def setUp(self):
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.example = Example()
self.test_folder = "test_folder"
self.trans = "test_folder/trans"
self.out = "test_folder/output"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.terms = "test_folder/terms"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.out)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.terms)
args = self.mock_args.mock()
args.tsss = self.tsss
args.trans = self.trans
args.out_folder = self.out
self.utr = UTRDetection(args)
def utr_detection(self):
"""Run UTR detection."""
print("Running UTR detection...")
self.check_folder([self._args.annotation_folder,
self._args.transcript_assembly_folder,
self._args.TSS_folder])
self.check_no_require_folder([self._args.terminator_folder])
project_creator.create_subfolders(self._paths.required_folders("utr"))
args_utr = self.args_container.container_utr(
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_assembly_folder,
self._args.terminator_folder,
self._args.terminator_fuzzy, self._paths.utr_folder,
self._args.TSS_source, self._args.base_5UTR,
self._args.UTR_length, self._args.base_3UTR)
utr = UTRDetection(args_utr)
utr.run_utr_detection(args_utr)
def utr_detection(self):
"""Run UTR detection."""
print("Running UTR detection...")
self.check_folder([
self._args.annotation_folder,
self._args.transcript_assembly_folder, self._args.TSS_folder
])
self.check_no_require_folder([self._args.terminator_folder])
project_creator.create_subfolders(self._paths.required_folders("utr"))
args_utr = self.args_container.container_utr(
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_assembly_folder,
self._args.terminator_folder, self._args.terminator_fuzzy,
self._paths.utr_folder, self._args.TSS_source,
self._args.base_5UTR, self._args.UTR_length, self._args.base_3UTR)
utr = UTRDetection(args_utr)
utr.run_utr_detection(args_utr)
def utr_detection(self):
"""Run UTR detection."""
print("Running UTR detection")
self.check_multi_files(
[self._args.annotation_files, self._args.terminator_files,
self._args.transcript_files, self._args.tss_files],
["--annotation_files", "--terminator_files",
"--transcript_files", "--tss_files"])
project_creator.create_subfolders(self._paths.required_folders("utr"))
args_utr = self.args_container.container_utr(
self._args.tss_files, self._args.annotation_files,
self._args.transcript_files, self._args.terminator_files,
self._args.terminator_tolerance, self._paths.utr_folder,
self._args.tss_source, self._args.base_5utr,
self._args.utr_length, self._args.base_3utr,
self._args.tolerance_3utr, self._args.tolerance_5utr)
utr = UTRDetection(args_utr)
utr.run_utr_detection(args_utr)
class TestsTSSpredator(unittest.TestCase):
def setUp(self):
self.mock_args = MockClass()
self.mock = Mock_func()
self.mock_parser = Mock_Multiparser()
self.example = Example()
self.test_folder = "test_folder"
self.trans = "test_folder/trans"
self.out = "test_folder/output"
self.gffs = "test_folder/gffs"
self.tsss = "test_folder/tsss"
self.terms = "test_folder/terms"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.trans)
os.mkdir(os.path.join(self.trans, "tmp"))
os.mkdir(self.out)
os.mkdir(self.gffs)
os.mkdir(self.tsss)
os.mkdir(os.path.join(self.tsss, "tmp"))
os.mkdir(self.terms)
args = self.mock_args.mock()
args.tsss = self.tsss
args.trans = self.trans
args.out_folder = self.out
self.utr = UTRDetection(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_compute_utr(self):
ut.detect_5utr = self.mock.mock_detect_5utr
ut.detect_3utr = self.mock.mock_detect_3utr
term_path = os.path.join(self.terms, "tmp")
os.mkdir(term_path)
utr5_path = os.path.join(self.out, "5UTR")
utr3_path = os.path.join(self.out, "3UTR")
os.mkdir(utr5_path)
os.mkdir(utr3_path)
utr5_stat_path = os.path.join(utr5_path, "statistics")
utr3_stat_path = os.path.join(utr3_path, "statistics")
os.mkdir(utr5_stat_path)
os.mkdir(utr3_stat_path)
gen_file(os.path.join(self.gffs, "test.gff"), self.example.gff_file)
gen_file(os.path.join(self.trans, "test_transcript.gff"), self.example.tran_file)
gen_file(os.path.join(self.tsss, "test_TSS.gff"), self.example.tss_file)
gen_file(os.path.join(term_path, "test_term.gff"), self.example.term_file)
args = self.mock_args.mock()
args.gffs = self.gffs
args.tsss = self.tsss
args.trans = self.trans
args.terms = self.terms
self.utr._compute_utr(args)
self.assertTrue(os.path.exists(os.path.join(utr5_stat_path, "test_5utr_length.png")))
self.assertTrue(os.path.exists(os.path.join(utr3_stat_path, "test_3utr_length.png")))
def test_run_utr_detection(self):
self.utr._check_gff = self.mock.mock_check_gff
ut.detect_5utr = self.mock.mock_detect_5utr
ut.detect_3utr = self.mock.mock_detect_3utr
utr5_path = os.path.join(self.out, "5UTR")
utr3_path = os.path.join(self.out, "3UTR")
os.mkdir(utr5_path)
os.mkdir(utr3_path)
utr5_stat_path = os.path.join(utr5_path, "statistics")
utr3_stat_path = os.path.join(utr3_path, "statistics")
os.mkdir(utr5_stat_path)
os.mkdir(utr3_stat_path)
gen_file(os.path.join(self.gffs, "test.gff"), self.example.gff_file)
gen_file(os.path.join(self.trans, "test_transcript.gff"), self.example.tran_file)
gen_file(os.path.join(self.tsss, "test_TSS.gff"), self.example.tss_file)
gen_file(os.path.join(self.terms, "test_term.gff"), self.example.term_file)
args = self.mock_args.mock()
args.tsss = self.tsss
args.gffs = self.gffs
args.trans = self.trans
args.terms = self.terms
args.out_folder = self.out
self.utr.run_utr_detection(args)
self.assertTrue(os.path.exists(os.path.join(utr5_stat_path, "test_5utr_length.png")))
self.assertTrue(os.path.exists(os.path.join(utr3_stat_path, "test_3utr_length.png")))