class TestGetPolyT(unittest.TestCase):
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_genomes_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_merge_files(self):
gff_folder = os.path.join(self.gffs, "test.gff_folder")
if (not os.path.exists(gff_folder)):
os.mkdir(gff_folder)
test1_folder = os.path.join(self.go_folder, "test1")
if (not os.path.exists(test1_folder)):
os.mkdir(test1_folder)
test2_folder = os.path.join(self.go_folder, "test2")
if (not os.path.exists(test2_folder)):
os.mkdir(test2_folder)
with open(os.path.join(gff_folder, "test1.gff"), "w") as fh:
fh.write("test1")
with open(os.path.join(gff_folder, "test2.gff"), "w") as fh:
fh.write("test2")
with open(os.path.join(test1_folder, "test1_uniprot.csv"), "w") as fh:
fh.write("test1")
with open(os.path.join(test2_folder, "test2_uniprot.csv"), "w") as fh:
fh.write("test2")
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.go._merge_files(self.gffs, self.go_folder, self.test_folder, log)
out_file = os.path.join(self.go_folder, "test", self.all_strain)
self.assertTrue(os.path.exists(out_file))
data = []
with open(out_file) as fh:
for line in fh:
data.append(line)
self.assertEqual(
"".join(data),
"Genome Strand Start End Protein_id Go_term\ntest1\ntest2\n")
log.close()
class TestGetPolyT(unittest.TestCase):
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_genomes_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_merge_files(self):
gff_folder = os.path.join(self.gffs, "test.gff_folder")
if (not os.path.exists(gff_folder)):
os.mkdir(gff_folder)
test1_folder = os.path.join(self.go_folder, "test1")
if (not os.path.exists(test1_folder)):
os.mkdir(test1_folder)
test2_folder = os.path.join(self.go_folder, "test2")
if (not os.path.exists(test2_folder)):
os.mkdir(test2_folder)
with open(os.path.join(gff_folder, "test1.gff"), "w") as fh:
fh.write("test1")
with open(os.path.join(gff_folder, "test2.gff"), "w") as fh:
fh.write("test2")
with open(os.path.join(test1_folder, "test1_uniprot.csv"), "w") as fh:
fh.write("test1")
with open(os.path.join(test2_folder, "test2_uniprot.csv"), "w") as fh:
fh.write("test2")
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.go._merge_files(self.gffs, self.go_folder, self.test_folder, log)
out_file = os.path.join(self.go_folder, "test", self.all_strain)
self.assertTrue(os.path.exists(out_file))
data = []
with open(out_file) as fh:
for line in fh:
data.append(line)
self.assertEqual("".join(data), "Genome Strand Start End Protein_id Go_term\ntest1\ntest2\n")
log.close()
class TestGetPolyT(unittest.TestCase):
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_strains_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_merge_files(self):
gff_folder = os.path.join(self.gffs, "test.gff_folder")
if (not os.path.exists(gff_folder)):
os.mkdir(gff_folder)
test1_folder = os.path.join(self.go_folder, "test1")
if (not os.path.exists(test1_folder)):
os.mkdir(test1_folder)
test2_folder = os.path.join(self.go_folder, "test2")
if (not os.path.exists(test2_folder)):
os.mkdir(test2_folder)
with open(os.path.join(gff_folder, "test1.gff"), "w") as fh:
fh.write("test1")
with open(os.path.join(gff_folder, "test2.gff"), "w") as fh:
fh.write("test2")
with open(os.path.join(test1_folder, "test1_uniprot.csv"), "w") as fh:
fh.write("test1")
with open(os.path.join(test2_folder, "test2_uniprot.csv"), "w") as fh:
fh.write("test2")
self.go._merge_files(self.gffs, self.go_folder, self.test_folder)
out_file = os.path.join(self.go_folder, "test", self.all_strain)
self.assertTrue(os.path.exists(out_file))
with open(out_file) as fh:
for line in fh:
self.assertEqual(line, "test1test2")
class TestGetPolyT(unittest.TestCase):
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_strains_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_merge_files(self):
gff_folder = os.path.join(self.gffs, "test.gff_folder")
if (not os.path.exists(gff_folder)):
os.mkdir(gff_folder)
test1_folder = os.path.join(self.go_folder, "test1")
if (not os.path.exists(test1_folder)):
os.mkdir(test1_folder)
test2_folder = os.path.join(self.go_folder, "test2")
if (not os.path.exists(test2_folder)):
os.mkdir(test2_folder)
with open(os.path.join(gff_folder, "test1.gff"), "w") as fh:
fh.write("test1")
with open(os.path.join(gff_folder, "test2.gff"), "w") as fh:
fh.write("test2")
with open(os.path.join(test1_folder, "test1_uniprot.csv"), "w") as fh:
fh.write("test1")
with open(os.path.join(test2_folder, "test2_uniprot.csv"), "w") as fh:
fh.write("test2")
self.go._merge_files(self.gffs, self.go_folder, self.test_folder)
out_file = os.path.join(self.go_folder, "test", self.all_strain)
self.assertTrue(os.path.exists(out_file))
with open(out_file) as fh:
for line in fh:
self.assertEqual(line, "test1test2")
def goterm(self):
"""Go term discovery"""
print("Running GO term mapping...")
self.check_folder([self._args.annotation_path])
self.check_no_require_folder([self._args.transcript_path])
self.check_file(
[self._args.UniProt_id, self._args.go_obo, self._args.goslim_obo],
["--UniProt_id", "--go.obo", "--goslim_obo"], True)
project_creator.create_subfolders(
self._paths.required_folders("go_term"))
args_go = self.args_container.container_goterm(
self._args.annotation_path, self._paths.goterm_output_folder,
self._args.UniProt_id, self._args.go_obo, self._args.goslim_obo,
self._args.transcript_path)
goterm = GoTermFinding(args_go)
goterm.run_go_term(args_go)
def goterm(self):
"""Go term discovery"""
print("Running GO term mapping...")
self.check_folder([self._args.annotation_path])
self.check_no_require_folder([self._args.transcript_path])
self.check_file([self._args.UniProt_id, self._args.go_obo,
self._args.goslim_obo],
["--UniProt_id", "--go.obo", "--goslim_obo"], True)
project_creator.create_subfolders(
self._paths.required_folders("go_term"))
args_go = self.args_container.container_goterm(
self._args.annotation_path,
self._paths.goterm_output_folder, self._args.UniProt_id,
self._args.go_obo, self._args.goslim_obo,
self._args.transcript_path)
goterm = GoTermFinding(args_go)
goterm.run_go_term(args_go)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_genomes_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gffs = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gffs)):
os.mkdir(self.gffs)
self.go_folder = os.path.join(self.test_folder, "go_folder")
if (not os.path.exists(self.go_folder)):
os.mkdir(self.go_folder)
self.all_strain = "all_genomes_uniprot.csv"
self.trans = os.path.join(self.test_folder, "tran_folder")
if (not os.path.exists(self.trans)):
os.mkdir(self.trans)
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.gffs = self.gffs
args.trans = self.trans
self.go = GoTermFinding(args)