Ejemplo n.º 1
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 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)
Ejemplo n.º 2
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 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)
Ejemplo n.º 3
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 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)
Ejemplo n.º 4
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 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)
Ejemplo n.º 5
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 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)
Ejemplo n.º 6
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 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)
Ejemplo n.º 7
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 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)
Ejemplo n.º 8
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 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)
Ejemplo n.º 9
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 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)
Ejemplo n.º 10
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 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)