def setUp(self, get_raw_reads_function):
#self.raw_reads = self.mock_get_raw_reads("", "")
self.reads = short_mock_get_alignments('', '')
self.raw_reads = mock_get_raw_reads('', '')
self.matrix = DepthMatrix(3, allow_orphans=True)
self.matrix.make_seq_matrix("", "")
def setUp(self, get_raw_reads_function):
#self.raw_reads = self.mock_get_raw_reads("", "")
self.reads = short_mock_get_alignments('', '')
self.raw_reads = mock_get_raw_reads('', '')
self.matrix = DepthMatrix(3, allow_orphans=True)
self.matrix.make_seq_matrix("", "")
class SimpleTest(unittest.TestCase):
#@mock.patch("subsample_mindepth.get_raw_reads", side_effect=short_mock_get_raw_reads)
@mock.patch("subsample_mindepth.get_alignments",
side_effect=short_mock_get_alignments)
def setUp(self, get_raw_reads_function):
#self.raw_reads = self.mock_get_raw_reads("", "")
self.reads = short_mock_get_alignments('', '')
self.raw_reads = mock_get_raw_reads('', '')
self.matrix = DepthMatrix(3, allow_orphans=True)
self.matrix.make_seq_matrix("", "")
@mock.patch("subsample_mindepth.get_raw_reads",
side_effect=mock_get_raw_reads)
def complexSetUp(self, func):
self.matrix.make_seq_matrix('', '')
pass
def test_simple_get_depths(self):
expected_depths = np.array([3, 2, 1])
result = self.matrix.get_depths(self.reads)
#print(result)
assert_equal(expected_depths, result)
def test_get_candidate_sequences(self):
# use the reads from setup and at position 0
expected = self.reads
result = self.matrix.get_candidate_sequences(0)
self.assertEquals(expected, result)
def test_get_candidate_sequences_no_candidates(self):
result = self.matrix.get_candidate_sequences(5)
self.assertEquals([], result)
def test_yield_greatest_overlaps(self):
expected = [Alignment('', '', 0, 'A' * 1, 0x2)]
def test_parse_alignment(self):
expected = Alignment(
self.raw_reads[0],
"gi|110640213|ref|NC_008253.1|_2_451_1:0:0_1:0:0_12b/1", 0, "GCT",
0)
result = sub.parse_alignment(self.raw_reads[0])
self.assertEquals(expected, result)
@mock.patch("subsample_mindepth.get_raw_reads",
side_effect=mock_get_raw_reads)
def test_make_seq_matrix(self, get_reads_function):
expected_lengths = [4, 2, 2]
self.matrix.make_seq_matrix("mockecoli.sam",
"gi|110640213|ref|NC_008253.1|")
actual_lengths = map(len, self.matrix.seq_matrix)
self.assertEquals(expected_lengths, actual_lengths)
def test_get_raw_reads(self):
pass
def test_yield_greatest_overlaps_ecoli(self):
self.complexSetUp()
expected = [
sub.parse_alignment(self.raw_reads[-2]),
sub.parse_alignment(self.raw_reads[4])
]
for seq in expected:
seq.pick()
result = list(self.matrix.yield_greatest_overlaps(3, 2))
self.assertEquals(expected, result)
#expected = self.matrix.seq_matrix[2][0]
pass
def test_pickreads(self):
pass
def test_minimize_depths_complex(self):
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [[seqs[0], seqs[1], seqs[3]], [seqs[4]],
[seqs[6], seqs[7]]]
expected_list = [seqs[0], seqs[1], seqs[3], seqs[4], seqs[6], seqs[7]]
for seq in expected_list:
seq.pick()
expected_depths = np.array([3, 4, 6, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list],
sub.flatten_and_filter_matrix(
self.matrix.seq_matrix))
def check_files(self, mock_stdout, expected_file):
samfile = os.path.join(THISD, expected_file)
expected = open(samfile, 'r').read().strip()
result = str(mock_stdout.getvalue().strip().decode('UTF-8'))
if expected_file == 'simplein.sam':
with open('tests/result.sam', 'w') as out:
out.write(result)
return expected, result
@mock.patch('subsample_mindepth.random.choice',
side_effect=not_random_subsample)
@mock.patch("subsamplebam.parse_args", side_effect=mock_args)
@mock.patch('subsamplebam.sys.stdout', new_callable=BytesIO)
def test_main(self, mock_stdout, func, func2):
sub.main()
self.assertEquals(*self.check_files(mock_stdout, 'test40.sam'))
''' The order of these mocks is the order they appear as arguments to the test method. '''
# @mock.patch('subsample_mindepth.random.sample', side_effect=not_random_subsample)
# @mock.patch("subsamplebam.parse_args", side_effect=more_random_mock_args)
# @mock.patch('subsamplebam.sys.stdout', new_callable=BytesIO)
# def test_main_more_random(self, mock_stdout, func, func2):
# #Expected will equal the input file becasue all reads are subsampled in this case
# sub.main()
# self.maxDiff = None
# expected, result = self.check_files(mock_stdout, 'simplein.sam')
# self.assertEquals(expected, result)
@mock.patch('subsample_mindepth.random.choice',
side_effect=not_random_subsample)
def test_minimize_depths_complex_more_random(self, func):
#TODO: Refactor this so as not to duplicate code with non-random ecoli test
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [[seqs[0], seqs[1], seqs[2], seqs[3]],
[seqs[4], seqs[5]], [seqs[6], seqs[7]]]
expected_list = seqs
for seq in expected_list:
seq.pick()
expected_depths = np.array([4, 6, 7, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.more_random = True
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list],
sub.flatten_and_filter_matrix(
self.matrix.seq_matrix))
class SimpleTest(unittest.TestCase):
#@mock.patch("subsample_mindepth.get_raw_reads", side_effect=short_mock_get_raw_reads)
@mock.patch("subsample_mindepth.get_alignments", side_effect=short_mock_get_alignments)
def setUp(self, get_raw_reads_function):
#self.raw_reads = self.mock_get_raw_reads("", "")
self.reads = short_mock_get_alignments('', '')
self.raw_reads = mock_get_raw_reads('', '')
self.matrix = DepthMatrix(3, allow_orphans=True)
self.matrix.make_seq_matrix("", "")
@mock.patch("subsample_mindepth.get_raw_reads", side_effect=mock_get_raw_reads)
def complexSetUp(self, func):
self.matrix.make_seq_matrix('', '')
pass
def test_simple_get_depths(self):
expected_depths = np.array([3, 2, 1])
result = self.matrix.get_depths(self.reads)
#print(result)
assert_equal(expected_depths, result)
def test_get_candidate_sequences(self):
# use the reads from setup and at position 0
expected = self.reads
result = self.matrix.get_candidate_sequences(0)
self.assertEquals(expected, result)
def test_get_candidate_sequences_no_candidates(self):
result = self.matrix.get_candidate_sequences(5)
self.assertEquals([], result)
def test_yield_greatest_overlaps(self):
expected = [Alignment('', '', 0, 'A'*1, 0x2)]
def test_parse_alignment(self):
expected = Alignment(self.raw_reads[0], "gi|110640213|ref|NC_008253.1|_2_451_1:0:0_1:0:0_12b/1", 0, "GCT", 0)
result = sub.parse_alignment(self.raw_reads[0])
self.assertEquals(expected, result)
@mock.patch("subsample_mindepth.get_raw_reads", side_effect=mock_get_raw_reads)
def test_make_seq_matrix(self, get_reads_function):
expected_lengths = [4, 2, 2]
self.matrix.make_seq_matrix("mockecoli.sam", "gi|110640213|ref|NC_008253.1|")
actual_lengths = map(len, self.matrix.seq_matrix)
self.assertEquals(expected_lengths, actual_lengths)
def test_get_raw_reads(self):
pass
def test_yield_greatest_overlaps_ecoli(self):
self.complexSetUp()
expected = [sub.parse_alignment(self.raw_reads[-2]), sub.parse_alignment(self.raw_reads[4])]
for seq in expected:
seq.pick()
result = list(self.matrix.yield_greatest_overlaps(3, 2))
self.assertEquals(expected, result)
#expected = self.matrix.seq_matrix[2][0]
pass
def test_pickreads(self):
pass
def test_minimize_depths_complex(self):
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [
[seqs[0], seqs[1], seqs[3]],
[seqs[4]],
[seqs[6], seqs[7]]
]
expected_list = [ seqs[0], seqs[1], seqs[3], seqs[4], seqs[6], seqs[7] ]
for seq in expected_list:
seq.pick()
expected_depths = np.array([3, 4, 6, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list], sub.flatten_and_filter_matrix(self.matrix.seq_matrix))
def check_files(self, mock_stdout, expected_file):
samfile = os.path.join(THISD, expected_file)
expected = open(samfile, 'r').read().strip()
result = str(mock_stdout.getvalue().strip().decode('UTF-8'));
if expected_file == 'simplein.sam':
with open('tests/result.sam', 'w') as out: out.write(result)
return expected, result
@mock.patch('subsample_mindepth.random.choice', side_effect=not_random_subsample)
@mock.patch("subsamplebam.parse_args", side_effect=mock_args)
@mock.patch('subsamplebam.sys.stdout', new_callable=BytesIO)
def test_main(self, mock_stdout, func, func2):
sub.main()
self.assertEquals(*self.check_files(mock_stdout, 'test40.sam'))
''' The order of these mocks is the order they appear as arguments to the test method. '''
# @mock.patch('subsample_mindepth.random.sample', side_effect=not_random_subsample)
# @mock.patch("subsamplebam.parse_args", side_effect=more_random_mock_args)
# @mock.patch('subsamplebam.sys.stdout', new_callable=BytesIO)
# def test_main_more_random(self, mock_stdout, func, func2):
# #Expected will equal the input file becasue all reads are subsampled in this case
# sub.main()
# self.maxDiff = None
# expected, result = self.check_files(mock_stdout, 'simplein.sam')
# self.assertEquals(expected, result)
@mock.patch('subsample_mindepth.random.choice', side_effect=not_random_subsample)
def test_minimize_depths_complex_more_random(self, func):
#TODO: Refactor this so as not to duplicate code with non-random ecoli test
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [
[seqs[0], seqs[1], seqs[2], seqs[3]],
[seqs[4], seqs[5]],
[seqs[6], seqs[7]]
]
expected_list = seqs
for seq in expected_list:
seq.pick()
expected_depths = np.array([4, 6, 7, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.more_random = True
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list], sub.flatten_and_filter_matrix(self.matrix.seq_matrix))
