def _paths(finished_paths, path_so_far, start, muts):
"""Return all paths from the start position through the mutation graph
:param finished_paths: completed paths
:param path_so_far: the accumulated mutation->mutation path so far
:param start: the start position to travers the muts from
:param muts: a dictionary in the form {start_position: [Mutation]}
:return: All paths through adjacent mutations starting with mutations at chromosome position start
"""
if muts == [] or start not in muts:
# No mutations available to continue this chain
finished_paths.append(path_so_far)
else:
# return reduce(operator.concat, lambda mut: OnpCombiner._paths(path + [mut], mut.end+1, muts), [])
# path = map(lambda mut: OnpQueue._paths(path + [mut], int(mut.end)+1, muts), muts[start])
for mut in muts[start]:
if len(path_so_far) > 0 and not PhasingUtils.is_in_phase(
path_so_far[-1], mut):
# Next mutation not in phase, so stop this path here.
finished_paths.append(path_so_far)
else:
OnpQueue._paths(finished_paths, path_so_far + [mut],
int(mut.end) + 1, muts)
return finished_paths
def test_phasing_info_missing(self):
"""Test whether we accurately say whether the phasing info present test works"""
m1 = MutationData()
m2 = MutationData()
m3 = MutationData()
m4 = MutationData()
m1.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_genotype", "0|1")
m4.createAnnotation("phasing_genotype", "0|1")
# m1 missing gt, m2 complete, m3 missing everything, m4 missing ID
self.assertFalse(PhasingUtils.has_phasing_information(m1))
self.assertTrue(PhasingUtils.has_phasing_information(m2))
self.assertFalse(PhasingUtils.has_phasing_information(m3))
self.assertFalse(PhasingUtils.has_phasing_information(m4))
def test_phasing_info_missing(self):
"""Test whether we accurately say whether the phasing info present test works"""
m1 = MutationData()
m2 = MutationData()
m3 = MutationData()
m4 = MutationData()
m1.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_genotype", "0|1")
m4.createAnnotation("phasing_genotype", "0|1")
# m1 missing gt, m2 complete, m3 missing everything, m4 missing ID
self.assertFalse(PhasingUtils.has_phasing_information(m1))
self.assertTrue(PhasingUtils.has_phasing_information(m2))
self.assertFalse(PhasingUtils.has_phasing_information(m3))
self.assertFalse(PhasingUtils.has_phasing_information(m4))
def _paths(finished_paths, path_so_far, start, muts):
"""Return all paths from the start position through the mutation graph
:param finished_paths: completed paths
:param path_so_far: the accumulated mutation->mutation path so far
:param start: the start position to travers the muts from
:param muts: a dictionary in the form {start_position: [Mutation]}
:return: All paths through adjacent mutations starting with mutations at chromosome position start
"""
if muts == [] or start not in muts:
# No mutations available to continue this chain
finished_paths.append(path_so_far)
else:
# return reduce(operator.concat, lambda mut: OnpCombiner._paths(path + [mut], mut.end+1, muts), [])
# path = map(lambda mut: OnpQueue._paths(path + [mut], int(mut.end)+1, muts), muts[start])
for mut in muts[start]:
if len(path_so_far) > 0 and not PhasingUtils.is_in_phase(path_so_far[-1], mut):
# Next mutation not in phase, so stop this path here.
finished_paths.append(path_so_far)
else:
OnpQueue._paths(finished_paths, path_so_far + [mut], int(mut.end) + 1, muts)
return finished_paths
def test_phasing_check(self):
"""
Test the actual phasing check.
"""
m1 = MutationData()
m2 = MutationData()
m3 = MutationData()
m4 = MutationData()
m5 = MutationData()
m6 = MutationData()
m7 = MutationData()
m1.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_genotype", "0|1")
m4.createAnnotation("phasing_genotype", "0|1")
m5.createAnnotation("phasing_id", "blah")
m5.createAnnotation("phasing_genotype", "0|1")
m6.createAnnotation("phasing_id", "blahdifferent")
m6.createAnnotation("phasing_genotype", "0|1")
# m1 and m2 should not be in phase, even though they share IDs, since m1 is missing the genotype info
unknown_val = True
self.assertFalse(PhasingUtils.is_in_phase(m1, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m1, unknown_val))
unknown_val = False
self.assertFalse(PhasingUtils.is_in_phase(m1, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m1, unknown_val))
# m2 and m4 should not be in phase, since m4 is missing the ID
unknown_val = True
self.assertFalse(PhasingUtils.is_in_phase(m4, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m4, unknown_val))
unknown_val = False
self.assertFalse(PhasingUtils.is_in_phase(m4, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m4, unknown_val))
# m3 and m7 should be unknown_val, since phasing info is missing.
unknown_val = True
self.assertTrue(PhasingUtils.is_in_phase(m3, m7, unknown_val) == unknown_val)
self.assertTrue(PhasingUtils.is_in_phase(m7, m3, unknown_val) == unknown_val)
unknown_val = False
self.assertTrue(PhasingUtils.is_in_phase(m3, m7, unknown_val) == unknown_val)
self.assertTrue(PhasingUtils.is_in_phase(m7, m3, unknown_val) == unknown_val)
# m2 and m5 should be in phase, regardless of the unknown_val parameter
self.assertTrue(PhasingUtils.is_in_phase(m2, m5, True))
self.assertTrue(PhasingUtils.is_in_phase(m5, m2, False))
self.assertTrue(PhasingUtils.is_in_phase(m2, m5, False))
self.assertTrue(PhasingUtils.is_in_phase(m5, m2, True))
# m2 and m6 should not be in phase, since the ID is different, regardless of the unknown_val parameter
self.assertFalse(PhasingUtils.is_in_phase(m2, m6, True))
self.assertFalse(PhasingUtils.is_in_phase(m6, m2, False))
self.assertFalse(PhasingUtils.is_in_phase(m2, m6, False))
self.assertFalse(PhasingUtils.is_in_phase(m6, m2, True))
def test_phasing_check(self):
"""
Test the actual phasing check.
"""
m1 = MutationData()
m2 = MutationData()
m3 = MutationData()
m4 = MutationData()
m5 = MutationData()
m6 = MutationData()
m7 = MutationData()
m1.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_id", "blah")
m2.createAnnotation("phasing_genotype", "0|1")
m4.createAnnotation("phasing_genotype", "0|1")
m5.createAnnotation("phasing_id", "blah")
m5.createAnnotation("phasing_genotype", "0|1")
m6.createAnnotation("phasing_id", "blahdifferent")
m6.createAnnotation("phasing_genotype", "0|1")
# m1 and m2 should not be in phase, even though they share IDs, since m1 is missing the genotype info
unknown_val = True
self.assertFalse(PhasingUtils.is_in_phase(m1, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m1, unknown_val))
unknown_val = False
self.assertFalse(PhasingUtils.is_in_phase(m1, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m1, unknown_val))
# m2 and m4 should not be in phase, since m4 is missing the ID
unknown_val = True
self.assertFalse(PhasingUtils.is_in_phase(m4, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m4, unknown_val))
unknown_val = False
self.assertFalse(PhasingUtils.is_in_phase(m4, m2, unknown_val))
self.assertFalse(PhasingUtils.is_in_phase(m2, m4, unknown_val))
# m3 and m7 should be unknown_val, since phasing info is missing.
unknown_val = True
self.assertTrue(
PhasingUtils.is_in_phase(m3, m7, unknown_val) == unknown_val)
self.assertTrue(
PhasingUtils.is_in_phase(m7, m3, unknown_val) == unknown_val)
unknown_val = False
self.assertTrue(
PhasingUtils.is_in_phase(m3, m7, unknown_val) == unknown_val)
self.assertTrue(
PhasingUtils.is_in_phase(m7, m3, unknown_val) == unknown_val)
# m2 and m5 should be in phase, regardless of the unknown_val parameter
self.assertTrue(PhasingUtils.is_in_phase(m2, m5, True))
self.assertTrue(PhasingUtils.is_in_phase(m5, m2, False))
self.assertTrue(PhasingUtils.is_in_phase(m2, m5, False))
self.assertTrue(PhasingUtils.is_in_phase(m5, m2, True))
# m2 and m6 should not be in phase, since the ID is different, regardless of the unknown_val parameter
self.assertFalse(PhasingUtils.is_in_phase(m2, m6, True))
self.assertFalse(PhasingUtils.is_in_phase(m6, m2, False))
self.assertFalse(PhasingUtils.is_in_phase(m2, m6, False))
self.assertFalse(PhasingUtils.is_in_phase(m6, m2, True))
