class Core:
_DIC_FUNC = {
'd2': Dissimilarity.get_D2,
'Ch': Dissimilarity.get_Ch,
'Eu': Dissimilarity.get_Eu,
'Ma': Dissimilarity.get_Ma,
'd2S': Dissimilarity.get_D2S,
'd2Star': Dissimilarity.get_D2Star,
'Hao': Dissimilarity.get_Hao
}
def __init__(self,
k_list: List[int],
seq_file_list: List[str],
dissimilirary_list: List[str],
save_dir: str,
markov_list: List[int] = None):
self._k_list = k_list
self._seq_list = [
SequenceData(seq_file_list[i], i)
for i in range(len(seq_file_list))
]
self._dissimilarity = [
self._DIC_FUNC[name] for name in dissimilirary_list
]
self._markov_list = markov_list
self._dissimilarity_names = dissimilirary_list
self._result = Result(len(seq_file_list))
self._save_dir = save_dir
def n_to_n(self):
names = [seq.name for seq in self._seq_list]
for i in tqdm(range(len(self._seq_list) - 1)): # type: int
self.one_to_n(self._seq_list[i], self._seq_list[i + 1:])
self._seq_list[i] = None
self._result.save_to_file(self._save_dir, names)
def one_to_n(self, one: SequenceData, others: List[SequenceData]):
for seq in others:
Core._one_to_one(one, seq, self._k_list, self._dissimilarity,
self._result, self._markov_list)
@staticmethod
def _one_to_one(seq_x: SequenceData, seq_y: SequenceData,
k_list: List[int], func_list: List[Callable],
result: Result, markov_list: List[int]):
for k in k_list:
[func(seq_x, seq_y, k, result, markov_list) for func in func_list]
def _clear(self, k: int, r: int = None):
if 'd2S' in self._dissimilarity_names or 'd2Star' in self._dissimilarity_names:
if k in self._markov_list:
return
if 'Hao' in self._dissimilarity_names:
k -= 3
for seq in self._seq_list:
seq.clear(k)
@staticmethod
def star(k_list: List[int],
seq_dir: str,
dissimilirary_list: List[str],
save_dir: str,
markov_list: List[int] = None):
dirs = Core.recurrence_load(seq_dir)
for dir_ in dirs:
name = os.path.split(dir_)[-1]
print('{} start.................'.format(name))
seq_file_list = Core.get_file_path(dir_)
save = os.path.join(save_dir, name)
os.makedirs(save) if not os.path.exists(save) else None
Core(k_list, seq_file_list, dissimilirary_list, save,
markov_list).n_to_n()
@staticmethod
def recurrence_load(dir_path: str):
dirs = []
def _rec_load(path: str):
tmps = os.listdir(path)
p = os.path.join(path, tmps[0])
if os.path.isfile(p):
dirs.append(path)
elif os.path.isdir(p):
[_rec_load(os.path.join(path, sub_path)) for sub_path in tmps]
else:
return
_rec_load(dir_path)
return dirs
@staticmethod
def get_file_path(dir_path: str) -> List[str]:
tmps = os.listdir(dir_path)
return [os.path.join(dir_path, sub_path) for sub_path in tmps]
