示例#1
0
    def test_handle_reads_unmatedReadOk(self):
        read1 = MockRead(key=1, mate_key=None)
        handler1 = MockReadHandler()
        handlers = [handler1]
        transform1 = ()
        read_transformations = {1: transform1}
        read_iter = iter([read1])

        clipper._handle_reads(handlers, read_iter, read_transformations)
        self.assertEquals(1, handler1.begin_calls)

        self.assertEquals(1, len(handler1.handle_calls))
        actual_calls = handler1.handle_calls[0]
        self.assertEquals(read1, actual_calls[0])
        self.assertEquals(transform1, actual_calls[1])
        self.assertEquals(ReadTransformation.NULL, actual_calls[2])

        self.assertEquals(1, handler1.end_calls)
示例#2
0
    def test_handle_reads_unmatedReadOk(self):
        read1 = MockRead(key=1, mate_key=None)
        handler1 = MockReadHandler()
        handlers = [handler1]
        transform1 = ()
        read_transformations = {1: transform1}
        read_iter = iter([read1])

        clipper._handle_reads(handlers, read_iter, read_transformations)
        self.assertEquals(1, handler1.begin_calls)

        self.assertEquals(1, len(handler1.handle_calls))
        actual_calls = handler1.handle_calls[0]
        self.assertEquals(read1, actual_calls[0])
        self.assertEquals(transform1, actual_calls[1])
        self.assertEquals(ReadTransformation.NULL, actual_calls[2])

        self.assertEquals(1, handler1.end_calls)
示例#3
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    def test_handle_reads_stopIterationSkipsHandlers(self):
        read1 = MockRead(key=1, mate_key=11)
        read2 = MockRead(key=2, mate_key=12)
        read3 = MockRead(key=3, mate_key=13)
        handler1 = MockReadHandler()
        handler2 = MockReadHandler(handle_raise=lambda read, _: read.key == 2)
        handler3 = MockReadHandler()
        handlers = [handler1, handler2, handler3]
        transform1 = ()
        mate_transform1 = ()
        transform2 = ()
        mate_transform2 = ()
        transform3 = ()
        mate_transform3 = ()
        read_transformations = {
            1: transform1,
            2: transform2,
            3: transform3,
            11: mate_transform1,
            12: mate_transform2,
            13: mate_transform3
        }
        read_iter = iter([read1, read2, read3])

        clipper._handle_reads(handlers, read_iter, read_transformations)
        self.assertEquals(1, handler1.begin_calls)
        self.assertEquals(1, handler2.begin_calls)
        self.assertEquals(1, handler3.begin_calls)

        expected_calls12 = [(read1, transform1, mate_transform1),
                            (read2, transform2, mate_transform2),
                            (read3, transform3, mate_transform3)]
        expected_calls3 = [(read1, transform1, mate_transform1),
                           (read3, transform3, mate_transform3)]
        self.assertEquals(expected_calls12, handler1.handle_calls)
        self.assertEquals(expected_calls12, handler2.handle_calls)
        self.assertEquals(expected_calls3, handler3.handle_calls)
        self.assertEquals(1, handler1.end_calls)
        self.assertEquals(1, handler2.end_calls)
        self.assertEquals(1, handler3.end_calls)
示例#4
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    def test_handle_reads_stopIterationSkipsHandlers(self):
        read1 = MockRead(key=1, mate_key=11)
        read2 = MockRead(key=2, mate_key=12)
        read3 = MockRead(key=3, mate_key=13)
        handler1 = MockReadHandler()
        handler2 = MockReadHandler(handle_raise=lambda read,_: read.key==2)
        handler3 = MockReadHandler()
        handlers = [handler1, handler2, handler3]
        transform1 = ()
        mate_transform1=()
        transform2 = ()
        mate_transform2=()
        transform3 = ()
        mate_transform3=()
        read_transformations = {1: transform1,
                                2: transform2,
                                3:transform3,
                                11: mate_transform1,
                                12: mate_transform2,
                                13: mate_transform3}
        read_iter = iter([read1, read2, read3])

        clipper._handle_reads(handlers, read_iter, read_transformations)
        self.assertEquals(1, handler1.begin_calls)
        self.assertEquals(1, handler2.begin_calls)
        self.assertEquals(1, handler3.begin_calls)

        expected_calls12 = [(read1, transform1, mate_transform1),
                            (read2, transform2, mate_transform2),
                            (read3, transform3, mate_transform3)]
        expected_calls3 = [(read1, transform1, mate_transform1),
                           (read3, transform3, mate_transform3)]
        self.assertEquals(expected_calls12, handler1.handle_calls)
        self.assertEquals(expected_calls12, handler2.handle_calls)
        self.assertEquals(expected_calls3, handler3.handle_calls)
        self.assertEquals(1, handler1.end_calls)
        self.assertEquals(1, handler2.end_calls)
        self.assertEquals(1, handler3.end_calls)
示例#5
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    def test_handle_reads(self):
        handler1 = MockReadHandler()
        handler2 = MockReadHandler()
        handler3 = MockReadHandler()
        handlers = [handler1, handler2, handler3]
        read1 = MockRead(key=1, mate_key=11)
        read2 = MockRead(key=2, mate_key=12)
        read3 = MockRead(key=3, mate_key=13)
        transform1 = ()
        mate_transform1 = ()
        transform2 = ()
        mate_transform2 = ()
        transform3 = ()
        mate_transform3 = ()

        read_transformations = {
            1: transform1,
            2: transform2,
            3: transform3,
            11: mate_transform1,
            12: mate_transform2,
            13: mate_transform3
        }
        read_iter = iter([read1, read2, read3])
        clipper._handle_reads(handlers, read_iter, read_transformations)
        self.assertEquals(1, handler1.begin_calls)
        self.assertEquals(1, handler2.begin_calls)
        self.assertEquals(1, handler3.begin_calls)

        expected_calls = [(read1, transform1, mate_transform1),
                          (read2, transform2, mate_transform2),
                          (read3, transform3, mate_transform3)]
        self.assertEquals(expected_calls, handler1.handle_calls)
        self.assertEquals(expected_calls, handler2.handle_calls)
        self.assertEquals(expected_calls, handler3.handle_calls)
        self.assertEquals(1, handler1.end_calls)
        self.assertEquals(1, handler2.end_calls)
        self.assertEquals(1, handler3.end_calls)
示例#6
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    def test_handle_reads(self):
        handler1 = MockReadHandler()
        handler2 = MockReadHandler()
        handler3 = MockReadHandler()
        handlers = [handler1, handler2, handler3]
        read1 = MockRead(key=1, mate_key=11)
        read2 = MockRead(key=2, mate_key=12)
        read3 = MockRead(key=3, mate_key=13)
        transform1 = ()
        mate_transform1=()
        transform2 = ()
        mate_transform2=()
        transform3 = ()
        mate_transform3=()

        read_transformations = {1: transform1,
                                2: transform2,
                                3:transform3,
                                11: mate_transform1,
                                12: mate_transform2,
                                13: mate_transform3}
        read_iter = iter([read1, read2, read3])
        clipper._handle_reads(handlers, read_iter, read_transformations)
        self.assertEquals(1, handler1.begin_calls)
        self.assertEquals(1, handler2.begin_calls)
        self.assertEquals(1, handler3.begin_calls)

        expected_calls = [(read1, transform1, mate_transform1),
                          (read2, transform2, mate_transform2),
                          (read3, transform3, mate_transform3)]
        self.assertEquals(expected_calls, handler1.handle_calls)
        self.assertEquals(expected_calls, handler2.handle_calls)
        self.assertEquals(expected_calls, handler3.handle_calls)
        self.assertEquals(1, handler1.end_calls)
        self.assertEquals(1, handler2.end_calls)
        self.assertEquals(1, handler3.end_calls)