def __init__(self,
alignment=None,
tree=None,
working_dir=None,
out_file=None):
"""Initialize the codeml instance.
The user may optionally pass in strings specifying the locations
of the input alignment and tree files, the working directory and
the final output file. Other options found in the CODEML control
have typical settings by default to run site class models 0, 1 and
2 on a nucleotide alignment.
"""
Paml.__init__(self, alignment, working_dir, out_file)
if tree is not None:
if not os.path.exists(tree):
raise IOError("The specified tree file does not exist.")
self.tree = tree
self.ctl_file = "codeml.ctl"
self._options = {
"noisy": None,
"verbose": None,
"runmode": None,
"seqtype": None,
"CodonFreq": None,
"ndata": None,
"clock": None,
"aaDist": None,
"aaRatefile": None,
"model": None,
"NSsites": None,
"icode": None,
"Mgene": None,
"fix_kappa": None,
"kappa": None,
"fix_omega": None,
"omega": None,
"fix_alpha": None,
"alpha": None,
"Malpha": None,
"ncatG": None,
"getSE": None,
"RateAncestor": None,
"Small_Diff": None,
"cleandata": None,
"fix_blength": None,
"method": None,
"rho": None,
"fix_rho": None
}
def __init__(self, alignment = None, working_dir = None,
out_file = None):
"""Initialize the Yn00 instance.
The user may optionally pass in strings specifying the locations
of the input alignment, the working directory and
the final output file.
"""
Paml.__init__(self, alignment, working_dir, out_file)
self.ctl_file = "yn00.ctl"
self._options = {"verbose": None,
"icode": None,
"weighting": None,
"commonf3x4": None,
"ndata": None}
def __init__(self, alignment = None, working_dir = None,
out_file = None):
"""Initialize the Yn00 instance.
The user may optionally pass in strings specifying the locations
of the input alignment, the working directory and
the final output file.
"""
Paml.__init__(self, alignment, working_dir, out_file)
self.ctl_file = "yn00.ctl"
self._options = {"verbose": None,
"icode": None,
"weighting": None,
"commonf3x4": None,
"ndata": None}
def __init__(self, alignment = None, tree = None, working_dir = None,
out_file = None):
"""Initialize the codeml instance.
The user may optionally pass in strings specifying the locations
of the input alignment and tree files, the working directory and
the final output file. Other options found in the CODEML control
have typical settings by default to run site class models 0, 1 and
2 on a nucleotide alignment.
"""
Paml.__init__(self, alignment, working_dir, out_file)
if tree is not None:
if not os.path.exists(tree):
raise IOError, "The specified tree file does not exist."
self.tree = tree
self.ctl_file = "codeml.ctl"
self._options = {"noisy": None,
"verbose": None,
"runmode": None,
"seqtype": None,
"CodonFreq": None,
"ndata": None,
"clock": None,
"aaDist": None,
"aaRatefile": None,
"model": None,
"NSsites": None,
"icode": None,
"Mgene": None,
"fix_kappa": None,
"kappa": None,
"fix_omega": None,
"omega": None,
"fix_alpha": None,
"alpha": None,
"Malpha": None,
"ncatG": None,
"getSE": None,
"RateAncestor": None,
"Small_Diff": None,
"cleandata": None,
"fix_blength": None,
"method": None,
"rho": None,
"fix_rho": None}
def __init__(self,
alignment=None,
tree=None,
working_dir=None,
out_file=None):
"""Initialize the Baseml instance.
The user may optionally pass in strings specifying the locations
of the input alignment and tree files, the working directory and
the final output file.
"""
Paml.__init__(self, alignment, working_dir, out_file)
if tree is not None:
if not os.path.exists(tree):
raise IOError("The specified tree file does not exist.")
self.tree = tree
self.ctl_file = "baseml.ctl"
self._options = {
"noisy": None,
"verbose": None,
"runmode": None,
"model": None,
"model_options": None,
"Mgene": None,
"ndata": None,
"clock": None,
"fix_kappa": None,
"kappa": None,
"fix_alpha": None,
"alpha": None,
"Malpha": None,
"ncatG": None,
"fix_rho": None,
"rho": None,
"nparK": None,
"nhomo": None,
"getSE": None,
"RateAncestor": None,
"Small_Diff": None,
"cleandata": None,
"icode": None,
"fix_blength": None,
"method": None
}
def __init__(self, alignment = None, tree = None, working_dir = None,
out_file = None):
"""Initialize the Baseml instance.
The user may optionally pass in strings specifying the locations
of the input alignment and tree files, the working directory and
the final output file.
"""
Paml.__init__(self, alignment, working_dir, out_file)
if tree is not None:
if not os.path.exists(tree):
raise IOError, "The specified tree file does not exist."
self.tree = tree
self.ctl_file = "baseml.ctl"
self._options = {"noisy": None,
"verbose": None,
"runmode": None,
"model": None,
"model_options": None,
"Mgene": None,
"ndata": None,
"clock": None,
"fix_kappa": None,
"kappa": None,
"fix_alpha": None,
"alpha": None,
"Malpha": None,
"ncatG": None,
"fix_rho": None,
"rho": None,
"nparK": None,
"nhomo": None,
"getSE": None,
"RateAncestor": None,
"Small_Diff": None,
"cleandata": None,
"icode": None,
"fix_blength": None,
"method": None}