zreader = fastq_reader.FastqReader.from_file(
self.zipped_fastq,
fastq_pb2.FastqReaderOptions(
compression_type=fastq_pb2.FastqReaderOptions.GZIP))
with zreader:
ziterable = zreader.iterate()
self.assertIsInstance(ziterable, clif_postproc.WrappedCppIterable)
self.assertEqual(test_utils.iterable_len(ziterable), 3)
def setUp(self):
self.fastq = test_utils.genomics_core_testdata('test_reads.fastq')
self.options = fastq_pb2.FastqReaderOptions()
