def _compute_intersection_forward_reverse(
self, prefixs, merge_path, wig_path, merge_wigs, args_term):
for prefix in prefixs:
tmp_seq = os.path.join(args_term.out_folder,
"_".join(["inter_seq", prefix]))
tmp_sec = os.path.join(args_term.out_folder,
"_".join(["inter_sec", prefix]))
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
gff_file = os.path.join(merge_path, prefix + ".gff")
print("Extracting seq of {0}".format(prefix))
intergenic_seq(os.path.join(self.fasta_path, prefix + ".fa"),
tran_file, gff_file, tmp_seq)
self._run_rnafold(args_term.RNAfold_path, tmp_seq, tmp_sec, prefix)
tmp_cand = os.path.join(args_term.out_folder,
"_".join(["term_candidates", prefix]))
poly_t(tmp_seq, tmp_sec, gff_file, tran_file, tmp_cand, args_term)
print("detection of terminator")
detect_coverage(
tmp_cand, os.path.join(merge_path, prefix + ".gff"),
os.path.join(self.tran_path, "_".join([
prefix, "transcript.gff"])),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(wig_path, "_".join([prefix, "forward.wig"])),
os.path.join(wig_path, "_".join([prefix, "reverse.wig"])),
os.path.join(self.tmps["hp_path"], "_".join([
prefix, self.tmps["hp_gff"]])), merge_wigs,
os.path.join(self.outfolder["term"], "_".join([
prefix, self.suffixs["gff"]])),
os.path.join(self.tmps["term_table"], "_".join([
prefix, "term_raw.csv"])), args_term)
self.multiparser.combine_gff(args_term.gffs, self.outfolder["term"],
None, "term")
self._move_file(self.outfolder["term"], self.outfolder["csv"])
def _compute_intersection_forward_reverse(
self, prefixs, merge_path, wig_path, merge_wigs, args_term, log):
'''the approach for searching gene converged region terminator'''
log.write("Searching terminators which located in gene converged "
"region.\n")
for prefix in prefixs:
tmp_seq = os.path.join(args_term.out_folder,
"_".join(["inter_seq", prefix]))
tmp_index = os.path.join(args_term.out_folder,
"_".join(["inter_index", prefix]))
tmp_sec = os.path.join(args_term.out_folder,
"_".join(["inter_sec", prefix]))
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
gff_file = os.path.join(merge_path, prefix + ".gff")
tmp_cand = tmp_cand = os.path.join(args_term.out_folder,
"_".join(["term_candidates", prefix]))
if os.path.exists(tran_file):
print("Extracting sequences of {0}".format(prefix))
log.write("Running get_inter_seq.py to extract the potential "
"sequences from {0}.\n".format(prefix))
intergenic_seq(os.path.join(self.fasta_path, prefix + ".fa"),
tran_file, gff_file, tmp_seq, tmp_index, args_term)
log.write("\t" + tmp_seq + " is generated for storing the "
"potential sequences.\n")
self._run_rnafold(args_term.RNAfold_path, tmp_seq, tmp_sec,
prefix, log)
log.write("Running extract_sec_info.py to extract the "
"information of secondary structure from {0}.\n".format(
prefix))
extract_info_sec(tmp_sec, tmp_seq, tmp_index)
os.remove(tmp_index)
log.write("Running get_polyT.py to detect the "
"terminator candidates for {0}.\n".format(prefix))
poly_t(tmp_seq, tmp_sec, gff_file, tran_file, tmp_cand, args_term)
log.write("\t" + tmp_cand + " which temporary stores terminator "
"candidates is generated.\n")
print("Detecting terminators for " + prefix)
log.write("Running detect_coverage_term.py to gain "
"high-confidence terminators for {0}.\n".format(prefix))
detect_coverage(
tmp_cand, os.path.join(merge_path, prefix + ".gff"),
os.path.join(self.tran_path, "_".join([
prefix, "transcript.gff"])),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(wig_path, "_".join([prefix, "forward.wig"])),
os.path.join(wig_path, "_".join([prefix, "reverse.wig"])),
os.path.join(self.tmps["hp_path"], "_".join([
prefix, self.tmps["hp_gff"]])), merge_wigs,
os.path.join(self.outfolder["term"], "_".join([
prefix, self.suffixs["gff"]])),
os.path.join(self.tmps["term_table"], "_".join([
prefix, "term_raw.csv"])), args_term)
self.multiparser.combine_gff(args_term.gffs, self.outfolder["term"],
None, "term")
self._move_file(self.outfolder["term"], self.outfolder["csv"])
def _compute_intersection_forward_reverse(self, prefixs, merge_path,
wig_path, merge_wigs, args_term):
'''the approach for searching gene converged region terminator'''
for prefix in prefixs:
tmp_seq = os.path.join(args_term.out_folder,
"_".join(["inter_seq", prefix]))
tmp_index = os.path.join(args_term.out_folder,
"_".join(["inter_index", prefix]))
tmp_sec = os.path.join(args_term.out_folder,
"_".join(["inter_sec", prefix]))
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
gff_file = os.path.join(merge_path, prefix + ".gff")
tmp_cand = tmp_cand = os.path.join(
args_term.out_folder, "_".join(["term_candidates", prefix]))
if os.path.exists(tran_file):
print("Extracting sequences of {0}".format(prefix))
intergenic_seq(os.path.join(self.fasta_path,
prefix + ".fa"), tran_file,
gff_file, tmp_seq, tmp_index, args_term)
self._run_rnafold(args_term.RNAfold_path, tmp_seq, tmp_sec,
prefix)
extract_info_sec(tmp_sec, tmp_seq, tmp_index)
os.remove(tmp_index)
poly_t(tmp_seq, tmp_sec, gff_file, tran_file, tmp_cand,
args_term)
print("Detecting terminators for " + prefix)
detect_coverage(
tmp_cand, os.path.join(merge_path, prefix + ".gff"),
os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"])),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(wig_path, "_".join([prefix, "forward.wig"])),
os.path.join(wig_path, "_".join([prefix, "reverse.wig"])),
os.path.join(self.tmps["hp_path"],
"_".join([prefix, self.tmps["hp_gff"]])),
merge_wigs,
os.path.join(self.outfolder["term"],
"_".join([prefix, self.suffixs["gff"]])),
os.path.join(self.tmps["term_table"],
"_".join([prefix, "term_raw.csv"])), args_term)
self.multiparser.combine_gff(args_term.gffs, self.outfolder["term"],
None, "term")
self._move_file(self.outfolder["term"], self.outfolder["csv"])
def _compute_intersection_forward_reverse(self, prefixs, merge_path,
wig_path, merge_wigs, args_term,
log):
'''the approach for searching gene converged region terminator'''
log.write("Searching terminators which located in gene converged "
"region.\n")
for prefix in prefixs:
tmp_seq = os.path.join(args_term.out_folder,
"_".join(["inter_seq", prefix]))
tmp_index = os.path.join(args_term.out_folder,
"_".join(["inter_index", prefix]))
tmp_sec = os.path.join(args_term.out_folder,
"_".join(["inter_sec", prefix]))
tran_file = os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"]))
gff_file = os.path.join(merge_path, prefix + ".gff")
tmp_cand = tmp_cand = os.path.join(
args_term.out_folder, "_".join(["term_candidates", prefix]))
if os.path.exists(tran_file):
print("Extracting sequences of {0}".format(prefix))
log.write("Running get_inter_seq.py to extract the potential "
"sequences from {0}.\n".format(prefix))
intergenic_seq(os.path.join(self.fasta_path,
prefix + ".fa"), tran_file,
gff_file, tmp_seq, tmp_index, args_term)
log.write("\t" + tmp_seq + " is generated for storing the "
"potential sequences.\n")
self._run_rnafold(args_term.RNAfold_path, tmp_seq, tmp_sec,
prefix, log)
log.write(
"Running extract_sec_info.py to extract the "
"information of secondary structure from {0}.\n".format(
prefix))
extract_info_sec(tmp_sec, tmp_seq, tmp_index)
os.remove(tmp_index)
log.write("Running get_polyT.py to detect the "
"terminator candidates for {0}.\n".format(prefix))
poly_t(tmp_seq, tmp_sec, gff_file, tran_file, tmp_cand,
args_term)
log.write("\t" + tmp_cand +
" which temporary stores terminator "
"candidates is generated.\n")
print("Detecting terminators for " + prefix)
log.write("Running detect_coverage_term.py to gain "
"high-confidence terminators for {0}.\n".format(prefix))
detect_coverage(
tmp_cand, os.path.join(merge_path, prefix + ".gff"),
os.path.join(self.tran_path,
"_".join([prefix, "transcript.gff"])),
os.path.join(self.fasta_path, prefix + ".fa"),
os.path.join(wig_path, "_".join([prefix, "forward.wig"])),
os.path.join(wig_path, "_".join([prefix, "reverse.wig"])),
os.path.join(self.tmps["hp_path"],
"_".join([prefix, self.tmps["hp_gff"]])),
merge_wigs,
os.path.join(self.outfolder["term"],
"_".join([prefix, self.suffixs["gff"]])),
os.path.join(self.tmps["term_table"],
"_".join([prefix, "term_raw.csv"])), args_term)
self.multiparser.combine_gff(args_term.gffs, self.outfolder["term"],
None, "term")
self._move_file(self.outfolder["term"], self.outfolder["csv"])