本文整理汇总了Python中_paml.Paml.__init__方法的典型用法代码示例。如果您正苦于以下问题：Python Paml.__init__方法的具体用法？Python Paml.__init__怎么用？Python Paml.__init__使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类_paml.Paml的用法示例。
在下文中一共展示了Paml.__init__方法的3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: __init__
# 需要导入模块: from _paml import Paml [as 别名]
# 或者: from _paml.Paml import __init__ [as 别名]
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2: __init__
# 需要导入模块: from _paml import Paml [as 别名]
# 或者: from _paml.Paml import __init__ [as 别名]
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3: __init__
# 需要导入模块: from _paml import Paml [as 别名]
# 或者: from _paml.Paml import __init__ [as 别名]
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}