本文整理汇总了Python中oncotator.utils.MutUtils.MutUtils.retrievePrecedingBaseFromAnnotationForInsertions方法的典型用法代码示例。如果您正苦于以下问题：Python MutUtils.retrievePrecedingBaseFromAnnotationForInsertions方法的具体用法？Python MutUtils.retrievePrecedingBaseFromAnnotationForInsertions怎么用？Python MutUtils.retrievePrecedingBaseFromAnnotationForInsertions使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类oncotator.utils.MutUtils.MutUtils的用法示例。
在下文中一共展示了MutUtils.retrievePrecedingBaseFromAnnotationForInsertions方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: testRetrievePrecedingBaseFromAnnotationForInsertions
# 需要导入模块: from oncotator.utils.MutUtils import MutUtils [as 别名]
# 或者: from oncotator.utils.MutUtils.MutUtils import retrievePrecedingBaseFromAnnotationForInsertions [as 别名]
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))