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, 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()