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)