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)