def testRetrievePrecedingBaseFromAnnotationForDeletions(self):
chrom = "1"
start = 1234568
end = 1234569 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "G"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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.retrievePrecedingBaseFromAnnotationForDeletions(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 = "GTCT"
alt_allele = "GTC"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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.retrievePrecedingBaseFromAnnotationForDeletions(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 = 152497145
end = 152497145 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "CCCGAGCTGCTTACGATAGCCTTCTT"
alt_allele = "C"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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.retrievePrecedingBaseFromAnnotationForDeletions(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 testRetrievePrecedingBaseFromAnnotationForDeletions(self):
chrom = "1"
start = 1234568
end = 1234569 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "G"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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.retrievePrecedingBaseFromAnnotationForDeletions(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 = "GTCT"
alt_allele = "GTC"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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.retrievePrecedingBaseFromAnnotationForDeletions(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 = 152497145
end = 152497145 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "CCCGAGCTGCTTACGATAGCCTTCTT"
alt_allele = "C"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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.retrievePrecedingBaseFromAnnotationForDeletions(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 testRetrievePrecedingBasesForDeletions(self):
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "G"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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 == 1234568, "Mut start should be 1234568 but was %s." % mut.start)
self.assertTrue(mut.end == 1234569, "Mut end should be 1234569 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "TC", "Ref allele should be TC but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "-", "Alt allele should be - but was %s." % mut.alt_allele)
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTCT"
alt_allele = "GTC"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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 == 1234570, "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 == "T", "Ref allele should be T but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "-", "Alt allele should be - but was %s." % mut.alt_allele)
chrom = "1"
start = 152497145
end = 152497145 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "CCCGAGCTGCTTACGATAGCCTTCTT"
alt_allele = "C"
build = "19"
mut = MutationDataFactory.default_create(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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 == 152497146, "Mut start should be 1234570 but was %s." % mut.start)
self.assertTrue(mut.end == 152497170, "Mut end should be 1234570 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "CCGAGCTGCTTACGATAGCCTTCTT", "Ref allele should be T but was %s."
% mut.ref_allele)
self.assertTrue(mut.alt_allele == "-", "Alt allele should be - but was %s." % mut.alt_allele)
def testRetrievePrecedingBasesForDeletions(self):
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTC"
alt_allele = "G"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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 == 1234568,
"Mut start should be 1234568 but was %s." % mut.start)
self.assertTrue(mut.end == 1234569,
"Mut end should be 1234569 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "TC",
"Ref allele should be TC but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "-",
"Alt allele should be - but was %s." % mut.alt_allele)
chrom = "1"
start = 1234567
end = 1234567 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "GTCT"
alt_allele = "GTC"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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 == 1234570,
"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 == "T",
"Ref allele should be T but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "-",
"Alt allele should be - but was %s." % mut.alt_allele)
chrom = "1"
start = 152497145
end = 152497145 # incorrect, but doesn't matter for the purposed of testing
ref_allele = "CCCGAGCTGCTTACGATAGCCTTCTT"
alt_allele = "C"
build = "19"
mut = MutationData(chrom, start, end, ref_allele, alt_allele, build)
preceding_bases, updated_ref_allele, updated_start, updated_end = \
MutUtils.retrievePrecedingBasesForDeletions(mut)
mut.ref_allele = updated_ref_allele
mut.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 == 152497146,
"Mut start should be 1234570 but was %s." % mut.start)
self.assertTrue(mut.end == 152497170,
"Mut end should be 1234570 but was %s." % mut.end)
self.assertTrue(mut.ref_allele == "CCGAGCTGCTTACGATAGCCTTCTT",
"Ref allele should be T but was %s." % mut.ref_allele)
self.assertTrue(mut.alt_allele == "-",
"Alt allele should be - but was %s." % mut.alt_allele)