def test_process(self):
"""Bypass the UI and test the main logic function directly."""
m = StringIO.StringIO(self.maf1 + "\n\n" + self.maf2)
ga = GenomeAlignment([x for x in genome_alignment_iterator(m, "A")])
prof = processBED(StringIO.StringIO(self.roi), ga, 4, CENTRE)
expect = [0.53333333, 0.66666666, 0.83333333, 0.73333333]
self.assertEqual(len(prof), len(expect))
for i in range(0, len(expect)):
self.assertAlmostEqual(prof[i], expect[i])
def test_process(self):
"""Bypass the UI and test the main logic function directly."""
m = StringIO.StringIO(self.maf1 + "\n\n" + self.maf2)
ga = GenomeAlignment([x for x in genome_alignment_iterator(m, "A")])
prof = processBED(StringIO.StringIO(self.roi), ga, 4, CENTRE)
expect = [0.53333333, 0.66666666, 0.83333333, 0.73333333]
self.assertEqual(len(prof), len(expect))
for i in range(0, len(expect)):
self.assertAlmostEqual(prof[i], expect[i])
def test_conservation_profile_pid(self):
"""Test getting conservation profiles (PID) from genome alignments."""
m = StringIO.StringIO(self.maf1 + "\n\n" + self.maf2)
ga = GenomeAlignment([x for x in genome_alignment_iterator(m, "A")])
# here we're testing directly; the actual script will adjust the regions
# before it does this step.
expect_raw = [[0.66666666, 1.00000000, 1.00000000, 1.0000000],
[0.66666666, 0.33333333, None],
[0.33333333, 0.33333333, 0.66666666, 0.33333333],
[None, None, 1.00000000, 1.00000000],
[0.33333333, 0.66666666],
[0.33333333, 1.00000000, 1.00000000],
[0.66666666, 1.00000000, 0.66666666]]
in_regions = [r for r in BEDIterator(StringIO.StringIO(self.roi))]
res = [conservtion_profile_pid(r, ga) for r in in_regions]
self.assertEqual(len(expect_raw), len(res))
for i in range(0, len(expect_raw)):
self.assertEqual(len(expect_raw[i]), len(res[i]))
for j in range(0, len(expect_raw[i])):
self.assertAlmostEqual(expect_raw[i][j], res[i][j])
# now we test with the adjusted regions
for l in in_regions:
transform_locus(l, CENTRE, 4)
res_adjusted = [conservtion_profile_pid(r, ga) for r in in_regions]
expect_adjusted = [[0.66666666, 1.00000000, 1.00000000, 1.0000000],
[0.66666666, 0.33333333, None, None],
[0.33333333, 0.33333333, 0.66666666, 0.33333333],
[None, None, 1.00000000, 1.00000000],
[None, 0.33333333, 0.66666666, 0.66666666],
[0.33333333, 1.00000000, 1.00000000, 0.66666666],
[0.66666666, 1.00000000, 0.66666666, None]]
self.assertEqual(len(expect_adjusted), len(res_adjusted))
for i in range(0, len(expect_adjusted)):
self.assertEqual(len(expect_adjusted[i]), len(res_adjusted[i]))
for j in range(0, len(expect_adjusted[i])):
self.assertAlmostEqual(expect_adjusted[i][j],
res_adjusted[i][j])
def test_conservation_profile_pid(self):
"""Test getting conservation profiles (PID) from genome alignments."""
m = StringIO.StringIO(self.maf1 + "\n\n" + self.maf2)
ga = GenomeAlignment([x for x in genome_alignment_iterator(m, "A")])
# here we're testing directly; the actual script will adjust the regions
# before it does this step.
expect_raw = [[0.66666666, 1.00000000, 1.00000000, 1.0000000],
[0.66666666, 0.33333333, None],
[0.33333333, 0.33333333, 0.66666666, 0.33333333],
[None, None, 1.00000000, 1.00000000],
[0.33333333, 0.66666666],
[0.33333333, 1.00000000, 1.00000000],
[0.66666666, 1.00000000, 0.66666666]]
in_regions = [r for r in BEDIterator(StringIO.StringIO(self.roi))]
res = [conservtion_profile_pid(r, ga) for r in in_regions]
self.assertEqual(len(expect_raw), len(res))
for i in range(0, len(expect_raw)):
self.assertEqual(len(expect_raw[i]), len(res[i]))
for j in range(0, len(expect_raw[i])):
self.assertAlmostEqual(expect_raw[i][j], res[i][j])
# now we test with the adjusted regions
for l in in_regions:
transform_locus(l, CENTRE, 4)
res_adjusted = [conservtion_profile_pid(r, ga) for r in in_regions]
expect_adjusted = [[0.66666666, 1.00000000, 1.00000000, 1.0000000],
[0.66666666, 0.33333333, None, None],
[0.33333333, 0.33333333, 0.66666666, 0.33333333],
[None, None, 1.00000000, 1.00000000],
[None, 0.33333333, 0.66666666, 0.66666666],
[0.33333333, 1.00000000, 1.00000000, 0.66666666],
[0.66666666, 1.00000000, 0.66666666, None]]
self.assertEqual(len(expect_adjusted), len(res_adjusted))
for i in range(0, len(expect_adjusted)):
self.assertEqual(len(expect_adjusted[i]), len(res_adjusted[i]))
for j in range(0, len(expect_adjusted[i])):
self.assertAlmostEqual(expect_adjusted[i][j], res_adjusted[i][j])