本文整理汇总了Python中_paml.Paml类的典型用法代码示例。如果您正苦于以下问题：Python Paml类的具体用法？Python Paml怎么用？Python Paml使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Paml类的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: run
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示例2: _set_rel_paths
def _set_rel_paths(self):
"""Convert all file/directory locations to paths relative to the current working directory.
CODEML requires that all paths specified in the control file be
relative to the directory from which it is called rather than
absolute paths.
"""
Paml._set_rel_paths(self)
if self.tree is not None:
self._rel_tree = _relpath(self.tree, self.working_dir)示例3: __init__
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}示例4: __init__
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}示例5: run
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 示例6: __init__
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}