def summarize(self):
"""Summarize the activities of this :class:`Adapter`.
"""
total_front = sum(self.lengths_front.values())
total_back = sum(self.lengths_back.values())
stats = MergingDict(adapter_class=self.__class__.__name__,
total_front=total_front,
total_back=total_back,
total=total_front + total_back,
match_probabilities=Const(
self.random_match_probabilities()))
where = self.where
assert (where in (ANYWHERE, LINKED)
or (where in (BACK, SUFFIX) and total_front == 0)
or (where in (FRONT, PREFIX) and total_back == 0))
stats["where"] = where_int_to_dict(where)
stats["sequence"] = Const(self.sequence)
stats["max_error_rate"] = Const(self.max_error_rate)
if where in (ANYWHERE, FRONT, PREFIX):
stats["lengths_front"] = self.lengths_front
stats["errors_front"] = self.errors_front
if where in (ANYWHERE, BACK, SUFFIX):
stats["lengths_back"] = self.lengths_back
stats["errors_back"] = self.errors_back
if where in (BACK, SUFFIX):
stats["adjacent_bases"] = self.adjacent_bases
return stats
def summarize(self):
"""Returns the summary dict for this adapter.
"""
total_front = sum(self.front_adapter.lengths_front.values())
total_back = sum(self.back_adapter.lengths_back.values())
stats = MergingDict(total_front=total_front,
total_back=total_back,
total=total_front + total_back)
where = self.where
assert (where in (ANYWHERE, LINKED)
or (where in (BACK, SUFFIX) and total_front == 0)
or (where in (FRONT, PREFIX) and total_back == 0))
stats["where"] = where_int_to_dict(where)
stats["front_sequence"] = Const(self.front_adapter.sequence)
stats["front_match_probabilities"] = Const(
self.front_adapter.random_match_probabilities())
stats["back_sequence"] = Const(self.back_adapter.sequence)
stats["back_match_probabilities"] = Const(
self.back_adapter.random_match_probabilities())
stats["front_max_error_rate"] = Const(
self.front_adapter.max_error_rate)
stats["back_max_error_rate"] = Const(self.back_adapter.max_error_rate)
stats["front_lengths_front"] = self.front_adapter.lengths_front
stats["front_lengths_back"] = self.front_adapter.lengths_back
stats["back_lengths_front"] = self.back_adapter.lengths_front
stats["back_lengths_back"] = self.back_adapter.lengths_back
# have to clone these nested dicts and set them
# up with a custom merge function
stats["front_errors_front"] = self.front_adapter.errors_front
stats["front_errors_back"] = self.front_adapter.errors_back
stats["back_errors_front"] = self.back_adapter.errors_front
stats["back_errors_back"] = self.back_adapter.errors_back
return stats
def asdict(self):
"""Returns AdapterType fields in a dict.
"""
return dict(name=self.name, desc=self.desc, flags=Const(self.flags))