def _combine_file(self, prefixs, args_pro):
'''combine all TSS file in the input folder to generate the
global TSS for detecting the global promoter'''
if args_pro.source:
for tss in os.listdir(self.tss_path):
if tss.endswith("_TSS.gff"):
self.helper.merge_file(os.path.join(self.tss_path, tss),
self.all_tss)
for fasta in os.listdir(args_pro.fastas):
if (fasta.endswith(".fa")) or (fasta.endswith(".fna")) or (
fasta.endswith(".fasta")):
self.helper.merge_file(
os.path.join(args_pro.fastas, fasta), self.all_fasta)
else:
for tss in os.listdir(
os.path.join(args_pro.output_folder, "TSS_class")):
if tss.endswith("_TSS.gff"):
self.helper.merge_file(os.path.join(self.tss_path, tss),
self.all_tss)
for fasta in os.listdir(args_pro.fastas):
if (fasta.endswith(".fa")) or (fasta.endswith(".fna")) or (
fasta.endswith(".fasta")):
self.helper.merge_file(
os.path.join(args_pro.fastas, fasta), self.all_fasta)
print("Generating fasta file of all fasta files")
prefixs.append("allfasta")
input_path = os.path.join(self.out_fasta, "allfasta")
self.helper.check_make_folder(
os.path.join(args_pro.output_folder, "allfasta"))
self.helper.check_make_folder(os.path.join(self.out_fasta, "allfasta"))
args_pro.source = True
upstream(self.all_tss, self.all_fasta, None, None, args_pro, None)
self._move_and_merge_fasta(input_path, "allfasta")
def _combine_file(self, prefixs, args_pro):
if args_pro.source:
for tss in os.listdir(self.tss_path):
if tss.endswith("_TSS.gff"):
self.helper.merge_file(os.path.join(
self.tss_path, tss), self.all_tss)
for fasta in os.listdir(args_pro.fastas):
if (fasta.endswith(".fa")) or (
fasta.endswith(".fna")) or (
fasta.endswith(".fasta")):
self.helper.merge_file(os.path.join(
args_pro.fastas, fasta), self.all_fasta)
else:
for tss in os.listdir(os.path.join(
args_pro.output_folder, "TSS_class")):
if tss.endswith("_TSS.gff"):
self.helper.merge_file(os.path.join(
self.tss_path, tss), self.all_tss)
for fasta in os.listdir(args_pro.fastas):
if (fasta.endswith(".fa")) or (
fasta.endswith(".fna")) or (
fasta.endswith(".fasta")):
self.helper.merge_file(os.path.join(
args_pro.fastas, fasta), self.all_fasta)
print("generating fasta file of all fasta files")
prefixs.append("allfasta")
input_path = os.path.join(self.out_fasta, "allfasta")
self.helper.check_make_folder(os.path.join(
args_pro.output_folder, "allfasta"))
self.helper.check_make_folder(os.path.join(
self.out_fasta, "allfasta"))
args_pro.source = True
upstream(self.all_tss, self.all_fasta, None,
None, args_pro)
self._move_and_merge_fasta(input_path, "allfasta")
def _get_upstream(self, args_pro, prefix, tss, fasta):
'''get upstream sequence of TSS'''
if args_pro.source:
print("Generating fasta file of {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
None, None, args_pro, prefix)
else:
if (args_pro.gffs is None):
print("Error: Please assign proper annotation!!!")
sys.exit()
if "TSS_classes" not in os.listdir(args_pro.output_folder):
os.mkdir(os.path.join(args_pro.output_folder, "TSS_classes"))
print("Classifying TSSs and extracting sequence of {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
os.path.join(self.gff_path, prefix + ".gff"),
os.path.join(args_pro.output_folder, "TSS_classes",
"_".join([prefix, "TSS.gff"])), args_pro, prefix)
def _get_upstream(self, args_pro, prefix, tss, fasta):
'''get upstream sequence of TSS'''
if args_pro.source:
print("Generating fasta file of {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
None, None, args_pro, prefix)
else:
if (args_pro.gffs is None):
print("Error: Please assign proper annotation!!!")
sys.exit()
if "TSS_classes" not in os.listdir(args_pro.output_folder):
os.mkdir(os.path.join(args_pro.output_folder, "TSS_classes"))
print("Classifying TSSs and extracting sequence of {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
os.path.join(self.gff_path, prefix + ".gff"),
os.path.join(args_pro.output_folder, "TSS_classes",
"_".join([prefix, "TSS.gff"])), args_pro, prefix)
def _get_upstream(self, args_pro, prefix, tss, fasta):
if args_pro.source:
print("generating fasta file of {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta), None, None,
args_pro)
else:
if (args_pro.gffs is None) or (args_pro.wigs is None) or (
args_pro.input_libs is None):
print("Error:please assign proper annotation, tex +/- "
"wig folder and tex treated libs!!!")
sys.exit()
if "TSS_class" not in os.listdir(args_pro.output_folder):
os.mkdir(os.path.join(args_pro.output_folder, "TSS_class"))
print("classifying TSS and extracting fasta {0}".format(prefix))
upstream(
os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
os.path.join(self.gff_path, prefix + ".gff"),
os.path.join(args_pro.output_folder, "TSS_class",
"_".join([prefix, "TSS.gff"])), args_pro)
def _get_upstream(self, args_pro, prefix, tss, fasta):
if args_pro.source:
print("generating fasta file of {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
None, None, args_pro)
else:
if (args_pro.gffs is None) or (
args_pro.wigs is None) or (
args_pro.input_libs is None):
print("Error:please assign proper annotation, tex +/- "
"wig folder and tex treated libs!!!")
sys.exit()
if "TSS_class" not in os.listdir(args_pro.output_folder):
os.mkdir(os.path.join(args_pro.output_folder, "TSS_class"))
print("classifying TSS and extracting fasta {0}".format(prefix))
upstream(os.path.join(self.tss_path, tss),
os.path.join(args_pro.fastas, fasta),
os.path.join(self.gff_path, prefix + ".gff"),
os.path.join(args_pro.output_folder, "TSS_class",
"_".join([prefix, "TSS.gff"])), args_pro)