class TestFastqParser(unittest.TestCase):
def setUp(self):
self.fastq_parser = FastqParser()
self.example_data = ExampleData()
def test_parse_1(self):
fastq_fh = StringIO(self.example_data.fastq_seqs_1)
self.assertEqual(
list(self.fastq_parser.entries(fastq_fh)),
[('test_1 a random sequence', 'TTTAGAAATTACACA'),
('test_2 another random sequence', 'ACGAGAAATTAAATTAAATT'),
('test_3 another random sequence', 'TAGAGACATTGGATTTTATT')])
def test_parse_empty_file(self):
fastq_fh = StringIO("")
self.assertEqual(
list(self.fastq_parser.entries(fastq_fh)), [])
def test_single_entry_file_header(self):
fastq_fh = StringIO(self.example_data.fastq_seqs_2)
self.assertEqual(self.fastq_parser.single_entry_file_header(fastq_fh),
"test_4 a random sequence")
def test_header_id_1(self):
self.assertEqual(
self.fastq_parser.header_id("seq_10101 An important protein"),
"seq_10101")
def test_header_id_2(self):
self.assertEqual(
self.fastq_parser.header_id("seq_10101\tAn important protein"),
"seq_10101")
class TestFastqParser(unittest.TestCase):
def setUp(self):
self.fastq_parser = FastqParser()
self.example_data = ExampleData()
def test_parse_1(self):
fastq_fh = StringIO(self.example_data.fastq_seqs_1)
self.assertEqual(
list(self.fastq_parser.entries(fastq_fh)),
[('test_1 a random sequence', 'TTTAGAAATTACACA'),
('test_2 another random sequence', 'ACGAGAAATTAAATTAAATT'),
('test_3 another random sequence', 'TAGAGACATTGGATTTTATT')])
def test_parse_empty_file(self):
fastq_fh = StringIO("")
self.assertEqual(list(self.fastq_parser.entries(fastq_fh)), [])
def test_single_entry_file_header(self):
fastq_fh = StringIO(self.example_data.fastq_seqs_2)
self.assertEqual(self.fastq_parser.single_entry_file_header(fastq_fh),
"test_4 a random sequence")
def test_header_id_1(self):
self.assertEqual(
self.fastq_parser.header_id("seq_10101 An important protein"),
"seq_10101")
def test_header_id_2(self):
self.assertEqual(
self.fastq_parser.header_id("seq_10101\tAn important protein"),
"seq_10101")
def setUp(self):
self.fastq_parser = FastqParser()
self.example_data = ExampleData()
def setUp(self):
self.fastq_parser = FastqParser()
self.example_data = ExampleData()