def test_copy(self):
"""Test annotation copy """
m = MutationData()
m.createAnnotation("foo", "3", "blah_source", annotationDescription="testing", tags=["superblah"], number="A")
m.createCopyAnnotation(m.getAnnotation("foo"), "bar")
# Note that getAnnotation returns an instance of Annotation, not simply the value
self.assertEqual(m.getAnnotation("foo"), m.getAnnotation("bar"))
def testAnnotationSourceIsPopulated(self):
''' Tests that the annotation source is not blank for the example tsv datasource. '''
geneDS = DatasourceFactory.createDatasource("testdata/small_tsv_ds/small_tsv_ds.config", "testdata/small_tsv_ds/")
self.assertTrue(geneDS <> None, "gene indexed datasource was None.")
m = MutationData()
m.createAnnotation('gene',"ABL1")
m = geneDS.annotate_mutation(m)
self.assertTrue(m['CGC_Abridged_Name'] == "v-abl Abelson murine leukemia viral oncogene homolog 1","Test gene TSV datasource did not annotate properly.")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource() <> "Unknown", "Annotation source was unknown")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource().strip() <> "", "Annotation source was blank")
def testAnnotationSourceIsPopulated(self):
''' Tests that the annotation source is not blank for the example tsv datasource. '''
geneDS = DatasourceFactory.createDatasource("testdata/small_tsv_ds/small_tsv_ds.config", "testdata/small_tsv_ds/")
self.assertTrue(geneDS <> None, "gene indexed datasource was None.")
m = MutationData()
m.createAnnotation('gene',"ABL1")
m = geneDS.annotate_mutation(m)
self.assertTrue(m['CGC_Abridged_Name'] == "v-abl Abelson murine leukemia viral oncogene homolog 1","Test gene TSV datasource did not annotate properly.")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource() <> "Unknown", "Annotation source was unknown")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource().strip() <> "", "Annotation source was blank")
def test_copy(self):
"""Test annotation copy """
m = MutationData()
m.createAnnotation("foo",
"3",
"blah_source",
annotationDescription="testing",
tags=["superblah"],
number="A")
m.createCopyAnnotation(m.getAnnotation("foo"), "bar")
# Note that getAnnotation returns an instance of Annotation, not simply the value
self.assertEqual(m.getAnnotation("foo"), m.getAnnotation("bar"))
def testAddTag(self):
''' Test adding a tag to an annotation '''
m = MutationData()
m.createAnnotation("fake1", "1")
m.addTagToAnnotation("fake1", "fakeTag")
self.assertTrue("fakeTag" in m.getAnnotation("fake1").getTags(),
"Tag was not added properly.")
def testAddTag(self):
''' Test adding a tag to an annotation '''
m = MutationData()
m.createAnnotation("fake1", "1")
m.addTagToAnnotation("fake1", "fakeTag")
self.assertTrue("fakeTag" in m.getAnnotation("fake1").getTags(), "Tag was not added properly.")
def test_hash(self):
"""Test that hashing works for a mutation data"""
m = MutationData()
m.start = 1
m.createAnnotation("foo",
"3",
"blah_source",
annotationDescription="testing",
tags=["superblah"],
number="A")
m.createCopyAnnotation(m.getAnnotation("foo"), "bar")
# Not unique
m2 = MutationData()
m2.start = 1
m2.createAnnotation("foo",
"3",
"blah_source",
annotationDescription="testing",
tags=["superblah"],
number="A")
m2.createCopyAnnotation(m.getAnnotation("foo"), "bar")
m3 = MutationData()
m3.start = 1
m3.createAnnotation("foo",
"3",
"blah_source",
annotationDescription="testing 2",
tags=["superblah"],
number="A")
m3.createCopyAnnotation(m.getAnnotation("foo"), "bar")
m4 = MutationData()
m4.start = 1
m4.createAnnotation("foo",
"3",
"blah_source",
annotationDescription="testing 2",
tags=["superblah", "testy blah"],
number="A")
m4.createCopyAnnotation(m.getAnnotation("foo"), "bar")
m5 = MutationData()
m5.start = 10
m5.createAnnotation("foo",
"3",
"blah_source",
annotationDescription="testing 2",
tags=["superblah", "testy blah"],
number="A")
m5.createCopyAnnotation(m.getAnnotation("foo"), "bar")
result = set()
result.add(m)
result.add(m2)
result.add(m3)
result.add(m4)
result.add(m5)
self.assertEqual(len(result), 4)