def test_minlen_greater_than_all(self):
"Test input when --minlen is greater than 2 out of 2 sequences"
expected = FastaStats(num_seqs=0,
num_bases=0,
min_len=None,
max_len=None,
average=None)
self.do_test(">header1\nATGC\nAGG\n>header2\nTT\n", 8, expected)
def test_minlen_less_than_all(self):
"Test input when --minlen is less than 2 out of 2 sequences"
expected = FastaStats(num_seqs=2,
num_bases=9,
min_len=2,
max_len=7,
average=4)
self.do_test(">header1\nATGC\nAGG\n>header2\nTT\n", 2, expected)
def test_minlen_greater_than_one(self):
"Test input when --minlen is less than 1 out of 2 sequences"
expected = FastaStats(num_seqs=1,
num_bases=7,
min_len=7,
max_len=7,
average=7)
self.do_test(">header1\nATGC\nAGG\n>header2\nTT\n", 3, expected)
def test_two_sequences(self):
"Test input containing two sequences"
expected = FastaStats(num_seqs=2,
num_bases=9,
min_len=2,
max_len=7,
average=4)
self.do_test(">header1\nATGC\nAGG\n>header2\nTT\n", 0, expected)
def test_no_header(self):
"Test input containing sequence without preceding header"
expected = FastaStats(num_seqs=0,
num_bases=0,
min_len=None,
max_len=None,
average=None)
self.do_test("no header\n", 0, expected)
def test_one_sequence(self):
"Test input containing one sequence"
expected = FastaStats(num_seqs=1,
num_bases=5,
min_len=5,
max_len=5,
average=5)
self.do_test(">header\nATGC\nA", 0, expected)
def test_single_greater_than_input(self):
"Test input containing a single greater-than (>) character"
expected = FastaStats(num_seqs=1,
num_bases=0,
min_len=0,
max_len=0,
average=0)
self.do_test('>', 0, expected)
def test_single_newline_input(self):
"Test input containing a newline (\n) character"
expected = FastaStats(num_seqs=0,
num_bases=0,
min_len=None,
max_len=None,
average=None)
self.do_test('\n', 0, expected)
def test_zero_byte_input(self):
"Test input containing zero bytes"
expected = FastaStats(num_seqs=0,
num_bases=0,
min_len=None,
max_len=None,
average=None)
self.do_test('', 0, expected)
def do_test(self, input_str, minlen, expected):
"Wrapper function for testing FastaStats"
result = FastaStats().from_file(StringIO(input_str), minlen)
self.assertEqual(expected, result)