def _compare_term_tran(self, args_term, prefixs): '''searching the associated terminator to transcript''' self.multiparser.combine_gff(args_term.gffs, self.tran_path, None, "transcript") prefixs = [] print("Comparing terminators with transcripts now") for file_ in os.listdir(self.tran_path): if file_.endswith("_transcript.gff"): prefixs.append(file_.replace("_transcript.gff", "")) for type_ in ("best_candidates", "expressed_candidates", "all_candidates"): compare_term_tran(self.tran_path, os.path.join(self.outfolder["term"], type_), args_term.fuzzy_up_ta, args_term.fuzzy_down_ta, args_term.out_folder, "terminator", self.outfolder["term"], args_term.trans) for prefix in prefixs: shutil.move( os.path.join( args_term.out_folder, "statistics", "stat_compare_transcript_terminator_" + prefix + ".csv"), os.path.join( args_term.out_folder, "statistics", "_".join([ "stat_compare_terminator_transcript", prefix, type_ + ".csv" ])))
def _compare_term_tran(self, args_term, prefixs, log): '''searching the associated terminator to transcript''' self.multiparser.combine_gff(args_term.gffs, self.tran_path, None, "transcript") prefixs = [] print("Comparing terminators with transcripts now") for file_ in os.listdir(self.tran_path): if file_.endswith("_transcript.gff"): prefixs.append(file_.replace("_transcript.gff", "")) log.write("Running compare_tran_term.py for comparing transcripts " "and terminators.\n") log.write("The following files are generated:\n") for type_ in ("best_candidates", "expressed_candidates", "all_candidates"): compare_term_tran(self.tran_path, os.path.join(self.outfolder["term"], type_), args_term.fuzzy_up_ta, args_term.fuzzy_down_ta, args_term.out_folder, "terminator", self.outfolder["term"], args_term.trans) for prefix in prefixs: shutil.move( os.path.join( args_term.out_folder, "statistics", "stat_compare_transcript_terminator_" + prefix + ".csv"), os.path.join( args_term.out_folder, "statistics", "_".join(["stat_compare_terminator_transcript", prefix, type_ + ".csv"]))) log.write("\t" + os.path.join( args_term.out_folder, "statistics", "_".join(["stat_compare_terminator_transcript", prefix, type_ + ".csv"])) + "\n")
def _compare_term_tran(self, args_tran): if args_tran.terms is not None: print("comparing between terminators and transcripts...") self.multiparser.parser_gff(args_tran.terms, "term") self.multiparser.combine_gff( args_tran.gffs, os.path.join(args_tran.terms, "tmp"), None, "term") compare_term_tran(self.gff_outfolder, os.path.join(args_tran.terms, "tmp"), args_tran.fuzzy_term, args_tran.fuzzy_term, args_tran.out_folder, "transcript")
def _compare_term_tran(self, args_tran): '''searching the associated terminator to transcript''' if args_tran.terms is not None: print("comparing between terminators and transcripts...") self.multiparser.parser_gff(args_tran.terms, "term") self.multiparser.combine_gff(args_tran.gffs, os.path.join(args_tran.terms, "tmp"), None, "term") compare_term_tran(self.gff_outfolder, os.path.join(args_tran.terms, "tmp"), args_tran.fuzzy_term, args_tran.fuzzy_term, args_tran.out_folder, "transcript", args_tran.terms, self.gff_outfolder)
def _compare_term_tran(self, args_term): self.multiparser.combine_gff(args_term.gffs, self.tran_path, None, "transcript") for type_ in ("best", "express", "all_candidates"): compare_term_tran(self.tran_path, os.path.join(self.outfolder["term"], type_), args_term.fuzzy_up_ta, args_term.fuzzy_down_ta, args_term.out_folder, "terminator") shutil.move( os.path.join( args_term.out_folder, "statistics", "stat_comparison_terminator_transcript.csv"), os.path.join( args_term.out_folder, "statistics", "stat_comparison_terminator_transcript_" + type_ + ".csv"))
def _compare_term_tran(self, args_tran, log): '''searching the associated terminator to transcript''' if args_tran.terms is not None: print("Comparing between terminators and transcripts") self.multiparser.parser_gff(args_tran.terms, "term") if args_tran.gffs is not None: self.multiparser.combine_gff( args_tran.gffs, os.path.join(args_tran.terms, "tmp"), None, "term") log.write("Running compare_tran_term.py to compare transcripts " "with terminators.\n") compare_term_tran(self.gff_outfolder, os.path.join(args_tran.terms, "tmp"), args_tran.fuzzy_term, args_tran.fuzzy_term, args_tran.out_folder, "transcript", args_tran.terms, self.gff_outfolder) for file_ in os.listdir(os.path.join(args_tran.out_folder, "statistics")): if file_.startswith("stat_compare_transcript_terminator_"): log.write("\t" + file_ + " is generated.\n")