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| # Copyright (C) 2011 by Brandon Invergo ([email protected]) | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Base class for the support of PAML, Phylogenetic Analysis by Maximum Likelihood.""" | |
| import os | |
| import subprocess | |
| class PamlError(EnvironmentError): | |
| """paml has failed. | |
| Run with verbose=True to view the error message. | |
| """ | |
| class Paml: | |
| """Base class for wrapping PAML commands.""" | |
| def __init__(self, alignment=None, working_dir=None, out_file=None): | |
| """Initialize the class.""" | |
| if working_dir is None: | |
| self.working_dir = os.getcwd() | |
| else: | |
| self.working_dir = working_dir | |
| if alignment is not None: | |
| if not os.path.exists(alignment): | |
| raise FileNotFoundError("The specified alignment file does not exist.") | |
| self.alignment = alignment | |
| self.out_file = out_file | |
| self._options = {} # will be set in subclasses | |
| def write_ctl_file(self): | |
| """Write control file.""" | |
| pass | |
| def read_ctl_file(self): | |
| """Read control file.""" | |
| pass | |
| def print_options(self): | |
| """Print out all of the options and their current settings.""" | |
| for option in self._options.items(): | |
| print(f"{option[0]} = {option[1]}") | |
| def set_options(self, **kwargs): | |
| """Set the value of an option. | |
| This function abstracts the options dict to prevent the user from | |
| adding options that do not exist or misspelling options. | |
| """ | |
| for option, value in kwargs.items(): | |
| if option not in self._options: | |
| raise KeyError("Invalid option: " + option) | |
| else: | |
| self._options[option] = value | |
| def get_option(self, option): | |
| """Return the value of an option.""" | |
| if option not in self._options: | |
| raise KeyError("Invalid option: " + option) | |
| else: | |
| return self._options.get(option) | |
| def get_all_options(self): | |
| """Return the values of all the options.""" | |
| return list(self._options.items()) | |
| def _set_rel_paths(self): | |
| """Convert all file/directory locations to paths relative to the current working directory (PRIVATE). | |
| paml requires that all paths specified in the control file be | |
| relative to the directory from which it is called rather than | |
| absolute paths. | |
| """ | |
| if self.working_dir is not None: | |
| self._rel_working_dir = os.path.relpath(self.working_dir) | |
| if self.alignment is not None: | |
| self._rel_alignment = os.path.relpath(self.alignment, self.working_dir) | |
| if self.out_file is not None: | |
| self._rel_out_file = os.path.relpath(self.out_file, self.working_dir) | |
| def run(self, ctl_file, verbose, command): | |
| """Run a paml program using the current configuration. | |
| Check that the class attributes exist and raise an error | |
| if not. Then run the command and check if it succeeds with | |
| a return code of 0, otherwise raise an error. | |
| The arguments may be passed as either absolute or relative | |
| paths, despite the fact that paml requires relative paths. | |
| """ | |
| if self.alignment is None: | |
| raise ValueError("Alignment file not specified.") | |
| if not os.path.exists(self.alignment): | |
| raise FileNotFoundError("The specified alignment file does not exist.") | |
| if self.out_file is None: | |
| raise ValueError("Output file not specified.") | |
| if self.working_dir is None: | |
| raise ValueError("Working directory not specified.") | |
| # Get the current working directory | |
| cwd = os.getcwd() | |
| # Move to the desired working directory | |
| if not os.path.exists(self.working_dir): | |
| os.mkdir(self.working_dir) | |
| os.chdir(self.working_dir) | |
| # If no external control file was specified... | |
| if ctl_file is None: | |
| # Dynamically build a control file | |
| self.write_ctl_file() | |
| ctl_file = self.ctl_file | |
| else: | |
| if not os.path.exists(ctl_file): | |
| raise FileNotFoundError("The specified control file does not exist.") | |
| if verbose: | |
| result_code = subprocess.call([command, ctl_file]) | |
| else: | |
| with open(os.devnull) as dn: | |
| result_code = subprocess.call([command, ctl_file], stdout=dn, stderr=dn) | |
| os.chdir(cwd) | |
| if result_code > 0: | |
| # If the program fails for any reason | |
| raise PamlError( | |
| "%s has failed (return code %i). Run with verbose = True to view error message" | |
| % (command, result_code) | |
| ) | |
| if result_code < 0: | |
| # If the paml process is killed by a signal somehow | |
| raise OSError( | |
| "The %s process was killed (return code %i)." % (command, result_code) | |
| ) | |