Esempio n. 1
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 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
Esempio n. 2
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 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
Esempio n. 3
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    def _set_rel_paths(self):
        """Convert all file/directory locations to paths relative to the current working directory.

        BASEML 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)
Esempio n. 4
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 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)
Esempio n. 5
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    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
        }
Esempio n. 6
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 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}
Esempio n. 7
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 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}
Esempio n. 8
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 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}
Esempio n. 9
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    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
        }
Esempio n. 10
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    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
Esempio n. 11
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 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        
Esempio n. 12
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 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}