Exemplo n.º 1
0
 def __init__(self, jar="snpEff.jar", javatmp=os.getcwd(), max_memory=None):
     if not jar:
         raise IOError("Fail to load snpEff tools~")
     self.jar = os.path.abspath(jar)
     JavaTool.__init__(self,
                       self.jar,
                       tmp_path=os.path.abspath(javatmp),
                       max_memory=max_memory)
Exemplo n.º 2
0
 def __init__(self,
              jar_path="",
              javatmp=os.getcwd(),
              max_memory=None,
              **kwargs):
     if not jar_path:
         raise IOError("Fail to load picard tools~")
     JavaTool.__init__(self,
                       os.path.abspath(jar_path),
                       tmp_path=os.path.abspath(javatmp),
                       max_memory=max_memory)
Exemplo n.º 3
0
	def __init__(self, jar="", javatmp=os.getcwd(), max_memory=None, **kwargs):
		if not jar:
			raise IOError("Fail to load GATK3 tools~")
		JavaTool.__init__(self, os.path.abspath(jar), tmp_path=os.path.abspath(javatmp), max_memory=max_memory)
Exemplo n.º 4
0
	def __init__(self, jar="snpEff.jar", javatmp=os.getcwd(), max_memory=None):
		if not jar:
			raise IOError("Fail to load snpEff tools~")
		self.jar = os.path.abspath(jar)
		JavaTool.__init__(self, self.jar, tmp_path=os.path.abspath(javatmp), max_memory=max_memory)