def _run_normal(self, prefix, gff, tran, fuzzy_tss, args_srna):
'''detection of intergenic and antisense sRNA'''
tex_datas = None
frag_datas = None
if "tmp_cutoff_inter" in os.listdir(args_srna.out_folder):
os.remove(os.path.join(args_srna.out_folder, "tmp_cutoff_inter"))
files = {
"frag_gff": None,
"frag_csv": None,
"tex_gff": None,
"tex_csv": None,
"merge_gff": None,
"merge_csv": None
}
if self.tss_path is not None:
tss = self.helper.get_correct_file(self.tss_path, "_TSS.gff",
prefix, None, None)
else:
tss = None
if self.pro_path is not None:
pro = self.helper.get_correct_file(self.pro_path,
"_processing.gff", prefix, None,
None)
else:
pro = None
if args_srna.frag_wigs is not None:
files["frag_gff"] = os.path.join(args_srna.out_folder,
"_".join(["tmp_frag", prefix]))
files["frag_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_frag_table", prefix]))
args_srna = self.args_container.container_intersrna(
"frag", files, args_srna, prefix,
os.path.join(args_srna.gffs, gff), tran, tss, pro, fuzzy_tss)
frag_datas = self._read_lib_wig(args_srna)
intergenic_srna(args_srna, frag_datas[0], frag_datas[1],
frag_datas[2], frag_datas[3])
if args_srna.tex_wigs is not None:
files["tex_gff"] = os.path.join(args_srna.out_folder,
"_".join(["tmp_tex", prefix]))
files["tex_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_tex_table", prefix]))
args_srna = self.args_container.container_intersrna(
"tex", files, args_srna, prefix,
os.path.join(args_srna.gffs, gff), tran, tss, pro, fuzzy_tss)
tex_datas = self._read_lib_wig(args_srna)
intergenic_srna(args_srna, tex_datas[0], tex_datas[1],
tex_datas[2], tex_datas[3])
files["merge_csv"] = "_".join([self.prefixs["normal_table"], prefix])
files["merge_gff"] = "_".join([self.prefixs["normal"], prefix])
self._merge_frag_tex_file(files, args_srna)
if ("TSS_class" in os.listdir(
args_srna.out_folder)) and (not args_srna.tss_source):
tss = os.path.join(args_srna.out_folder, "TSS_class",
prefix + "_TSS.gff")
return tss, frag_datas, tex_datas
def _run_normal(self, prefix, gff, tran, fuzzy_tss, args_srna):
if "tmp_cutoff_inter" in os.listdir(args_srna.out_folder):
os.remove(os.path.join(args_srna.out_folder, "tmp_cutoff_inter"))
files = {"frag_gff": None, "frag_csv": None,
"tex_gff": None, "tex_csv": None,
"merge_gff": None, "merge_csv": None}
if ("tss" in args_srna.import_info):
tss = self.helper.get_correct_file(self.tss_path, "_TSS.gff",
prefix, None, None)
else:
tss = None
if self.pro_path is not None:
pro = self.helper.get_correct_file(
self.pro_path, "_processing.gff", prefix, None, None)
else:
pro = None
if args_srna.frag_wigs is not None:
files["frag_gff"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_frag", prefix]))
files["frag_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_frag_table", prefix]))
args_srna = self.args_container.container_intersrna(
"frag", files, args_srna, prefix,
os.path.join(args_srna.gffs, gff), tran, tss,
pro, fuzzy_tss)
intergenic_srna(args_srna)
if args_srna.tex_wigs is not None:
files["tex_gff"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_tex", prefix]))
files["tex_csv"] = os.path.join(
args_srna.out_folder, "_".join(["tmp_tex_table", prefix]))
args_srna = self.args_container.container_intersrna(
"tex", files, args_srna, prefix,
os.path.join(args_srna.gffs, gff), tran, tss,
pro, fuzzy_tss)
intergenic_srna(args_srna)
files["merge_csv"] = "_".join([self.prefixs["normal_table"], prefix])
files["merge_gff"] = "_".join([self.prefixs["normal"], prefix])
self._merge_frag_tex_file(files, args_srna)
if "TSS_class" in os.listdir(args_srna.out_folder):
tss = os.path.join(args_srna.out_folder,
"TSS_class", prefix + "_TSS.gff")
return tss
def test_intergenic_srna(self):
si.read_libs = self.mock.mock_read_libs
si.read_wig = self.mock.mock_read_wig
gff_file = os.path.join(self.test_folder, "aaa.gff")
tss_file = os.path.join(self.test_folder, "aaa_TSS.gff")
tran_file = os.path.join(self.test_folder, "aaa_tran.gff")
pro_file = os.path.join(self.test_folder, "aaa_processing.gff")
wig_f_file = os.path.join(self.wig_folder, "wig_f.wig")
wig_r_file = os.path.join(self.wig_folder, "wig_r.wig")
gen_file(gff_file, self.example.gff_file)
gen_file(tss_file, self.example.gff_file)
gen_file(tran_file, self.example.gff_file)
gen_file(pro_file, self.example.gff_file)
output_file = os.path.join(self.test_folder, "output")
output_table = os.path.join(self.test_folder, "table")
coverage = [0, 0, 0, 50, 10]
si.replicate_comparison = self.mock.mock_replicate_comparison
si.coverage_comparison = self.mock.mock_coverage_comparison
args = self.mock_args.mock()
args.gff_file = gff_file
args.tran_file = tran_file
args.pro_file = pro_file
args.tss_file = tss_file
args.table_best = True
args.cutoffs = coverage
args.out_folder = self.test_folder
args.file_type = "frag"
args.cut_notex = coverage
args.input_libs = "input_libs"
args.wig_folder = self.wig_folder
args.wig_f_file = wig_f_file
args.wig_r_file = wig_r_file
args.tss_source = True
args.output_file = output_file
args.output_table = output_table
args.in_cds = False
args.wigs_f = None
args.wigs_r = None
args.ex_srna = False
si.intergenic_srna(args, args.input_libs, None,
args.wigs_f, args.wigs_r, tss_file)
self.assertTrue(os.path.exists(output_file))
self.assertTrue(os.path.exists(output_table))
def test_intergenic_srna(self):
si.read_libs = self.mock.mock_read_libs
si.read_wig = self.mock.mock_read_wig
gff_file = os.path.join(self.test_folder, "aaa.gff")
tss_file = os.path.join(self.test_folder, "aaa_TSS.gff")
tran_file = os.path.join(self.test_folder, "aaa_tran.gff")
pro_file = os.path.join(self.test_folder, "aaa_processing.gff")
wig_f_file = os.path.join(self.wig_folder, "wig_f.wig")
wig_r_file = os.path.join(self.wig_folder, "wig_r.wig")
gen_file(gff_file, self.example.gff_file)
gen_file(tss_file, self.example.gff_file)
gen_file(tran_file, self.example.gff_file)
gen_file(pro_file, self.example.gff_file)
output_file = os.path.join(self.test_folder, "output")
output_table = os.path.join(self.test_folder, "table")
coverage = [0, 0, 0, 50, 10]
si.replicate_comparison = self.mock.mock_replicate_comparison
si.coverage_comparison = self.mock.mock_coverage_comparison
args = self.mock_args.mock()
args.gff_file = gff_file
args.tran_file = tran_file
args.pro_file = pro_file
args.tss_file = tss_file
args.table_best = True
args.cutoffs = coverage
args.out_folder = self.test_folder
args.file_type = "frag"
args.cut_notex = coverage
args.input_libs = "input_libs"
args.wig_folder = self.wig_folder
args.wig_f_file = wig_f_file
args.wig_r_file = wig_r_file
args.tss_source = True
args.output_file = output_file
args.output_table = output_table
args.in_cds = False
args.wigs_f = None
args.wigs_r = None
args.ex_srna = False
si.intergenic_srna(args, args.input_libs, None, args.wigs_f,
args.wigs_r)
self.assertTrue(os.path.exists(output_file))
self.assertTrue(os.path.exists(output_table))