class TestTargetFasta(unittest.TestCase):
def setUp(self):
self.root_folder = "a_test_project"
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
self.ref_folder = os.path.join(self.root_folder, "ref")
self.tar_folder = os.path.join(self.root_folder, "tar")
self.fasta_folder = os.path.join(self.root_folder, "fasta_files")
os.mkdir(self.root_folder)
os.mkdir(self.ref_folder)
os.mkdir(self.tar_folder)
os.mkdir(os.path.join(self.root_folder, "fasta_files"))
self.target_fasta = TargetFasta(self.tar_folder, self.ref_folder)
self.target_fasta.seq_editer = Mock_seq_editer
self.target_fasta.multiparser = Mock_multiparser
self.target_fasta.helper = Mock_helper
self.example = ExampleData()
def tearDown(self):
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
def test_get_target_fasta(self):
gen_file("a_test_project/ref/bbb.fa", self.example.fasta_file2)
gen_file("a_test_project/mut", self.example.mutation_table)
log = open(os.path.join(self.root_folder, "test.log"), "w")
self.target_fasta.get_target_fasta("a_test_project/mut",
self.tar_folder,
["a_test_project/ref/bbb.fa"],
"test", self.root_folder, log)
self.assertTrue(
os.path.exists(os.path.join(self.fasta_folder, "test.fa")))
log.close()
class TestTargetFasta(unittest.TestCase):
def setUp(self):
self.root_folder = "a_test_project"
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
self.ref_folder = os.path.join(self.root_folder, "ref")
self.tar_folder = os.path.join(self.root_folder, "tar")
os.mkdir(self.root_folder)
os.mkdir(self.ref_folder)
os.mkdir(self.tar_folder)
self.target_fasta = TargetFasta(self.tar_folder, self.ref_folder)
self.target_fasta.seq_editer = Mock_seq_editer
self.target_fasta.multiparser = Mock_multiparser
self.target_fasta.helper = Mock_helper
self.example = ExampleData()
def tearDown(self):
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
def test_get_target_fasta(self):
self.target_fasta.get_target_fasta(None,
self.tar_folder,
self.ref_folder,
["ccc:aaa,bbb"])
self.assertTrue(os.path.exists(os.path.join(self.tar_folder, "ccc.fa")))
class TestTargetFasta(unittest.TestCase):
def setUp(self):
self.root_folder = "a_test_project"
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
self.ref_folder = os.path.join(self.root_folder, "ref")
self.tar_folder = os.path.join(self.root_folder, "tar")
self.fasta_folder = os.path.join(self.root_folder, "fasta_files")
os.mkdir(self.root_folder)
os.mkdir(self.ref_folder)
os.mkdir(self.tar_folder)
os.mkdir(os.path.join(self.root_folder, "fasta_files"))
self.target_fasta = TargetFasta(self.tar_folder, self.ref_folder)
self.target_fasta.seq_editer = Mock_seq_editer
self.target_fasta.multiparser = Mock_multiparser
self.target_fasta.helper = Mock_helper
self.example = ExampleData()
def tearDown(self):
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
def test_get_target_fasta(self):
gen_file("a_test_project/ref/bbb.fa", self.example.fasta_file2)
gen_file("a_test_project/mut", self.example.mutation_table)
log = open(os.path.join(self.root_folder, "test.log"), "w")
self.target_fasta.get_target_fasta("a_test_project/mut",
self.tar_folder,
["a_test_project/ref/bbb.fa"],
"test",
self.root_folder,log)
self.assertTrue(os.path.exists(
os.path.join(self.fasta_folder, "test.fa")))
log.close()
def setUp(self):
self.root_folder = "a_test_project"
if os.path.exists(self.root_folder):
shutil.rmtree(self.root_folder)
self.ref_folder = os.path.join(self.root_folder, "ref")
self.tar_folder = os.path.join(self.root_folder, "tar")
os.mkdir(self.root_folder)
os.mkdir(self.ref_folder)
os.mkdir(self.tar_folder)
self.target_fasta = TargetFasta(self.tar_folder, self.ref_folder)
self.target_fasta.seq_editer = Mock_seq_editer
self.target_fasta.multiparser = Mock_multiparser
self.target_fasta.helper = Mock_helper
self.example = ExampleData()
def get_target_fasta(self):
"""Get target fasta"""
print("Running update genome fasta")
self.check_multi_files([self._args.related_fasta_files],
["--related_fasta_files"])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.related_fasta_files)
target.get_target_fasta(
self._args.mutation_table, self._paths.tar_fasta_folder,
self._args.related_fasta_files, self._args.combine_to_one_fasta,
self._paths.target_base_folder)
def get_target_fasta(self):
"""Get target fasta"""
print("Running get target fasta...")
self.check_parameter([self._args.output_format], ["--output_format"])
self.check_folder([self._args.ref_fasta_folder])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
outputs = self._args.output_format.split(",")
for output in outputs:
output = output.strip()
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.ref_fasta_folder)
target.get_target_fasta(
self._args.mutation_table, self._paths.tar_fasta_folder,
self._args.ref_fasta_folder, outputs)
def get_target_fasta(self):
"""Get target fasta"""
print("Running get target fasta...")
self.check_parameter([self._args.output_format], ["--output_format"])
self.check_folder([self._args.ref_fasta_folder])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
outputs = self._args.output_format.split(",")
for output in outputs:
output = output.strip()
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.ref_fasta_folder)
target.get_target_fasta(self._args.mutation_table,
self._paths.tar_fasta_folder,
self._args.ref_fasta_folder, outputs)
def get_target_fasta(self):
"""Get target fasta"""
print("Running get target fasta")
self.check_multi_files([self._args.ref_fasta_files], ["--ref_fasta_files"])
self.check_parameter([self._args.output_format], ["--output_format"])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
for output in self._args.output_format:
output = output.strip()
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.ref_fasta_files)
target.get_target_fasta(
self._args.mutation_table, self._paths.tar_fasta_folder,
self._args.ref_fasta_files, self._args.output_format,
self._paths.target_base_folder)