Ejemplo n.º 1
0
class TestEventMapping():

	def __init__(self):
		self.template_model = EventModel("models/template_model_5.model")
		self.complement_model = EventModel("models/complement_model_5.model")
		self.event_mapper = EventMapper()

		self.my_seq = Seq("CAAAACGTGT")
		self.forward_template_events = Seq2Events(self.my_seq, self.template_model).events
		self.reverse_template_events = Seq2Events(self.my_seq.reverse_complement(), self.template_model).events
		
		self.reverse_complement_events = Seq2Events(self.my_seq.reverse_complement(), self.complement_model).events
		self.forward_complement_events = Seq2Events(self.my_seq, self.complement_model).events

		self.complement_seq = self.my_seq.reverse_complement()


	def test_make_simple_reference(self):
		forward_template_mapping_results = self.event_mapper.map(self.forward_template_events, self.forward_template_events)
		reverse_template_mapping_results = self.event_mapper.map(self.reverse_template_events, self.forward_template_events)
		forward_complement_mapping_results = self.event_mapper.map(self.forward_complement_events, self.forward_template_events)
		reverse_complement_mapping_results = self.event_mapper.map(self.reverse_complement_events, self.forward_template_events)


		assert len(forward_template_mapping_results.path[0]) == 6

		assert forward_template_mapping_results.path[0].tolist() == [0, 1, 2 ,3, 4, 5]
		assert forward_template_mapping_results.path[1].tolist() == [0, 1, 2 , 3 ,4, 5]

		assert min([sum(sum(forward_template_mapping_results.cost)),
					sum(sum(reverse_template_mapping_results.cost)),
					sum(sum(forward_complement_mapping_results.cost)),
					sum(sum(reverse_complement_mapping_results.cost))]) == sum(sum(forward_template_mapping_results.cost))

		assert min([forward_template_mapping_results.dist,
					reverse_template_mapping_results.dist, 
					forward_complement_mapping_results.dist, 
					reverse_complement_mapping_results.dist]) == forward_template_mapping_results.dist

	def test_complement_mapping(self):
		forward_template_mapping_results = self.event_mapper.map(self.forward_template_events, self.forward_complement_events)
		reverse_template_mapping_results = self.event_mapper.map(self.reverse_template_events, self.forward_complement_events)
		forward_complement_mapping_results = self.event_mapper.map(self.forward_complement_events, self.forward_complement_events)
		reverse_complement_mapping_results = self.event_mapper.map(self.reverse_complement_events, self.forward_complement_events)


		assert len(forward_complement_mapping_results.path[0]) == 6

		assert forward_complement_mapping_results.path[0].tolist() == [0, 1, 2 ,3, 4, 5]
		assert forward_complement_mapping_results.path[1].tolist() == [0, 1, 2 , 3 ,4, 5]

		assert min([sum(sum(forward_template_mapping_results.cost)),
					sum(sum(reverse_template_mapping_results.cost)),
					sum(sum(forward_complement_mapping_results.cost)),
					sum(sum(reverse_complement_mapping_results.cost))]) == sum(sum(forward_complement_mapping_results.cost))

		assert min([forward_template_mapping_results.dist,
					reverse_template_mapping_results.dist, 
					forward_complement_mapping_results.dist, 
					reverse_complement_mapping_results.dist]) == forward_complement_mapping_results.dist
Ejemplo n.º 2
0
	def __init__(self):
		self.template_model = EventModel("models/template_model_5.model")
		self.complement_model = EventModel("models/complement_model_5.model")
		self.event_mapper = EventMapper()

		self.my_seq = Seq("CAAAACGTGT")
		self.forward_template_events = Seq2Events(self.my_seq, self.template_model).events
		self.reverse_template_events = Seq2Events(self.my_seq.reverse_complement(), self.template_model).events
		
		self.reverse_complement_events = Seq2Events(self.my_seq.reverse_complement(), self.complement_model).events
		self.forward_complement_events = Seq2Events(self.my_seq, self.complement_model).events

		self.complement_seq = self.my_seq.reverse_complement()