def testRetrievePrecedingBaseFromAnnotationForInsertions(self):
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCT"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
updated_ref_allele, updated_alt_allele, updated_start = \
MutUtils.retrievePrecedingBaseFromAnnotationForInsertions(mut)
self.assertTrue(
updated_start == start,
"Mut start should be %s but was %s." % (start, updated_start))
self.assertTrue(
updated_ref_allele == ref_allele,
"Ref allele should be %s but was %s." %
(ref_allele, updated_ref_allele))
self.assertTrue(
updated_alt_allele == alt_allele,
"Alt allele should be %s but was %s." %
(alt_allele, updated_alt_allele))
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCTT"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
updated_ref_allele, updated_alt_allele, updated_start = \
MutUtils.retrievePrecedingBaseFromAnnotationForInsertions(mut)
self.assertTrue(
updated_start == start,
"Mut start should be %s but was %s." % (start, updated_start))
self.assertTrue(
updated_ref_allele == ref_allele,
"Ref allele should be %s but was %s." %
(ref_allele, updated_ref_allele))
self.assertTrue(
updated_alt_allele == alt_allele,
"Alt allele should be %s but was %s." %
(alt_allele, updated_alt_allele))
def testRetrievePrecedingBasesForInsertions(self):
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCT"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele,
alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
self.assertTrue("_preceding_bases" in mut,
"_preceding_bases is missing in the mutation data.")
self.assertTrue(mut.start == 1234569,
"Mut start should be 1234570 but was %s." % mut.start)
self.assertTrue(mut.end == 1234570,
"Mut end should be 1234570 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "-",
"Ref allele should be - but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "T",
"Alt allele should be T but was %s." % mut.alt_allele)
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCTT"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele,
alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(
annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME,
annotationValue=preceding_bases)
self.assertTrue("_preceding_bases" in mut,
"_preceding_bases is missing in the mutation data.")
self.assertTrue(mut.start == 1234569,
"Mut start should be 1234570 but was %s." % mut.start)
self.assertTrue(mut.end == 1234570,
"Mut end should be 1234571 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "-",
"Ref allele should be - but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "TT",
"Alt allele should be TT but was %s." % mut.alt_allele)
def testRetrievePrecedingBaseFromAnnotationForInsertions(self):
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCT"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue=preceding_bases)
updated_ref_allele, updated_alt_allele, updated_start = \
MutUtils.retrievePrecedingBaseFromAnnotationForInsertions(mut)
self.assertTrue(updated_start == start, "Mut start should be %s but was %s." % (start, updated_start))
self.assertTrue(updated_ref_allele == ref_allele, "Ref allele should be %s but was %s."
% (ref_allele, updated_ref_allele))
self.assertTrue(updated_alt_allele == alt_allele, "Alt allele should be %s but was %s."
% (alt_allele, updated_alt_allele))
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCTT"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue=preceding_bases)
updated_ref_allele, updated_alt_allele, updated_start = \
MutUtils.retrievePrecedingBaseFromAnnotationForInsertions(mut)
self.assertTrue(updated_start == start, "Mut start should be %s but was %s." % (start, updated_start))
self.assertTrue(updated_ref_allele == ref_allele, "Ref allele should be %s but was %s."
% (ref_allele, updated_ref_allele))
self.assertTrue(updated_alt_allele == alt_allele, "Alt allele should be %s but was %s."
% (alt_allele, updated_alt_allele))
def testRetrievePrecedingBasesForInsertions(self):
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCT"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue=preceding_bases)
self.assertTrue("_preceding_bases" in mut, "_preceding_bases is missing in the mutation data.")
self.assertTrue(mut.start == 1234569, "Mut start should be 1234570 but was %s." % mut.start)
self.assertTrue(mut.end == 1234570, "Mut end should be 1234570 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "-", "Ref allele should be - but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "T", "Alt allele should be T but was %s." % mut.alt_allele)
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "GTCTT"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_alt_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForInsertions(mut)
mut.ref_allele = "-"
mut.alt_allele = updated_alt_allele
mut.start = updated_start
mut.end = updated_end
mut.createAnnotation(annotationName=MutUtils.PRECEDING_BASES_ANNOTATION_NAME, annotationValue=preceding_bases)
self.assertTrue("_preceding_bases" in mut, "_preceding_bases is missing in the mutation data.")
self.assertTrue(mut.start == 1234569, "Mut start should be 1234570 but was %s." % mut.start)
self.assertTrue(mut.end == 1234570, "Mut end should be 1234571 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "-", "Ref allele should be - but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "TT", "Alt allele should be TT but was %s." % mut.alt_allele)
