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))
