def test_write(self):
"""
Check if GFF3 lines are written properly to the output file.
"""
test_input = Reader(self.__input_file)
with Writer(self.__output_file) as test_output:
for record in test_input.records():
test_output.write(record)
# compare the test output file to the original one
with open(self.__input_file) as test_input:
with open(self.__output_file) as test_output:
for input_line, output_line in zip(test_input,
test_output):
self.assertEqual(input_line, output_line)
def test_records(self):
"""
Check if the parse reads a file in the GFF3 format in the
correct way.
"""
# test against the correct input file
with open(self.__correct_file) as gff_file:
parser = Reader(gff_file)
for record in parser.records():
self.assertIsInstance(record, Record)
# check against an unsorted input file
with open(self.__correct_file) as gff_file:
parser = Reader(gff_file)
with self.assertRaises(Gff3Error):
for record in parser.records(check_order=True):
self.assertIsInstance(record, Record)
# test against incorrect input files
for i in self.__incorrect_files:
with open(i) as gff_file:
parser = Reader(gff_file)
with self.assertRaises(Gff3Error):
for _ in parser.records():
pass
def test_records(self):
"""
Check if the parse reads a file in the GFF3 format in the
correct way.
"""
# test against the correct input file
parser = Reader(self.__correct_file)
for record in parser.records():
self.assertIsInstance(record, Gff3Record)
# test against incorrect input files
for gff_file in self.__incorrect_files:
parser = Reader(os.path.join(self.__incorrect_file_dir,
gff_file))
with self.assertRaises(Gff3Error):
for _ in parser.records():
pass
