def _handleMissingAnnotations(self, m):
missingHeaderAnnotations = MutUtils.retrieveMissingAnnotations(m,
TcgaVcfOutputRenderer.requiredHeaderAnnotations)
missingMutAnnotations = MutUtils.retrieveMissingAnnotations(m, TcgaVcfOutputRenderer.requiredMutAnnotations)
if len(missingHeaderAnnotations) > 0:
sError = "The following annotations are required for rendering a TCGA VCF 1.1, but were not found: " + str(
missingHeaderAnnotations)
self.logger.error(sError)
raise MissingAnnotationException(sError)
if len(missingMutAnnotations) > 0:
sError = "The following annotations important for rendering a TCGA VCF 1.1. Proceeding... : " + str(
missingMutAnnotations)
self.logger.warn(sError)
def _handleMissingAnnotations(self, m):
missingHeaderAnnotations = MutUtils.retrieveMissingAnnotations(
m, TcgaVcfOutputRenderer.requiredHeaderAnnotations)
missingMutAnnotations = MutUtils.retrieveMissingAnnotations(
m, TcgaVcfOutputRenderer.requiredMutAnnotations)
if len(missingHeaderAnnotations) > 0:
sError = "The following annotations are required for rendering a TCGA VCF 1.1, but were not found: " + str(
missingHeaderAnnotations)
self.logger.error(sError)
raise MissingAnnotationException(sError)
if len(missingMutAnnotations) > 0:
sError = "The following annotations important for rendering a TCGA VCF 1.1. Proceeding... : " + str(
missingMutAnnotations)
self.logger.warn(sError)
def testRetrieveMissingAnnotations(self):
""" Test simple case.
"""
m = MutationDataFactory.default_create()
m.createAnnotation("a1", "1")
m.createAnnotation("a2", "1")
m.createAnnotation("a3", "1")
m.createAnnotation("a4", "1")
annotationNames = ["a3", "a2"]
result = MutUtils.retrieveMissingAnnotations(m,annotationNames)
self.assertIsNotNone(result)
self.assertTrue(len(result) == 0, "Result was not empty: " + str(result))
annotationNames = ["zztop", "a1", "blah", "dummy"]
result = MutUtils.retrieveMissingAnnotations(m,annotationNames)
self.assertTrue(result[0] == "blah", "Result was not sorted")
self.assertTrue("blah" in result and "dummy" in result and "zztop" in result, "Incorrect elements (Truth: [zztop, blah, dummy]): " + str(result))
def testRetrieveMissingAnnotations(self):
""" Test simple case.
"""
m = MutationData()
m.createAnnotation("a1", "1")
m.createAnnotation("a2", "1")
m.createAnnotation("a3", "1")
m.createAnnotation("a4", "1")
annotationNames = ["a3", "a2"]
result = MutUtils.retrieveMissingAnnotations(m, annotationNames)
self.assertIsNotNone(result)
self.assertTrue(
len(result) == 0, "Result was not empty: " + str(result))
annotationNames = ["zztop", "a1", "blah", "dummy"]
result = MutUtils.retrieveMissingAnnotations(m, annotationNames)
self.assertTrue(result[0] == "blah", "Result was not sorted")
self.assertTrue(
"blah" in result and "dummy" in result and "zztop" in result,
"Incorrect elements (Truth: [zztop, blah, dummy]): " + str(result))
