def test_native_gff_header(self, gff_filename):
gff_path = test_utils.genomics_core_testdata(gff_filename)
with gff.GffReader(gff_path) as reader:
self.assertEqual(EXPECTED_GFF_VERSION, reader.header.gff_version)
with gff.NativeGffReader(gff_path) as native_reader:
self.assertEqual(EXPECTED_GFF_VERSION,
native_reader.header.gff_version)
def test_iterate_gff_reader(self, gff_filename):
gff_path = test_utils.genomics_core_testdata(gff_filename)
expected = [('ctg123', 999, 9000), ('ctg123', 999, 1012)]
with gff.GffReader(gff_path) as reader:
records = list(reader.iterate())
self.assertLen(records, 2)
self.assertEqual([(r.range.reference_name, r.range.start, r.range.end)
for r in records], expected)
def test_roundtrip_writer(self, filename):
output_path = test_utils.test_tmpfile(filename)
with gff.GffWriter(output_path, header=self.header) as writer:
for record in self.records:
writer.write(record)
with gff.GffReader(output_path) as reader:
v2_records = list(reader.iterate())
self.assertEqual(self.records, v2_records)