def test_pattern_count_extra_dataset(self):
"""
Test the pattern_count method using the PatternCount.txt fixture
The course prompt called this the "Extra Dataset"
"""
file_util_obj = FileUtil(FIXTURE2_FPATH)
inputs = file_util_obj.inputs
expected = int(file_util_obj.outputs[0])
sequence_obj = DnaFreqCalc(inputs[0])
actual = sequence_obj.pattern_count(inputs[1])
self.assertEqual(expected, actual)
def test_pattern_count_test_four(self):
"""
Test the pattern_count method using the TEST DATASET 3 fixture
Saved in PatternCountTest3.txt
This test dataset checks if your code is also counting occurrences of
the Reverse Complement of Pattern (which would have an output of 4),
which is out of the scope of this problem (that will come up later in
the chapter). Your code should only be looking for perfect matches of
Pattern in Text at this point.
"""
fname = PATTERN_COUNT_TEST_FNAMES[3]
fpath = os.path.join(FIXTURE_PATH, fname)
file_util_obj = FileUtil(fpath)
inputs = file_util_obj.inputs
expected = int(file_util_obj.outputs[0])
sequence_obj = DnaFreqCalc(inputs[0])
actual = sequence_obj.pattern_count(inputs[1])
self.assertEqual(expected, actual)
def test_pattern_count_test_two(self):
"""
Test the pattern_count method using the TEST DATASET 2 fixture
Saved in PatternCountTest2.txt
This dataset checks if your code correctly handles cases where there
is an occurrence of Pattern at the very beginning of Text.
Note that there are no overlapping occurrences of Pattern (i.e. AAAA),
and there is no occurrence of Pattern at the very end of Text,
so assuming your code passed Test Dataset 1, this test would only check
for off-by-one errors at the beginning of Text.
"""
fname = PATTERN_COUNT_TEST_FNAMES[1]
fpath = os.path.join(FIXTURE_PATH, fname)
file_util_obj = FileUtil(fpath)
inputs = file_util_obj.inputs
expected = int(file_util_obj.outputs[0])
sequence_obj = DnaFreqCalc(inputs[0])
actual = sequence_obj.pattern_count(inputs[1])
self.assertEqual(expected, actual)
def test_pattern_count_test_one(self):
"""
Test the pattern_count method using the TEST DATASET 1 fixture
Saved in PatternCountTest1.txt
This dataset just checks if you’re correctly counting.
It is the “easiest” test. Notice that all occurrences of CG in Text
(ACGTACGTACGT) are away from the very edges (so your code won’t fail
on off-by-one errors at the beginning or at the end of Text) and that
none of the occurrences of Pattern overlap (so your code won’t fail if
you fail to account for overlaps).
"""
fname = PATTERN_COUNT_TEST_FNAMES[0]
fpath = os.path.join(FIXTURE_PATH, fname)
file_util_obj = FileUtil(fpath)
inputs = file_util_obj.inputs
expected = int(file_util_obj.outputs[0])
sequence_obj = DnaFreqCalc(inputs[0])
actual = sequence_obj.pattern_count(inputs[1])
self.assertEqual(expected, actual)
def test_pattern_count_sample(self):
"""
Test the pattern_count method using the SamplePatternCount.txt inputs
From prompt: The sample dataset is not actually run on your code.
Notice that “GCG” occurs twice in Text: once at the beginning (GCGCG)
and once at the end (GCGCG). A common mistake for this problem is
incorrectly handling overlaps and not counting the second of these two
occurrences (because it begins at the end of the previous occurrence).
The sample dataset checks for the following things:
* Off-by-one at the beginning of Text (result would be 1)
* Off-by-one at the end of Text (result would be 1)
* Not counting overlaps (result would be 1)
"""
file_util_obj = FileUtil(FIXTURE1_FPATH)
inputs = file_util_obj.inputs
expected = int(file_util_obj.outputs[0])
sequence_obj = DnaFreqCalc(inputs[0])
actual = sequence_obj.pattern_count(inputs[1])
self.assertEqual(expected, actual)