def _run_utrsrna(self, gff, tran, prefix, tss, pro, args_srna):
if "tmp_median" in os.listdir(args_srna.out_folder):
os.remove(os.path.join(args_srna.out_folder, "tmp_median"))
files = {"frag_gff": None, "frag_csv": None,
"tex_gff": None, "tex_csv": None,
"merge_gff": None, "merge_csv": None}
if args_srna.tex_wigs is not None:
files["tex_gff"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_utr_tex", prefix]))
files["tex_csv"] = os.path.join(
args_srna.out_folder,
"_".join(["tmp_utr_tex_table", prefix]))
args_srna = self.args_container.container_utrsrna(
os.path.join(args_srna.gffs, gff), tran, tss, files,
pro, os.path.join(self.fasta_path, prefix + ".fa"),
"tex", prefix, args_srna)
utr_derived_srna(args_srna)
if args_srna.frag_wigs is not None:
files["frag_gff"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_utr_frag", prefix]))
files["frag_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_utr_frag_table", prefix]))
args_srna = self.args_container.container_utrsrna(
os.path.join(args_srna.gffs, gff), tran, tss, files,
pro, os.path.join(self.fasta_path, prefix + ".fa"),
"frag", prefix, args_srna)
utr_derived_srna(args_srna)
files["merge_csv"] = "_".join([self.prefixs["utr_table"], prefix])
files["merge_gff"] = "_".join([self.prefixs["utr"], prefix])
self._merge_frag_tex_file(files, args_srna)
filter_utr(files["merge_gff"], files["merge_csv"], args_srna.min_utr)
def _filter_min_utr(self, prefixs, min_utr):
'''filter out the low expressed UTR-derived sRNA'''
for prefix in prefixs:
filter_utr(
os.path.join(self.all_best["all_gff"],
"_".join([prefix, "sRNA.gff"])),
os.path.join(self.all_best["all_table"],
"_".join([prefix, "sRNA.csv"])), min_utr)
def _run_utrsrna(self, gff, tran, prefix, tss, pro, args_srna, frag_datas,
tex_datas):
'''detection of UTR-derived sRNA'''
if "tmp_median" in os.listdir(args_srna.out_folder):
os.remove(os.path.join(args_srna.out_folder, "tmp_median"))
files = {
"frag_gff": None,
"frag_csv": None,
"tex_gff": None,
"tex_csv": None,
"merge_gff": None,
"merge_csv": None
}
if args_srna.tex_wigs is not None:
files["tex_gff"] = os.path.join(args_srna.out_folder,
"_".join(["tmp_utr_tex", prefix]))
files["tex_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_utr_tex_table", prefix]))
args_srna = self.args_container.container_utrsrna(
os.path.join(args_srna.gffs, gff), tran, tss, files, pro,
os.path.join(self.fasta_path, prefix + ".fa"), "tex", prefix,
args_srna)
utr_derived_srna(args_srna, tex_datas[0], tex_datas[1],
tex_datas[2], tex_datas[3])
if args_srna.frag_wigs is not None:
files["frag_gff"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_utr_frag", prefix]))
files["frag_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_utr_frag_table", prefix]))
args_srna = self.args_container.container_utrsrna(
os.path.join(args_srna.gffs, gff), tran, tss, files, pro,
os.path.join(self.fasta_path, prefix + ".fa"), "frag", prefix,
args_srna)
utr_derived_srna(args_srna, frag_datas[0], frag_datas[1],
frag_datas[2], frag_datas[3])
files["merge_csv"] = "_".join([self.prefixs["utr_table"], prefix])
files["merge_gff"] = "_".join([self.prefixs["utr"], prefix])
self._merge_frag_tex_file(files, args_srna)
filter_utr(files["merge_gff"], files["merge_csv"], args_srna.min_utr)
def _filter_min_utr(self, prefixs, min_utr):
for prefix in prefixs:
filter_utr(os.path.join(self.all_best["all_gff"],
"_".join([prefix, "sRNA.gff"])),
os.path.join(self.all_best["all_table"],
"_".join([prefix, "sRNA.csv"])), min_utr)