def run(self, ctl_file=None, verbose=False, command="yn00", parse=True):
Paml.run(self, ctl_file, verbose, command)
if parse:
results = read(self.out_file)
else:
results = None
return results
def run(self, ctl_file = None, verbose = False, command = "yn00",
parse = True):
Paml.run(self, ctl_file, verbose, command)
if parse:
results = read(self.out_file)
else:
results = None
return results
def run(self, ctl_file=None, verbose=False, command="baseml", parse=True):
"""Run baseml using the current configuration and then parse the results.
Return a process signal so the user can determine if
the execution was successful (return code 0 is successful, -N
indicates a failure). The arguments may be passed as either
absolute or relative paths, despite the fact that BASEML
requires relative paths.
"""
if self.tree is None:
raise ValueError("Tree file not specified.")
if not os.path.exists(self.tree):
raise IOError("The specified tree file does not exist.")
Paml.run(self, ctl_file, verbose, command)
if parse:
results = read(self.out_file)
else:
results = None
return results
def run(self, ctl_file = None, verbose = False, command = "codeml",
parse = True):
"""Run codeml using the current configuration and then parse the results.
Return a process signal so the user can determine if
the execution was successful (return code 0 is successful, -N
indicates a failure). The arguments may be passed as either
absolute or relative paths, despite the fact that CODEML
requires relative paths.
"""
if self.tree is None:
raise ValueError, "Tree file not specified."
if not os.path.exists(self.tree):
raise IOError, "The specified tree file does not exist."
Paml.run(self, ctl_file, verbose, command)
if parse:
results = read(self.out_file)
else:
results = None
return results