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/"