def __init__(self, mothurExe, commands, stdout=None, stderr=None):
# Validate the supplied Mothur executable
try:
assert is_executable(mothurExe)
self._mothur = mothurExe
except AssertionError:
raise ValueError("Mothur executable is not valid!")
# Validate the supplied Mothur commands
self._commands = []
for command in commands:
try:
assert isinstance(command, MothurCommand)
self._commands.append( command )
except:
raise ValueError("Argument is not a MothurCommand!")
self.stdout = stdout
self.stderr = stderr
def validateSettings(self):
# Search for Mothur executable if not supplied
if self.mothurExe is None:
self.mothur = which('mothur')
if self.mothur is None:
raise OSError('Mothur executable not found!')
# If an argument was given, check that it's executable
elif is_executable( self.mothurExe ):
self.mothur = self.mothurExe
else:
raise OSError('Supplied Mothur executable not valid!')
# Validate the Num_Processes argument
try:
assert self.numProc >= 1
except AssertionError:
raise ValueError("Number of processes must be >= 1!")
self.numProc = str(self.numProc)
