def screenshot(self, args_sc): lib_dict = {"ft": [], "fn": [], "rt": [], "rn": [], "ff": [], "rf": []} f_texs = [] r_texs = [] if args_sc.tlibs is not None: for lib in args_sc.tlibs: lib_datas = lib.split(":") if not lib_datas[0].endswith(".wig"): print("Error: Exist a not proper wig files!") sys.exit() else: if lib_datas[-1] == "+": f_texs.append(lib_datas) else: r_texs.append(lib_datas) f_texs = sorted(f_texs, key=lambda x: (x[1], x[2], x[3])) r_texs = sorted(r_texs, key=lambda x: (x[1], x[2], x[3])) self._import_libs(f_texs, "+", lib_dict) self._import_libs(r_texs, "-", lib_dict) if args_sc.flibs is not None: for lib in args_sc.flibs: lib_datas = lib.split(":") if not lib_datas[0].endswith(".wig"): print("Error: Exist a not proper wig files!") sys.exit() else: if lib_datas[-1] == "+": lib_dict["ff"].append(lib_datas[0]) else: lib_dict["rf"].append(lib_datas[0]) gen_screenshot(args_sc, lib_dict, self.forward_file + ".txt", self.reverse_file + ".txt", self.strain) if (args_sc.tlibs is None) and (args_sc.flibs is None): print("Error: There are no wig file assigned!") sys.exit()
def screenshot(self, args_sc, log): lib_dict = {"ft": [], "fn": [], "rt": [], "rn": [], "ff": [], "rf": []} f_texs = [] r_texs = [] if args_sc.tlibs is not None: for lib in args_sc.tlibs: lib_datas = lib.split(":") if not lib_datas[0].endswith(".wig"): log.write("Wiggle files should end with .wig.\n") print("Error: Wiggle files should end with .wig!") sys.exit() else: if lib_datas[-1] == "+": f_texs.append(lib_datas) else: r_texs.append(lib_datas) f_texs = sorted(f_texs, key=lambda x: (x[1], x[2], x[3])) r_texs = sorted(r_texs, key=lambda x: (x[1], x[2], x[3])) self._import_libs(f_texs, "+", lib_dict) self._import_libs(r_texs, "-", lib_dict) if args_sc.flibs is not None: for lib in args_sc.flibs: lib_datas = lib.split(":") if not lib_datas[0].endswith(".wig"): log.write("Wiggle files should end with .wig.\n") print("Error: Wiggle files should end with .wig!") sys.exit() else: if lib_datas[-1] == "+": lib_dict["ff"].append(lib_datas[0]) else: lib_dict["rf"].append(lib_datas[0]) log.write("Running gen_screenshots.py to generate IGV batch script.\n") gen_screenshot(args_sc, lib_dict, self.forward_file + ".txt", self.reverse_file + ".txt", self.strain) log.write("\t" + self.forward_file + ".txt is generated.\n") log.write("\t" + self.reverse_file + ".txt is generated.\n") if (args_sc.tlibs is None) and (args_sc.flibs is None): log.write("No wig files can be found.\n") print("Error: There is no wig file assigned!") sys.exit()
def screenshot(self, args_sc): lib_dict = {"ft": [], "fn": [], "rt": [], "rn": [], "ff": [], "rf": []} f_texs = [] r_texs = [] if args_sc.tlibs is not None: for lib in args_sc.tlibs: lib_datas = lib.split(":") if not lib_datas[0].endswith(".wig"): print("Error:Exist a not proper wig files!!") sys.exit() else: if lib_datas[-1] == "+": f_texs.append(lib_datas) else: r_texs.append(lib_datas) f_texs = sorted(f_texs, key=lambda x: (x[1], x[2], x[3])) r_texs = sorted(r_texs, key=lambda x: (x[1], x[2], x[3])) self._import_libs(f_texs, "+", args_sc.tex_wigs, lib_dict) self._import_libs(r_texs, "-", args_sc.tex_wigs, lib_dict) if args_sc.flibs is not None: for lib in args_sc.flibs: lib_datas = lib.split(":") if not lib_datas[0].endswith(".wig"): print("Error:Exist a not proper wig files!!") sys.exit() else: if lib_datas[-1] == "+": lib_dict["ff"].append(os.path.join( args_sc.frag_wigs, lib_datas[0])) else: lib_dict["rf"].append(os.path.join( args_sc.frag_wigs, lib_datas[0])) gen_screenshot(args_sc, lib_dict, self.forward_file + ".txt", self.reverse_file + ".txt", self.strain) if (args_sc.tlibs is None) and (args_sc.flibs is None): print("Error: There are no wig file assigned!!!") sys.exit()