def __init__(self,
threads=None,
runfiles=None,
path=None,
output_dir=None,
extra_params=None):
if output_dir:
self.output_dir = os.path.abspath(output_dir)
else:
self.output_dir = os.getcwd()
if threads:
self.threads = threads
else:
self.threads = 16
if not os.path.isdir(self.output_dir):
os.makedirs(self.output_dir)
if runfiles:
self.runfiles = runfiles
else:
self.path = path
self.runfiles = fileparser.RunFiles(self.path,
output_dir=output_dir)
if extra_params:
self.extra_params = " ".join(extra_params)
else:
self.extra_params = ""
self.spades_out_dir = self.output_dir + "/spades_output/"
def __init__(self, runfiles=None, path=None, output_dir = ""):
if output_dir:
self.output_dir = os.path.abspath(output_dir)
else:
self.output_dir = os.getcwd()
if not os.path.isdir(self.output_dir):
os.makedirs(self.output_dir)
if runfiles:
self.runfiles = runfiles
else:
self.path = path
self.runfiles = fileparser.RunFiles(self.path, output_dir=output_dir)
self.cg_out_dir = self.output_dir + "/cg_pipeline_output/"
def __init__(self, runfiles=None, path=None, output_dir = None):
reference_dir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))[:-4] + "/PT_genomes"
if output_dir:
self.output_dir = os.path.abspath(output_dir)
else:
self.output_dir = os.getcwd()
if not os.path.isdir(self.output_dir):
os.makedirs(self.output_dir)
if runfiles:
self.runfiles = runfiles
else:
self.path = path
self.runfiles = fileparser.RunFiles(self.path, output_dir=output_dir)
self.db=reference_dir
self.cutshaw_out_dir = self.output_dir + "/CutShaw_output/"