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)
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)
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)
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)
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)