def test_01_g(self):
args = CLI([TESTS_EXAMPLE_ALIGNMENT_01, '--verbose'])
args.parameters.left_padding = 4
args.parameters.right_padding = 4
flaimapper = FlaiMapper(args)
i = 0
for region in flaimapper.regions():
if i == 0:
self.assertEqual(region.region[0], 'chr1')
self.assertEqual(region.region[1],
13 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
43 + 20 + args.parameters.right_padding)
else:
self.assertEqual(region.region[0], 'chr2')
self.assertEqual(region.region[1],
54 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
54 + 26 + args.parameters.right_padding)
i += 1
self.assertEqual(i, 2)
def test_01_b(self):
args = CLI([
TESTS_EXAMPLE_ALIGNMENT_01, '-p', TESTS_FUNCTIONAL_DUCK7_PARAMS,
'--verbose'
])
# Use custom file that must be set to a padding of 7
self.assertEqual(args.parameters.left_padding, 7)
self.assertEqual(args.parameters.right_padding, 7)
flaimapper = FlaiMapper(args)
i = 0
for region in flaimapper.regions():
if i == 0:
self.assertEqual(region.region[0], 'chr1')
self.assertEqual(region.region[1],
13 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
43 + 20 + args.parameters.right_padding)
elif i == 1:
self.assertEqual(region.region[0], 'chr2')
self.assertEqual(region.region[1],
54 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
54 + 26 + args.parameters.right_padding)
else:
self.asserTrue(False, "Race condition?")
i += 1
self.assertEqual(i, 2)
def test_04_b(self):
args = CLI([
TESTS_EXAMPLE_ALIGNMENT_01, '-p', TESTS_FUNCTIONAL_DUCK7_PARAMS,
'--verbose'
])
fm = FlaiMapper(args)
# First check whether it's looking in the right regions
i = 0
for region in fm:
if i == 0:
self.assertEqual(region.region[0], 'chr1')
self.assertEqual(region.region[1],
13 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
43 + 20 + args.parameters.right_padding)
elif i == 1:
self.assertEqual(region.region[0], 'chr2')
self.assertEqual(region.region[1],
54 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
54 + 26 + args.parameters.right_padding)
else:
self.asserTrue(False, "Race condition?")
i += 1
self.assertEqual(i, 2)
# Then detect the fragments
i = 0
for region in fm:
for fragment in region:
if i == 0:
self.assertEqual(region.region[1] + fragment.start, 13)
self.assertEqual(region.region[1] + fragment.stop, 36)
elif i == 1:
self.assertEqual(region.region[1] + fragment.start, 43)
self.assertEqual(region.region[1] + fragment.stop, 62)
elif i == 2:
self.assertEqual(region.region[1] + fragment.start, 54)
self.assertEqual(region.region[1] + fragment.stop, 79)
else:
self.asserTrue(False, "Race condition?")
i += 1
self.assertEqual(i, 3)
def test_02b(self):
fname = 'test_FlaiMapper_test_02b_output.gtf'
args = CLI([
TESTS_EXAMPLE_ALIGNMENT_01, '-o', fname, '--verbose', '--offset5p',
'5', '--offset3p', '5'
])
flaimapper = FlaiMapper(args)
# Run analysis
flaimapper.run()
# assert Contents:
assertion = (not filecmp.cmp(fname,
TESTS_FLAIMAPPER_TEST_02_OUTPUT_GTF))
self.assertTrue(assertion)
if assertion:
os.remove(fname)
def test_03_a(self):
fname = 'test_FlaiMapper_test_03_output.txt'
args = CLI([
TESTS_EXAMPLE_ALIGNMENT_01, '-o', fname, '-f', '1', '--verbose',
'--offset5p', '4', '--offset3p', '4'
])
flaimapper = FlaiMapper(args)
# Run analysis
flaimapper.run()
# assert Contents:
self.assertTrue(
filecmp.cmp(TESTS_FLAIMAPPER_TEST_03_a_OUTPUT_TXT, fname),
msg="diff '" + TESTS_FLAIMAPPER_TEST_03_a_OUTPUT_TXT + "' '" +
fname + "':\n" +
get_file_diff(TESTS_FLAIMAPPER_TEST_03_a_OUTPUT_TXT, fname))
os.remove(fname)
def test_02(self):
fname = 'test_FlaiMapper_test_02_output.gtf'
args = CLI([
TESTS_EXAMPLE_ALIGNMENT_01, '-o', fname, '--verbose', '--offset5p',
'4', '--offset3p', '4'
])
flaimapper = FlaiMapper(args)
# Run analysis
flaimapper.run()
# assert Contents:
self.assertTrue(
filecmp.cmp(TESTS_FLAIMAPPER_TEST_02_OUTPUT_GTF, fname),
msg="diff '" + TESTS_FLAIMAPPER_TEST_02_OUTPUT_GTF + "' '" +
fname + "':\n" +
get_file_diff(TESTS_FLAIMAPPER_TEST_02_OUTPUT_GTF, fname))
os.remove(fname) # does not get executed if assertion is False
def test_01_a(self):
args = CLI([TESTS_EXAMPLE_ALIGNMENT_01, '--verbose'])
args.parameters.left_padding = 1
args.parameters.right_padding = 1
flaimapper = FlaiMapper(args)
i = 0
for region in flaimapper.regions():
if i == 0:
self.assertEqual(region.region[0], 'chr1')
self.assertEqual(region.region[1],
13 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
13 + 20 + 4 + args.parameters.right_padding)
elif i == 1:
self.assertEqual(region.region[0], 'chr1')
self.assertEqual(region.region[1],
43 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
43 + 20 + args.parameters.right_padding)
elif i == 2:
self.assertEqual(region.region[0], 'chr2')
self.assertEqual(region.region[1],
54 - 1 - args.parameters.left_padding)
self.assertEqual(region.region[2],
54 + 26 + args.parameters.right_padding)
else:
self.asserTrue(False, "Race condition?")
i += 1
self.assertEqual(i, 3)
def test_02(self):
cli = CLI([TESTS_EXAMPLE_ALIGNMENT_01, "-p", PARAMETERS_DEFAULT])
self.assertTrue(cli.parameters.left_padding, 15)
self.assertTrue(cli.parameters.right_padding, 15)
def test_01(self):
cli = CLI([TESTS_EXAMPLE_ALIGNMENT_01])
self.assertTrue(cli.parameters.left_padding, 15)
self.assertTrue(cli.parameters.right_padding, 15)