def compile(self):
refresh_register()
debug("Available Commands: \n{}\n".format(available_commands))
for _ in self._steps_data:
# add to the steps title list
fname = get_step_title(_) # debug(fname)
self._steps_title.append(fname)
if fname in available_commands:
command = available_commands.find(fname)
args = get_step_args(_)
kwargs = get_step_kwargs(_)
# print(args)
# print(kwargs)
try:
command.validate(args, kwargs)
except ValueError as vErr:
self._arg_fail.add(fname)
error("{}: {}".format(command, vErr))
except TypeError as tErr:
self._arg_fail.add(fname)
error("{}: Attribute(s) Missing: {}".format(command, tErr))
command.set_args(args, kwargs)
self.steps.append(command)
temp(repr(command))
else:
fatal(fname)
self.commands_not_found.append(fname)
err = len(self.commands_not_found)
aerr = len(self._arg_fail)
if err:
error("{} command{} from the procedure not found.".format(
colored(err, "red"), "s" if err > 1 else ""))
if aerr:
error("{} command{} had an argument mismatch.".format(
colored(aerr, "yellow"), "s" if aerr > 1 else ""))
if err + aerr:
error(self)
error(self._arg_fail)
raise Exception("Compilation Failed Error")
exit(1)
debug(self)
info("Compilation Successfull.\n")
def get_genome():
temp("I got the genome")
def generate_primer_pool(method="primer3"):
temp("I did validate this snp region on the given target")
def filter_primer_pool(GC, del_g, free_energy, thermo=False):
temp("I did validate this snp region on the given target")
def select_target_region(width, symmetric=True):
temp("I did validate this snp region on the given target")
def print_allele_frequency(*selectors):
temp("I did validate this snp region on the given target")
def get_chromosome_location():
temp("I did validate this snp region on the given target")
def snp_id(*ids):
temp("I did validate this snp region on the given target")
def validate_snp_region_on_target():
temp("I did validate this snp region on the given target")