def setUp(self):
self.mock_args = MockClass()
self.example = Example()
self.mock = Mock_func()
self.test_folder = "test_folder"
self.gffs = "test_folder/gffs"
self.srnas = "test_folder/srnas"
self.out = "test_folder/output"
self.fastas = "test_folder/fastas"
self.seq = "test_folder/output/sRNA_seqs"
self.rnaup = "test_folder/output/RNAup"
self.rnaplex = "test_folder/output/RNAplex"
self.merge = "test_folder/output/merge"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.gffs)
os.mkdir(self.out)
os.mkdir(self.srnas)
os.mkdir(self.fastas)
os.mkdir(self.rnaup)
os.mkdir(self.rnaplex)
os.mkdir(self.seq)
os.mkdir(self.merge)
os.mkdir(os.path.join(self.rnaup, "test"))
args = self.mock_args.mock()
args.out_folder = self.out
args.srnas = self.srnas
args.fastas = self.fastas
args.gffs = self.gffs
self.star = sRNATargetPrediction(args)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction...")
self.check_folder([
self._args.fasta_path, self._args.sRNA_path,
self._args.annotation_path
])
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.Vienna_folder, self._args.annotation_path,
self._args.fasta_path, self._args.sRNA_path, self._args.query_sRNA,
self._args.program, self._args.interaction_length,
self._args.window_size_target, self._args.span_target,
self._args.window_size_srna, self._args.span_srna,
self._args.unstructured_region_RNAplex_target,
self._args.unstructured_region_RNAplex_srna,
self._args.unstructured_region_RNAup, self._args.energy_threshold,
self._args.duplex_distance, self._args.top,
self._paths.starget_output_folder, self._args.process_rnaplex,
self._args.process_rnaup, self._args.continue_rnaup,
self._args.potential_target_start, self._args.potential_target_end,
self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction")
self.check_multi_files(
[self._args.fasta_files, self._args.srna_files,
self._args.annotation_files],
["--fasta_files", "--srna_files",
"--annotation_files"])
if "RNAup" in self._args.program:
self._args.rnaup_path = self.check_execute_file(
self._args.rnaup_path)
if "RNAplex" in self._args.program:
for prop in ("rnaplfold_path", "rnaplex_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
if "IntaRNA" in self._args.program:
self._args.intarna_path = self.check_execute_file(
self._args.intarna_path)
if self._args.mode_intarna is None:
print("Error: --mode_IntaRNA need to be assigned!")
sys.exit()
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.rnaplfold_path, self._args.rnaplex_path,
self._args.rnaup_path, self._args.intarna_path,
self._args.annotation_files,
self._args.fasta_files, self._args.srna_files,
self._args.query_srnas, self._args.program,
self._args.interaction_length,
self._args.window_size_target_rnaplex,
self._args.span_target_rnaplex,
self._args.window_size_srna_rnaplfold,
self._args.span_srna_rnaplfold,
self._args.unstructured_region_rnaplex_target,
self._args.unstructured_region_rnaplex_srna,
self._args.unstructured_region_rnaup,
self._args.energy_threshold_rnaplex,
self._args.duplex_distance_rnaplex, self._args.top,
self._paths.starget_output_folder, self._args.parallels_rnaplex,
self._args.parallels_rnaup, self._args.parallels_intarna,
self._args.continue_rnaup,
self._args.slide_window_size_srna_intarna,
self._args.max_loop_length_srna_intarna,
self._args.slide_window_size_target_intarna,
self._args.max_loop_length_target_intarna,
self._args.mode_intarna, self._args.potential_target_start,
self._args.potential_target_end, self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction")
self.check_multi_files(
[self._args.fasta_files, self._args.srna_files,
self._args.annotation_files],
["--fasta_files", "--srna_files",
"--annotation_files"])
if (self._args.program.lower() == "both"):
for prop in ("rnaplfold_path", "rnaplex_path", "rnaup_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
elif self._args.program.lower() == "RNAup":
self._args.rnaup_path = self.check_execute_file(self._args.rnaup_path)
elif self._args.program.lower() == "RNAplex":
for prop in ("rnaplfold_path", "rnaplex_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.rnaplfold_path, self._args.rnaplex_path,
self._args.rnaup_path, self._args.annotation_files,
self._args.fasta_files, self._args.srna_files,
self._args.query_srnas, self._args.program,
self._args.interaction_length, self._args.window_size_target,
self._args.span_target, self._args.window_size_srna,
self._args.span_srna,
self._args.unstructured_region_rnaplex_target,
self._args.unstructured_region_rnaplex_srna,
self._args.unstructured_region_rnaup, self._args.energy_threshold,
self._args.duplex_distance, self._args.top,
self._paths.starget_output_folder, self._args.parallels_rnaplex,
self._args.parallels_rnaup, self._args.continue_rnaup,
self._args.potential_target_start, self._args.potential_target_end,
self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction...")
self.check_folder([self._args.fasta_path, self._args.sRNA_path,
self._args.annotation_path])
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.Vienna_folder, self._args.annotation_path,
self._args.fasta_path, self._args.sRNA_path,
self._args.query_sRNA, self._args.program,
self._args.interaction_length, self._args.window_size_target,
self._args.span_target, self._args.window_size_srna,
self._args.span_srna,
self._args.unstructured_region_RNAplex_target,
self._args.unstructured_region_RNAplex_srna,
self._args.unstructured_region_RNAup, self._args.energy_threshold,
self._args.duplex_distance, self._args.top,
self._paths.starget_output_folder, self._args.process_rnaplex,
self._args.process_rnaup, self._args.continue_rnaup,
self._args.potential_target_start, self._args.potential_target_end,
self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)