def test_mutation_combiner_ordering(self):
"""Test that ordering of combined attributes makes matches original order"""
mut1 = MutationDataFactory.default_create(chr=1,
start=100,
end=100,
ref_allele="G",
alt_allele="A")
mut1.createAnnotation("SomeDepth", "2")
mut1.createAnnotation("AnotherDepth", "1")
mut2 = MutationDataFactory.default_create(chr=1,
start=101,
end=101,
ref_allele="C",
alt_allele="T")
mut2.createAnnotation("SomeDepth", "1")
mut2.createAnnotation("AnotherDepth", "2")
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([mut1, mut2], mdf)
expected = MutationDataFactory.default_create(chr=1,
start=100,
end=101,
ref_allele="GC",
alt_allele="AT")
expected.createAnnotation("SomeDepth", "2|1")
expected.createAnnotation("AnotherDepth", "1|2")
self.assertTrue(result.attributesEqual(expected))
self.assertEqual(result, expected)
def test_mutation_combiner_identical_annotation(self):
"""Test that annotations with all identical values are not repeated with | between them"""
mut1 = MutationDataFactory.default_create(chr=1,
start=100,
end=100,
ref_allele="G",
alt_allele="A")
mut1.createAnnotation("SampleName", "John Doe")
mut2 = MutationDataFactory.default_create(chr=1,
start=101,
end=101,
ref_allele="C",
alt_allele="T")
mut2.createAnnotation("SampleName", "John Doe")
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([mut1, mut2], mdf)
expected = MutationDataFactory.default_create(chr=1,
start=100,
end=101,
ref_allele="GC",
alt_allele="AT")
expected.createAnnotation("SampleName", "John Doe")
self.assertTrue(result.attributesEqual(expected))
self.assertEqual(result, expected)
def test_mutation_combiner(self):
"""Test that attributes and annotations are set properly with combine mutations"""
mut1 = MutationDataFactory.default_create(chr=1,
start=100,
end=100,
ref_allele="G",
alt_allele="A")
mut1.createAnnotation("SomeValue", "value1", "INPUT", "STRING",
"a value")
mut2 = MutationDataFactory.default_create(chr=1,
start=101,
end=101,
ref_allele="C",
alt_allele="T")
mut2.createAnnotation("SomeValue", "value2", tags=["IT"])
mut2.createAnnotation("AnotherValue", "5")
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([mut1, mut2], mdf)
expected = MutationDataFactory.default_create(chr=1,
start=100,
end=101,
ref_allele="GC",
alt_allele="AT")
expected.createAnnotation("SomeValue",
"value1|value2",
"INPUT",
"STRING",
"a value",
tags=["IT"])
expected.createAnnotation("AnotherValue", "5")
self.assertTrue(result.attributesEqual(expected))
self.assertEqual(result, expected)
def test_mutation_combiner_identical_annotation(self):
"""Test that annotations with all identical values are not repeated with | between them"""
mut1 = MutationDataFactory.default_create(chr=1,start=100, end=100, ref_allele="G", alt_allele="A")
mut1.createAnnotation("SampleName", "John Doe")
mut2 = MutationDataFactory.default_create(chr=1,start=101, end=101, ref_allele="C", alt_allele="T")
mut2.createAnnotation("SampleName", "John Doe" )
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([mut1, mut2], mdf)
expected = MutationDataFactory.default_create(chr=1, start=100, end=101, ref_allele="GC", alt_allele="AT")
expected.createAnnotation("SampleName", "John Doe")
self.assertTrue(result.attributesEqual(expected))
self.assertEqual(result, expected)
def test_mutation_combiner(self):
"""Test that attributes and annotations are set properly with combine mutations"""
mut1 = MutationDataFactory.default_create(chr=1,start=100, end=100, ref_allele="G", alt_allele="A")
mut1.createAnnotation("SomeValue", "value1", "INPUT", "STRING", "a value")
mut2 = MutationDataFactory.default_create(chr=1,start=101, end=101, ref_allele="C", alt_allele="T")
mut2.createAnnotation("SomeValue", "value2", tags=["IT"])
mut2.createAnnotation("AnotherValue","5")
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([mut1, mut2], mdf)
expected = MutationDataFactory.default_create(chr=1, start=100, end=101, ref_allele="GC", alt_allele="AT")
expected.createAnnotation("SomeValue", "value1|value2", "INPUT", "STRING", "a value", tags=["IT"])
expected.createAnnotation("AnotherValue", "5")
self.assertTrue(result.attributesEqual(expected))
self.assertEqual(result, expected)
def test_mutation_combiner_ordering(self):
"""Test that ordering of combined attributes makes matches original order"""
mut1 = MutationDataFactory.default_create(chr=1,start=100, end=100, ref_allele="G", alt_allele="A")
mut1.createAnnotation("SomeDepth", "2")
mut1.createAnnotation("AnotherDepth", "1")
mut2 = MutationDataFactory.default_create(chr=1,start=101, end=101, ref_allele="C", alt_allele="T")
mut2.createAnnotation("SomeDepth", "1" )
mut2.createAnnotation("AnotherDepth", "2")
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([mut1, mut2], mdf)
expected = MutationDataFactory.default_create(chr=1, start=100, end=101, ref_allele="GC", alt_allele="AT")
expected.createAnnotation("SomeDepth", "2|1")
expected.createAnnotation("AnotherDepth","1|2")
self.assertTrue(result.attributesEqual(expected))
self.assertEqual(result, expected)
def test_mutation_combiner_no_mut(self):
"""Combining no mutations should return None"""
result = OnpQueue._combine_mutations([])
self.assertIsNone(result)
def test_mutation_combiner_no_mut(self):
"""Combining no mutations should return None"""
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([], mdf)
self.assertIsNone(result)
def test_mutation_combiner_no_mut(self):
"""Combining no mutations should return None"""
mdf = MutationDataFactory()
result = OnpQueue._combine_mutations([], mdf)
self.assertIsNone(result)
