class MaLocal(object):
__CB = {"A": "T", "T": "A", "G": "C", "C": "G"}
def __init__(self, path):
self.__db = MaDb(path)
self.__db.open()
def __complement(self, seq):
return "".join([self.__CB[base] if base in self.__CB else base for base in seq.upper()])
def get(self, chr, strand, start, ref, alt, var_id=None):
if ref == "-" or alt == "-" or len(ref) > 1 or len(alt) > 1:
return None
r = self.__db.get(chr, start, ref, alt, var_id=var_id)
if r is None and strand == "-":
r = self.__db.get(chr, start, self.__complement(ref), self.__complement(alt), var_id=var_id)
return r
def close(self):
self.__db.close()
def __init__(self, path):
self.__db = MaDb(path)
self.__db.open()