def testCompressed(self):
reader = genomics_reader.TFRecordReader(
test_utils.genomics_core_testdata('test_features.gff.tfrecord.gz'),
gff_pb2.GffRecord(),
)
records = list(reader.iterate())
self.assertEqual('GenBank', records[0].source)
self.assertEqual('ctg123', records[1].range.reference_name)
def setUp(self):
self.options = gff_pb2.GffReaderOptions()
self.first = gff_pb2.GffRecord()
self.first.range.reference_name = 'ctg123'
self.first.range.start = 999
self.first.range.end = 9000
self.first.source = 'GenBank'
self.first.type = 'gene'
self.first.score = 2.5
self.first.strand = gff_pb2.GffRecord.FORWARD_STRAND
self.first.phase = 0
self.first.attributes['ID'] = 'gene00001'
self.first.attributes['Name'] = 'EDEN'
self.second = gff_pb2.GffRecord()
self.second.range.reference_name = 'ctg123'
self.second.range.start = 999
self.second.range.end = 1012
self.second.phase = -1
self.second.score = -float('inf')
def setUp(self):
out_fname = test_utils.test_tmpfile('output.gff')
self.writer = gff_writer.GffWriter.to_file(out_fname,
gff_pb2.GffHeader(),
gff_pb2.GffWriterOptions())
self.expected_gff_content = open(
test_utils.genomics_core_testdata(
'test_features.gff')).readlines()
self.header = gff_pb2.GffHeader(
sequence_regions=[ranges.make_range('ctg123', 0, 1497228)])
self.record = gff_pb2.GffRecord(
range=ranges.make_range('ctg123', 1000, 1100))
def _raw_next(self):
record = gff_pb2.GffRecord()
not_done = self._cc_iterable.PythonNext(record)
return record, not_done
