def test_optimize_tss(self):
opt.Helper = Mock_helper
opt.Multiparser = Mock_multiparser
opt.optimization = Mock_func().mock_optimization
gen_file(os.path.join(self.gffs, "tmp", "test.gff"), "test")
gen_file(os.path.join(self.fastas, "tmp", "test.fa"), "test")
args = self.mock_args.mock()
args.fastas = self.fastas
args.gffs = self.gffs
args.wigs = self.wigs
args.tsspredator_path = "test"
args.manuals = self.manuals
gen_file(os.path.join(self.manuals, "tmp", "test.gff"), "test")
args.output_folder = self.test_folder
args.project_strain = "test"
args.height = 9
args.height_reduction = 9
args.factor = 9
args.factor_reduction = 9
args.base_height = 9
args.enrichment = 9
args.processing = 9
args.utr = 200
args.libs = "test"
args.replicate_name = "test"
args.cluster = 2
args.strain_lengths = {"test": 100}
args.cores = 4
args.program = "TSS"
args.replicate = 2
args.steps = 2000
opt.optimize_tss(args)
self.assertTrue(
os.path.exists(os.path.join(self.test_folder, "test.csv")))
def optimize(self):
"""opimize TSSpredator"""
self.check_folder([
self._args.wig_folder, self._args.fasta_file,
self._args.annotation_file
])
self.check_file([self._args.manual], ["--manual"], True)
self.check_parameter(
[self._args.strain_name, self._args.lib, self._args.output_prefix],
["--strain_name", "--lib", "--output_prefix"])
if self._args.program.lower() == "tss":
print("Running optimization of TSS prediction...")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "processing_site":
print("Running optimization of processing site prediction...")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error:No such program!!!!")
sys.exit()
args_ops = self.args_container.container_optimize(
self._args.TSSpredator_path, self._args.fasta_file,
self._args.annotation_file, self._args.wig_folder,
self._args.manual, out_folder, self._args.strain_name,
self._args.max_height, self._args.max_height_reduction,
self._args.max_factor, self._args.max_factor_reduction,
self._args.max_base_height, self._args.max_enrichment_factor,
self._args.max_processing_factor, self._args.utr_length,
self._args.lib, self._args.output_prefix, self._args.cluster,
self._args.length, self._args.core, self._args.program,
self._args.replicate_match, self._args.steps)
optimize_tss(args_ops)
def optimize(self):
"""opimize TSSpredator"""
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files,
self._args.manual_files],
["--fasta_files", "--annotation_files", "--manual_files"])
self._args.tsspredator_path = self.check_execute_file(
self._args.tsspredator_path)
self.check_parameter([self._args.tex_notex_libs,
self._args.condition_names],
["--tex_notex_lib",
"--condition_names"])
if self._args.program.lower() == "tss":
print("Running optimization of TSS prediction")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "ps":
print("Running optimization of processing site prediction")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error: No such program!")
sys.exit()
args_ops = self.args_container.container_optimize(
self._args.tsspredator_path, self._args.fasta_files,
self._args.annotation_files,
self._args.manual_files, out_folder, self._args.max_height,
self._args.max_height_reduction, self._args.max_factor,
self._args.max_factor_reduction, self._args.max_base_height,
self._args.max_enrichment_factor, self._args.max_processing_factor,
self._args.utr_length, self._args.tex_notex_libs,
self._args.condition_names, self._args.cluster,
self._args.curated_sequence_length, self._args.parallels,
self._args.program, self._args.replicate_tex,
self._args.steps)
optimize_tss(args_ops)
def test_optimize_tss(self):
opt.Helper = Mock_helper
opt.Multiparser = Mock_multiparser
opt.optimization = Mock_func().mock_optimization
gen_file(os.path.join(self.gffs, "tmp", "test.gff"), "test")
gen_file(os.path.join(self.fastas, "tmp", "test.fa"), "test")
args = self.mock_args.mock()
args.fastas = self.fastas
args.gffs = self.gffs
args.wigs = self.wigs
args.tsspredator_path = "test"
args.manuals = self.manuals
gen_file(os.path.join(self.manuals, "tmp", "test.gff"), "test")
args.output_folder = self.test_folder
args.project_strain = "test"
args.height = 9
args.height_reduction = 9
args.factor = 9
args.factor_reduction = 9
args.base_height = 9
args.enrichment = 9
args.processing = 9
args.utr = 200
args.libs = "test"
args.replicate_name = "test"
args.cluster = 2
args.strain_lengths = {"test": 100}
args.cores = 4
args.program = "TSS"
args.replicate = 2
args.steps = 2000
log = open(os.path.join(self.test_folder, "test.log"), "w")
opt.optimize_tss(args, log)
self.assertTrue(os.path.exists(os.path.join(
self.test_folder, "test.csv")))
log.close()
def optimize(self):
"""opimize TSSpredator"""
self.check_folder([self._args.wig_folder, self._args.fasta_file,
self._args.annotation_file])
self.check_file([self._args.manual],
["--manual"], True)
self.check_parameter([self._args.strain_name, self._args.lib,
self._args.output_prefix],
["--strain_name", "--lib", "--output_prefix"])
if self._args.program.lower() == "tss":
print("Running optimization of TSS prediction...")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "processing_site":
print("Running optimization of processing site prediction...")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error:No such program!!!!")
sys.exit()
args_ops = self.args_container.container_optimize(
self._args.TSSpredator_path, self._args.fasta_file,
self._args.annotation_file, self._args.wig_folder,
self._args.manual, out_folder,
self._args.strain_name, self._args.max_height,
self._args.max_height_reduction, self._args.max_factor,
self._args.max_factor_reduction, self._args.max_base_height,
self._args.max_enrichment_factor, self._args.max_processing_factor,
self._args.utr_length, self._args.lib,
self._args.output_prefix, self._args.cluster,
self._args.length, self._args.core,
self._args.program, self._args.replicate_match,
self._args.steps)
optimize_tss(args_ops)