def test_mikado_config(self):
namespace = Namespace(default=False)
namespace.scoring = None
namespace.intron_range = None
namespace.reference = ""
namespace.external = None
namespace.mode = ["permissive"]
namespace.threads = 1
namespace.blast_targets = []
namespace.junctions = []
out = os.path.join(tempfile.gettempdir(), "configuration.yaml")
with open(out, "w") as out_handle:
namespace.out = out_handle
Mikado.subprograms.configure.create_config(namespace)
self.assertGreater(os.stat(out).st_size, 0)
conf = Mikado.configuration.configurator.to_json(out)
conf = Mikado.configuration.configurator.check_json(conf)
conf = Mikado.configuration.configurator.check_json(conf)
os.remove(out)
def test_mikado_config(self):
namespace = Namespace(default=False)
namespace.scoring = None
namespace.intron_range = None
namespace.reference = ""
namespace.external = None
namespace.mode = ["permissive"]
namespace.threads = 1
namespace.blast_targets = []
namespace.junctions = []
out = os.path.join(tempfile.gettempdir(), "configuration.yaml")
with open(out, "w") as out_handle:
namespace.out = out_handle
Mikado.subprograms.configure.create_config(namespace)
self.assertGreater(os.stat(out).st_size, 0)
conf = Mikado.configuration.configurator.to_json(out)
conf = Mikado.configuration.configurator.check_json(conf)
conf = Mikado.configuration.configurator.check_json(conf)
os.remove(out)
def test_daijin_config(self):
# Check the basic function actually functions
_ = daijin_configurator.create_daijin_base_config()
namespace = Namespace(default=False)
namespace.r1 = []
namespace.r2 = []
namespace.samples = []
namespace.strandedness = []
namespace.asm_methods = []
namespace.aligners = []
namespace.modes = ["nosplit"]
namespace.cluster_config = None
namespace.scheduler = ""
namespace.flank = None
namespace.intron_range = None
namespace.prot_db = []
namespace.genome = self.__genomefile__.name
namespace.transcriptome = ""
namespace.name = "Daijin"
namespace.out_dir = tempfile.gettempdir()
namespace.threads = 1
namespace.scoring = random.choice(
pkg_resources.resource_listdir("Mikado.configuration",
"scoring_files"))
out = os.path.join(tempfile.gettempdir(), "configuration.yaml")
with open(out, "wt") as out_handle:
namespace.out = out_handle
daijin_configurator.create_daijin_config(namespace, level="ERROR")
self.assertGreater(os.stat(out).st_size, 0)
with open(out) as out_handle:
config = yaml.load(out_handle)
daijin_configurator.check_config(config)
def test_daijin_config(self):
# Check the basic function actually functions
_ = daijin_configurator.create_daijin_base_config()
namespace = Namespace(default=False)
namespace.r1 = []
namespace.r2 = []
namespace.samples = []
namespace.strandedness = []
namespace.asm_methods = []
namespace.aligners = []
namespace.modes = ["nosplit"]
namespace.cluster_config = None
namespace.scheduler = ""
namespace.flank = None
namespace.intron_range = None
namespace.prot_db = []
namespace.genome = self.__genomefile__.name
namespace.transcriptome = ""
namespace.name = "Daijin"
namespace.out_dir = tempfile.gettempdir()
namespace.threads = 1
namespace.scoring = random.choice(
pkg_resources.resource_listdir("Mikado.configuration", "scoring_files"))
out = os.path.join(tempfile.gettempdir(), "configuration.yaml")
with open(out, "wt") as out_handle:
namespace.out = out_handle
daijin_configurator.create_daijin_config(namespace, level="ERROR")
self.assertGreater(os.stat(out).st_size, 0)
with open(out) as out_handle:
config = yaml.load(out_handle)
daijin_configurator.check_config(config)