def initializeMutFromAttributes(chr, start, end, ref_allele, alt_allele, build, mutation_data_factory=None):
mutation_data_factory = MutationDataFactory() if mutation_data_factory is None else mutation_data_factory
mut = mutation_data_factory.create(str(chr), str(start), str(end), ref_allele, alt_allele, str(build))
varType = TranscriptProviderUtils.infer_variant_type(mut.ref_allele, mut.alt_allele)
if TranscriptProviderUtils.is_xnp(varType): # Snps and other xNPs
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue="")
if varType == VariantClassification.VT_DEL: # deletion
preceding_bases, updated_ref_allele, updated_start, updated_end =\
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut["ref_allele"] = updated_ref_allele
mut.alt_allele = "-"
mut["alt_allele"] = "-"
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
elif varType == VariantClassification.VT_INS: # insertion
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut["ref_allele"] = "-"
mut.alt_allele = updated_alt_allele
mut["alt_allele"] = updated_alt_allele
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
return mut
def test_annotation_overwriting_on(self):
"""Test that the factory can produce a mutation that allows overwriting. Just need to make sure no exception thrown."""
mdf = MutationDataFactory(allow_overwriting=True)
mut = mdf.create()
mut.createAnnotation("blah", "123")
self.assertTrue(mut['blah'] == "123")
mut.createAnnotation("blah", "456")
self.assertTrue(mut['blah'] == "456")
def test_annotation_overwriting_on(self):
"""Test that the factory can produce a mutation that allows overwriting. Just need to make sure no exception thrown."""
mdf = MutationDataFactory(allow_overwriting=True)
mut = mdf.create()
mut.createAnnotation("blah", "123")
self.assertTrue(mut['blah'] == "123")
mut.createAnnotation("blah", "456")
self.assertTrue(mut['blah'] == "456")
def test_annotation_overwriting_off(self):
"""Test that the factory can produce a mutation that does not allow overwriting. Make sure DuplicateAnnotationException is thrown."""
mdf = MutationDataFactory(allow_overwriting=False)
mut = mdf.create()
mut.createAnnotation("blah", "123")
self.assertTrue(mut['blah'] == "123")
is_exception_raised = False
try:
mut.createAnnotation("blah", "456")
except DuplicateAnnotationException as dae:
is_exception_raised = True
self.assertTrue(is_exception_raised, "DuplicateAnnotationException should have been seen, but wasn't")
def initializeMutFromAttributes(chr,
start,
end,
ref_allele,
alt_allele,
build,
mutation_data_factory=None):
mutation_data_factory = MutationDataFactory(
) if mutation_data_factory is None else mutation_data_factory
mut = mutation_data_factory.create(str(chr), str(start), str(end),
ref_allele, alt_allele, str(build))
varType = TranscriptProviderUtils.infer_variant_type(
mut.ref_allele, mut.alt_allele)
if TranscriptProviderUtils.is_xnp(varType): # Snps and other xNPs
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue="")
if varType == VariantClassification.VT_DEL: # deletion
preceding_bases, updated_ref_allele, updated_start, updated_end =\
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut["ref_allele"] = updated_ref_allele
mut.alt_allele = "-"
mut["alt_allele"] = "-"
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
elif varType == VariantClassification.VT_INS: # insertion
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut["ref_allele"] = "-"
mut.alt_allele = updated_alt_allele
mut["alt_allele"] = updated_alt_allele
mut.start = updated_start
mut["start"] = updated_start
mut.end = updated_end
mut["end"] = updated_end
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
return mut
def test_annotation_overwriting_off(self):
"""Test that the factory can produce a mutation that does not allow overwriting. Make sure DuplicateAnnotationException is thrown."""
mdf = MutationDataFactory(allow_overwriting=False)
mut = mdf.create()
mut.createAnnotation("blah", "123")
self.assertTrue(mut['blah'] == "123")
is_exception_raised = False
try:
mut.createAnnotation("blah", "456")
except DuplicateAnnotationException as dae:
is_exception_raised = True
self.assertTrue(
is_exception_raised,
"DuplicateAnnotationException should have been seen, but wasn't")
