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")