general_class.py 文件源码

def ref_dict_gen(self,FILEPATH=os.getcwd()):
            ## this function output the reference chromosome into a dict
            if '/' in self.filename:
                complete_path=self.filename
            else:
                complete_path=FILEPATH + '/' + self.filename

            reader=csv.reader(open(complete_path,'rU'),delimiter=self.SEP_CHAR,quoting=csv.QUOTE_NONE)
            row=reader.next()
            ref_dict= dict()
            while row[0][0]=="@":
                if row[0][1:3]=="SQ":
                    ref_name=row[1][3:]
                    ref_length=int(row[2][3:])
                    ref_dict[ref_name]=ref_length
                row=reader.next()
            return ref_dict