def terminator(self):
"""Run TransTermHP for detecting terminators."""
print("Running terminator prediction...")
if self._args.TransTermHP_path is None:
print("Please assign the folder where you install TransTermHP.")
self.check_folder([self._args.fasta_folder,
self._args.annotation_folder,
self._args.transcript_folder])
self.check_no_require_folder([self._args.sRNA])
project_creator.create_subfolders(
self._paths.required_folders("terminator"))
args_term = self.args_container.container_terminator(
self._args.TransTermHP_path, self._args.expterm_path,
self._args.RNAfold_path,
self._paths.transterm_folder, self._args.fasta_folder,
self._args.annotation_folder, self._args.transcript_folder,
self._args.sRNA, self._args.statistics,
self._args.tex_wig_folder, self._args.frag_wig_folder,
self._args.decrease, self._args.highest_coverage,
self._args.fuzzy_detect_coverage,
self._args.fuzzy_within_transcript,
self._args.fuzzy_downstream_transcript,
self._args.fuzzy_within_gene,
self._args.fuzzy_downstream_gene, self._paths.transtermhp_folder,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.tex_notex, self._args.replicates_tex,
self._args.replicates_frag, self._args.table_best,
self._args.min_loop_length, self._args.max_loop_length,
self._args.min_stem_length,
self._args.max_stem_length, self._args.min_U_tail_length,
self._args.miss_rate, self._args.range_U_tail)
terminator = Terminator(args_term)
terminator.run_terminator(args_term)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.test_folder = "test_folder"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.trans = "test_folder/trans"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out)
os.mkdir(self.fastas)
os.mkdir(self.gffs)
os.mkdir(self.srnas)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.out, "tables"))
os.mkdir(os.path.join(self.out, "gffs"))
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(os.path.join(self.fastas, "tmp"))
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.trans = self.trans
args.out_folder = self.out
args.srnas = self.srnas
self.term = Terminator(args)
def terminator(self):
"""Run TransTermHP for detecting terminators."""
print("Running terminator prediction...")
if self._args.TransTermHP_path is None:
print("Please assign the folder where you install TransTermHP.")
self.check_folder([
self._args.fasta_folder, self._args.annotation_folder,
self._args.transcript_folder
])
self.check_no_require_folder([self._args.sRNA])
project_creator.create_subfolders(
self._paths.required_folders("terminator"))
args_term = self.args_container.container_terminator(
self._args.TransTermHP_path, self._args.expterm_path,
self._args.RNAfold_path, self._paths.transterm_folder,
self._args.fasta_folder, self._args.annotation_folder,
self._args.transcript_folder, self._args.sRNA,
self._args.statistics, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.decrease,
self._args.highest_coverage, self._args.fuzzy_detect_coverage,
self._args.fuzzy_within_transcript,
self._args.fuzzy_downstream_transcript,
self._args.fuzzy_within_gene, self._args.fuzzy_downstream_gene,
self._paths.transtermhp_folder, self._args.tex_notex_libs,
self._args.frag_libs, self._args.tex_notex,
self._args.replicates_tex, self._args.replicates_frag,
self._args.table_best, self._args.min_loop_length,
self._args.max_loop_length, self._args.min_stem_length,
self._args.max_stem_length, self._args.min_U_tail_length,
self._args.miss_rate, self._args.range_U_tail)
terminator = Terminator(args_term)
terminator.run_terminator(args_term)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.test_folder = "test_folder"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.trans = "test_folder/trans"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out)
os.mkdir(self.fastas)
os.mkdir(self.gffs)
os.mkdir(self.srnas)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.out, "tables"))
os.mkdir(os.path.join(self.out, "gffs"))
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(os.path.join(self.fastas, "tmp"))
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.trans = self.trans
args.out_folder = self.out
args.srnas = self.srnas
self.term = Terminator(args)
def terminator(self):
"""Run TransTermHP and Gene converaged for detecting terminators"""
print("Running terminator prediction")
if self._args.transtermhp_path is None:
print("Please assign the folder where you install TransTermHP.")
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files,
self._args.transcript_files, self._args.srna_files],
["--fasta_files", "--annotation_files",
"--transcript_files", "--srna_files"])
for prop in ("transtermhp_path", "expterm_path", "rnafold_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
project_creator.create_subfolders(
self._paths.required_folders("terminator"))
args_term = self.args_container.container_terminator(
self._args.transtermhp_path, self._args.expterm_path,
self._args.rnafold_path,
self._paths.transterm_folder, self._args.fasta_files,
self._args.annotation_files, self._args.transcript_files,
self._args.srna_files, self._args.statistics,
self._args.decrease, self._args.highest_coverage,
self._args.fuzzy_detect_coverage,
self._args.fuzzy_within_transcript,
self._args.fuzzy_downstream_transcript,
self._args.fuzzy_within_gene,
self._args.fuzzy_downstream_gene, self._paths.transtermhp_folder,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.tex_notex, self._args.replicate_tex,
self._args.replicate_frag, self._args.table_best,
self._args.min_loop_length, self._args.max_loop_length,
self._args.min_stem_length, self._args.max_stem_length,
self._args.min_u_tail_length, self._args.miss_rate,
self._args.range_u_tail, self._args.keep_multi_term,
self._args.window_size, self._args.window_shift)
terminator = Terminator(args_term)
terminator.run_terminator(args_term)
class TestTerminator(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.test_folder = "test_folder"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.trans = "test_folder/trans"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out)
os.mkdir(self.fastas)
os.mkdir(self.gffs)
os.mkdir(self.srnas)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.out, "tables"))
os.mkdir(os.path.join(self.out, "gffs"))
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(os.path.join(self.fastas, "tmp"))
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.trans = self.trans
args.out_folder = self.out
args.srnas = self.srnas
self.term = Terminator(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
if os.path.exists("tmp_transterm"):
shutil.rmtree("tmp_transterm")
if os.path.exists("tmp_term_table"):
shutil.rmtree("tmp_term_table")
if os.path.exists("tmp_merge_gff"):
shutil.rmtree("tmp_merge_gff")
def test_convert_gff2rntptt(self):
os.mkdir(os.path.join(self.srnas, "tmp"))
gen_file(os.path.join(self.gffs, "aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.srnas, "aaa_sRNA.gff"),
self.example.srna_file)
gen_file(os.path.join(self.fastas, "aaa.fa"), self.example.fasta_file)
file_types, prefixs = self.term._convert_gff2rntptt(
self.gffs, self.fastas, self.srnas)
self.assertDictEqual(file_types, {'aaa': 'srna'})
self.assertListEqual(prefixs, ['aaa'])
def test_combine_annotation(self):
test1 = os.path.join(self.test_folder, "test1.ptt")
test2 = os.path.join(self.test_folder, "test2.ptt")
gen_file(test1, self.example.ptt)
gen_file(test2, self.example.ptt)
files = [test1, test2]
combine_file = os.path.join(self.test_folder, "combine")
self.term._combine_annotation(combine_file, files)
datas = import_data(combine_file)
result = self.example.ptt.split("\n")[3:]
self.assertEqual("\n".join(datas), "\n".join(result + result))
def test_run_TransTermHP(self):
self.term._TransTermHP = self.mock.mock_TransTermHP
os.mkdir(os.path.join(self.gffs, "tmp/combine"))
gen_file(os.path.join(self.gffs, "tmp/combine/aaa.ptt"),
self.example.ptt)
gen_file(os.path.join(self.fastas, "tmp/aaa.fa"),
self.example.fasta_file)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.hp_folder = self.out
self.term._run_TransTermHP(args)
self.assertTrue(os.path.exists(os.path.join(self.out, "aaa")))
def test_convert_to_gff(self):
self.term.multiparser = self.mock_parser
hp_folder = os.path.join(self.out, "aaa")
os.mkdir(hp_folder)
gen_file(os.path.join(hp_folder, "aaa_best_terminator_after_gene.bag"),
self.example.bag)
os.mkdir("tmp_transterm")
args = self.mock_args.mock()
args.hp_folder = self.out
args.gffs = self.gffs
self.term._convert_to_gff(["aaa"], args)
datas = import_data(
"/home/silas/ANNOgesic/tmp_transterm/aaa_transtermhp.gff")
self.assertEqual("\n".join(datas), self.example.gff_bag)
def test_merge_sRNA(self):
os.mkdir(os.path.join(self.srnas, "tmp"))
self.term.multiparser = self.mock_parser
gen_file(os.path.join(self.gffs, "aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.srnas, "tmp/aaa_sRNA.gff"),
self.example.srna_file)
merge = self.term._merge_sRNA(self.srnas, ["aaa"], self.gffs)
self.assertEqual(merge.split("/")[-1], "tmp_merge_gff")
shutil.rmtree("tmp_merge_gff")
def test_move_file(self):
term_outfolder = self.gffs
csv_outfolder = self.out
gen_file(os.path.join(term_outfolder, "aaa_term.gff"),
self.example.term_file)
if (not os.path.exists("tmp_term_table")):
os.mkdir("tmp_term_table")
gen_file("tmp_term_table/aaa_term_raw.csv", "test")
self.term._move_file(term_outfolder, csv_outfolder)
shutil.rmtree("tmp_term_table")
self.assertTrue(
"test_folder/output/gffs/all_candidates/aaa_term_all.gff")
self.assertTrue(
"test_folder/output/tables/all_candidates/aaa_term_all.csv")
def test_compute_intersection_forward_reverse(self):
self.term.multiparser = self.mock_parser
te.intergenic_seq = self.mock.mock_intergenic_seq
te.poly_t = self.mock.mock_poly_t
te.detect_coverage = self.mock.mock_detect_coverage
self.term._run_rnafold = self.mock.mock_run_rnafold
term_outfolder = os.path.join(self.out, "gffs")
csv_outfolder = os.path.join(self.out, "tables")
args = self.mock_args.mock()
args.trans = self.trans
args.fastas = self.fastas
args.tex_notex = "tex_notex"
args.libs = "libs"
args.replicates = "rep"
args.RNAfold_path = "test"
self.term._compute_intersection_forward_reverse(["aaa"],
self.test_folder,
"wig_path",
"merge_wigs", args)
self.assertTrue(os.path.join(self.out, "inter_seq_aaa"))
self.assertTrue(os.path.join(self.out, "inter_sec_aaa"))
def test_compute_stat(self):
term_outfolder = os.path.join(self.out, "gffs")
csv_outfolder = os.path.join(self.out, "tables")
te.stat_term = self.mock.mock_stat_term
gen_file(
os.path.join(term_outfolder, "all_candidates/aaa_term_all.gff"),
self.example.term_file)
gen_file(os.path.join(term_outfolder, "best/aaa_term.csv"),
self.example.term_file)
gen_file(os.path.join(term_outfolder, "express/aaa_term.csv"),
self.example.term_file)
gen_file(os.path.join(term_outfolder, "non_express/aaa_term.csv"),
self.example.term_file)
args = self.mock_args.mock()
args.stat = True
args.out_folder = self.out
self.term._compute_stat(args)
self.assertTrue(
os.path.exists(os.path.join(csv_outfolder,
"express/aaa_term.csv")))
self.assertTrue(
os.path.exists(os.path.join(csv_outfolder, "best/aaa_term.csv")))
self.assertTrue(
os.path.exists(
os.path.join(csv_outfolder, "non_express/aaa_term.csv")))
def test_run_terminator(self):
te.stat_term = self.mock.mock_stat_term
te.intergenic_seq = self.mock.mock_intergenic_seq
te.poly_t = self.mock.mock_poly_t
te.detect_coverage = self.mock.mock_detect_coverage
self.term.multiparser = self.mock_parser
self.term._run_rnafold = self.mock.mock_run_rnafold
self.term._TransTermHP = self.mock.mock_TransTermHP
self.term._compare_term_tran = self.mock.mock_compare_term_tran
self.term._remove_tmp_file = self.mock.mock_remove_tmp_file
os.mkdir(os.path.join(self.srnas, "tmp"))
os.mkdir(os.path.join(self.trans, "tmp"))
gen_file(os.path.join(self.gffs, "tmp/aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.fastas, "tmp/aaa.fa"),
self.example.fasta_file)
gen_file(os.path.join(self.srnas, "tmp/aaa_sRNA.gff"),
self.example.srna_file)
gen_file(os.path.join(self.trans, "tmp/aaa_transcript.gff"),
self.example.tran_file)
tex_wigs = os.path.join(self.test_folder, "tex")
frag_wigs = os.path.join(self.test_folder, "frag")
os.mkdir(tex_wigs)
os.mkdir(frag_wigs)
gen_file(os.path.join(frag_wigs, "frag.wig"), "text")
gen_file(os.path.join(tex_wigs, "tex.wig"), "text")
args = self.mock_args.mock()
args.out_folder = self.out
args.fastas = self.fastas
args.gffs = self.gffs
args.trans = self.trans
args.srnas = self.srnas
args.tex_wigs = tex_wigs
args.frag_wigs = frag_wigs
args.hp_folder = self.test_folder
args.tex_notex = "tex_notex"
args.wig_path = self.test_folder
args.merge_wigs = self.test_folder
args.RNAfold_path = "RNAfold_path"
args.stat = True
args.fuzzy_up_ta = 2
args.fuzzy_up_gene = 2
args.fuzzy_down_ta = 2
args.fuzzy_down_gene = 2
self.term.run_terminator(args)
self.assertTrue(
os.path.exists(os.path.join(self.out, "tables/all_candidates")))
self.assertTrue(
os.path.exists(os.path.join(self.out, "tables/express")))
self.assertTrue(os.path.exists(os.path.join(self.out, "tables/best")))
self.assertTrue(
os.path.exists(os.path.join(self.out, "gffs/all_candidates")))
self.assertTrue(os.path.exists(os.path.join(self.out, "gffs/express")))
self.assertTrue(os.path.exists(os.path.join(self.out, "gffs/best")))
class TestTerminator(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.test_folder = "test_folder"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.trans = "test_folder/trans"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out)
os.mkdir(self.fastas)
os.mkdir(self.gffs)
os.mkdir(self.srnas)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.out, "tables"))
os.mkdir(os.path.join(self.out, "gffs"))
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(os.path.join(self.fastas, "tmp"))
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.trans = self.trans
args.out_folder = self.out
args.srnas = self.srnas
self.term = Terminator(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
if os.path.exists("tmp_transterm"):
shutil.rmtree("tmp_transterm")
if os.path.exists("tmp_term_table"):
shutil.rmtree("tmp_term_table")
if os.path.exists("tmp_merge_gff"):
shutil.rmtree("tmp_merge_gff")
def test_convert_gff2rntptt(self):
os.mkdir(os.path.join(self.srnas, "tmp"))
gen_file(os.path.join(self.gffs, "aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.srnas, "aaa_sRNA.gff"), self.example.srna_file)
gen_file(os.path.join(self.fastas, "aaa.fa"), self.example.fasta_file)
file_types, prefixs = self.term._convert_gff2rntptt(self.gffs, self.fastas, self.srnas)
self.assertDictEqual(file_types, {'aaa': 'srna'})
self.assertListEqual(prefixs, ['aaa'])
def test_combine_annotation(self):
test1 = os.path.join(self.test_folder, "test1.ptt")
test2 = os.path.join(self.test_folder, "test2.ptt")
gen_file(test1, self.example.ptt)
gen_file(test2, self.example.ptt)
files = [test1, test2]
combine_file = os.path.join(self.test_folder, "combine")
self.term._combine_annotation(combine_file, files)
datas = import_data(combine_file)
result = self.example.ptt.split("\n")[3:]
self.assertEqual("\n".join(datas), "\n".join(result + result))
def test_run_TransTermHP(self):
self.term._TransTermHP = self.mock.mock_TransTermHP
os.mkdir(os.path.join(self.gffs, "tmp/combine"))
gen_file(os.path.join(self.gffs, "tmp/combine/aaa.ptt"), self.example.ptt)
gen_file(os.path.join(self.fastas, "tmp/aaa.fa"), self.example.fasta_file)
args = self.mock_args.mock()
args.gffs = self.gffs
args.fastas = self.fastas
args.hp_folder = self.out
self.term._run_TransTermHP(args)
self.assertTrue(os.path.exists(os.path.join(self.out, "aaa")))
def test_convert_to_gff(self):
self.term.multiparser = self.mock_parser
hp_folder = os.path.join(self.out, "aaa")
os.mkdir(hp_folder)
gen_file(os.path.join(hp_folder, "aaa_best_terminator_after_gene.bag"), self.example.bag)
os.mkdir("tmp_transterm")
args = self.mock_args.mock()
args.hp_folder = self.out
args.gffs = self.gffs
self.term._convert_to_gff(["aaa"], args)
datas = import_data("/home/silas/ANNOgesic/tmp_transterm/aaa_transtermhp.gff")
self.assertEqual("\n".join(datas), self.example.gff_bag)
def test_merge_sRNA(self):
os.mkdir(os.path.join(self.srnas, "tmp"))
self.term.multiparser = self.mock_parser
gen_file(os.path.join(self.gffs, "aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.srnas, "tmp/aaa_sRNA.gff"), self.example.srna_file)
merge = self.term._merge_sRNA(self.srnas, ["aaa"], self.gffs)
self.assertEqual(merge.split("/")[-1], "tmp_merge_gff")
shutil.rmtree("tmp_merge_gff")
def test_move_file(self):
term_outfolder = self.gffs
csv_outfolder = self.out
gen_file(os.path.join(term_outfolder, "aaa_term.gff"), self.example.term_file)
if (not os.path.exists("tmp_term_table")):
os.mkdir("tmp_term_table")
gen_file("tmp_term_table/aaa_term_raw.csv", "test")
self.term._move_file(term_outfolder, csv_outfolder)
shutil.rmtree("tmp_term_table")
self.assertTrue("test_folder/output/gffs/all_candidates/aaa_term_all.gff")
self.assertTrue("test_folder/output/tables/all_candidates/aaa_term_all.csv")
def test_compute_intersection_forward_reverse(self):
self.term.multiparser = self.mock_parser
te.intergenic_seq = self.mock.mock_intergenic_seq
te.poly_t = self.mock.mock_poly_t
te.detect_coverage = self.mock.mock_detect_coverage
self.term._run_rnafold = self.mock.mock_run_rnafold
term_outfolder = os.path.join(self.out, "gffs")
csv_outfolder = os.path.join(self.out, "tables")
args = self.mock_args.mock()
args.trans = self.trans
args.fastas = self.fastas
args.tex_notex = "tex_notex"
args.libs = "libs"
args.replicates = "rep"
args.RNAfold_path = "test"
self.term._compute_intersection_forward_reverse(["aaa"], self.test_folder,
"wig_path", "merge_wigs", args)
self.assertTrue(os.path.join(self.out, "inter_seq_aaa"))
self.assertTrue(os.path.join(self.out, "inter_sec_aaa"))
def test_compute_stat(self):
term_outfolder = os.path.join(self.out, "gffs")
csv_outfolder = os.path.join(self.out, "tables")
te.stat_term = self.mock.mock_stat_term
gen_file(os.path.join(term_outfolder, "all_candidates/aaa_term_all.gff"), self.example.term_file)
gen_file(os.path.join(term_outfolder, "best/aaa_term.csv"), self.example.term_file)
gen_file(os.path.join(term_outfolder, "express/aaa_term.csv"), self.example.term_file)
gen_file(os.path.join(term_outfolder, "non_express/aaa_term.csv"), self.example.term_file)
args = self.mock_args.mock()
args.stat = True
args.out_folder = self.out
self.term._compute_stat(args)
self.assertTrue(os.path.exists(os.path.join(csv_outfolder, "express/aaa_term.csv")))
self.assertTrue(os.path.exists(os.path.join(csv_outfolder, "best/aaa_term.csv")))
self.assertTrue(os.path.exists(os.path.join(csv_outfolder, "non_express/aaa_term.csv")))
def test_run_terminator(self):
te.stat_term = self.mock.mock_stat_term
te.intergenic_seq = self.mock.mock_intergenic_seq
te.poly_t = self.mock.mock_poly_t
te.detect_coverage = self.mock.mock_detect_coverage
self.term.multiparser = self.mock_parser
self.term._run_rnafold = self.mock.mock_run_rnafold
self.term._TransTermHP = self.mock.mock_TransTermHP
self.term._compare_term_tran = self.mock.mock_compare_term_tran
self.term._remove_tmp_file = self.mock.mock_remove_tmp_file
os.mkdir(os.path.join(self.srnas, "tmp"))
os.mkdir(os.path.join(self.trans, "tmp"))
gen_file(os.path.join(self.gffs, "tmp/aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.fastas, "tmp/aaa.fa"), self.example.fasta_file)
gen_file(os.path.join(self.srnas, "tmp/aaa_sRNA.gff"), self.example.srna_file)
gen_file(os.path.join(self.trans, "tmp/aaa_transcript.gff"), self.example.tran_file)
tex_wigs = os.path.join(self.test_folder, "tex")
frag_wigs = os.path.join(self.test_folder, "frag")
os.mkdir(tex_wigs)
os.mkdir(frag_wigs)
gen_file(os.path.join(frag_wigs, "frag.wig"), "text")
gen_file(os.path.join(tex_wigs, "tex.wig"), "text")
args = self.mock_args.mock()
args.out_folder = self.out
args.fastas = self.fastas
args.gffs = self.gffs
args.trans = self.trans
args.srnas = self.srnas
args.tex_wigs = tex_wigs
args.frag_wigs = frag_wigs
args.hp_folder = self.test_folder
args.tex_notex = "tex_notex"
args.wig_path = self.test_folder
args.merge_wigs = self.test_folder
args.RNAfold_path = "RNAfold_path"
args.stat = True
args.fuzzy_up_ta = 2
args.fuzzy_up_gene = 2
args.fuzzy_down_ta = 2
args.fuzzy_down_gene = 2
self.term.run_terminator(args)
self.assertTrue(os.path.exists(os.path.join(self.out, "tables/all_candidates")))
self.assertTrue(os.path.exists(os.path.join(self.out, "tables/express")))
self.assertTrue(os.path.exists(os.path.join(self.out, "tables/best")))
self.assertTrue(os.path.exists(os.path.join(self.out, "gffs/all_candidates")))
self.assertTrue(os.path.exists(os.path.join(self.out, "gffs/express")))
self.assertTrue(os.path.exists(os.path.join(self.out, "gffs/best")))