class TestScreen(unittest.TestCase):
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.output = os.path.join(self.test_folder, "output")
self.tex_wig = os.path.join(self.test_folder, "tex")
self.frag_wig = os.path.join(self.test_folder, "frag")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tex_wig)
os.mkdir(self.frag_wig)
os.mkdir(self.output)
self.fasta = os.path.join(self.test_folder, "aaa.fa")
gen_file(self.fasta, self.example.fasta)
args = self.mock_args.mock()
args.output_folder = self.output
args.fasta = self.fasta
self.screen = Screen(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_screenshot(self):
gen_file(os.path.join(self.tex_wig, "tex_1_f.wig"), self.example.wig_f)
gen_file(os.path.join(self.tex_wig, "notex_1_f.wig"), self.example.wig_f)
gen_file(os.path.join(self.frag_wig, "frag_f.wig"), self.example.wig_f)
gen_file(os.path.join(self.tex_wig, "tex_1_r.wig"), self.example.wig_r)
gen_file(os.path.join(self.tex_wig, "notex_1_r.wig"), self.example.wig_r)
gen_file(os.path.join(self.frag_wig, "frag_r.wig"), self.example.wig_r)
args = self.mock_args.mock()
args.fasta = self.fasta
args.main_gff = os.path.join(self.test_folder, "main.gff")
gen_file(args.main_gff, self.example.main_gff)
side_gff = os.path.join(self.test_folder, "side.gff")
args.side_gffs = [side_gff]
gen_file(side_gff, self.example.side_gff)
args.frag_wigs = self.frag_wig
args.tex_wigs = self.tex_wig
args.height = 1000
args.tlibs = ["tex_1_f.wig:tex:1:a:+", "tex_1_r.wig:tex:1:a:-",
"notex_1_f.wig:notex:1:a:+", "notex_1_r.wig:notex:1:a:-"]
args.flibs = ["frag_f.wig:frag:1:a:+", "frag_r.wig:frag:1:a:-"]
args.present = "expand"
args.output_folder = self.output
self.screen.screenshot(args)
self.assertTrue(os.path.exists(os.path.join(self.output, "screenshots", "aaa", "forward")))
self.assertTrue(os.path.exists(os.path.join(self.output, "screenshots", "aaa", "reverse")))
datas = import_data(os.path.join(self.output, "screenshots", "aaa", "forward.txt"))
datas = import_data(os.path.join(self.output, "screenshots", "aaa", "reverse.txt"))
self.assertEqual("\n".join(datas), self.example.out_r)
def test_import_libs(self):
texs = [["tex_1.wig", "tex", "1", "a", "+"], ["notex_1.wig", "notex", "1", "a", "+"]]
lib_dict = {"ft": [], "fn": [], "rt": [], "rn": [], "ff": [], "rf": []}
self.screen._import_libs(texs, "+", self.tex_wig, lib_dict)
self.assertDictEqual(lib_dict, {'fn': ['test_folder/tex/notex_1.wig'], 'rn': [],
'rt': [], 'ft': ['test_folder/tex/tex_1.wig'], 'rf': [], 'ff': []})
def screen(self):
"""generate screenshot"""
print("Running screenshot generation")
self.check_file([self._args.main_gff, self._args.fasta_file],
["--main_gff", "--fasta_file"], True)
if self._args.side_gffs is not None:
for gff in (self._args.side_gffs):
gff = gff.strip()
if not os.path.isfile(gff):
print("Error: The --side_gffs do not exist!")
sys.exit()
if self._args.output_folder is None:
print("Error: Please assign --output_folder!")
sys.exit()
if (self._args.present != "expand") and (
self._args.present != "collapse") and (
self._args.present != "squish"):
print("Error: Please assign \"expand\" or "
"\"collapse\" or \"squish\" to --present!")
sys.exit()
args_sc = self.args_container.container_screen(
self._args.main_gff, self._args.side_gffs,
self._args.fasta_file, self._args.height,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.present, self._args.output_folder)
screen = Screen(args_sc)
screen.screenshot(args_sc)
def screen(self):
"""generate screenshot"""
print("Running screenshot generating...")
self.check_file([self._args.main_gff, self._args.fasta],
["--main_gff", "--fasta"], True)
if self._args.side_gffs is not None:
for gff in (self._args.side_gffs.split(",")):
gff = gff.strip()
if not os.path.isfile(gff):
print("Error: The --side_gffs no exist!!")
sys.exit()
if self._args.output_folder is None:
print("Error: please assign --output_folder!!")
sys.exit()
if (self._args.present != "expand") and (
self._args.present != "collapse") and (
self._args.present != "squish"):
print("Error: please assign \"expand\" or "
"\"collapse\" or \"squish\" to --present!!")
sys.exit()
args_sc = self.args_container.container_screen(
self._args.main_gff, self._args.side_gffs,
self._args.fasta, self._args.frag_wig_folder,
self._args.tex_wig_folder, self._args.height,
self._args.tex_libs, self._args.frag_libs,
self._args.present, self._args.output_folder)
screen = Screen(args_sc)
screen.screenshot(args_sc)
def setUp(self):
self.example = Example()
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.output = os.path.join(self.test_folder, "output")
self.tex_wig = os.path.join(self.test_folder, "tex")
self.frag_wig = os.path.join(self.test_folder, "frag")
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.tex_wig)
os.mkdir(self.frag_wig)
os.mkdir(self.output)
self.fasta = os.path.join(self.test_folder, "aaa.fa")
gen_file(self.fasta, self.example.fasta)
args = self.mock_args.mock()
args.output_folder = self.output
args.fasta = self.fasta
self.screen = Screen(args, self.output)