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
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()