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# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import os
import os.path
from ._paml import Paml, _relpath
from . import _parse_codeml
class CodemlError(EnvironmentError):
"""CODEML has failed. Run with verbose = True to view CODEML's error
message"""
class Codeml(Paml):
"""This class implements an interface to CODEML, part of the PAML package."""
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 write_ctl_file(self):
"""Dynamically build a CODEML control file from the options.
The control file is written to the location specified by the
ctl_file property of the codeml class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
if True: # Dummy statement to preserve indentation for diff
with open(self.ctl_file, 'w') as ctl_handle:
ctl_handle.write("seqfile = %s\n" % self._rel_alignment)
ctl_handle.write("outfile = %s\n" % self._rel_out_file)
ctl_handle.write("treefile = %s\n" % self._rel_tree)
for option in self._options.items():
if option[1] is None:
# If an option has a value of None, there's no need
# to write it in the control file; it's normally just
# commented out.
continue
if option[0] == "NSsites":
# NSsites is stored in Python as a list but in the
# control file it is specified as a series of numbers
# separated by spaces.
NSsites = " ".join(str(site) for site in option[1])
ctl_handle.write("%s = %s\n" % (option[0], NSsites))
else:
ctl_handle.write("%s = %s\n" % (option[0], option[1]))
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the Codeml instance.
"""
temp_options = {}
if not os.path.isfile(ctl_file):
raise IOError("File not found: %r" % ctl_file)
else:
with open(ctl_file) as ctl_handle:
for line in ctl_handle:
line = line.strip()
uncommented = line.split("*", 1)[0]
if uncommented != "":
if "=" not in uncommented:
raise AttributeError(
"Malformed line in control file:\n%r" % line)
(option, value) = uncommented.split("=", 1)
option = option.strip()
value = value.strip()
if option == "seqfile":
self.alignment = value
elif option == "treefile":
self.tree = value
elif option == "outfile":
self.out_file = value
elif option == "NSsites":
site_classes = value.split(" ")
for n in range(len(site_classes)):
try:
site_classes[n] = int(site_classes[n])
except:
raise TypeError(
"Invalid site class: %s" % site_classes[n])
temp_options["NSsites"] = site_classes
elif option not in self._options:
raise KeyError("Invalid option: %s" % option)
else:
if "." in value:
try:
converted_value = float(value)
except:
converted_value = value
else:
try:
converted_value = int(value)
except:
converted_value = value
temp_options[option] = converted_value
for option in self._options:
if option in temp_options:
self._options[option] = temp_options[option]
else:
self._options[option] = None
def print_options(self):
"""Print out all of the options and their current settings."""
for option in self._options.items():
if option[0] == "NSsites" and option[1] is not None:
# NSsites is stored in Python as a list but in the
# control file it is specified as a series of numbers
# separated by spaces.
NSsites = " ".join(str(site) for site in option[1])
print("%s = %s" % (option[0], NSsites))
else:
print("%s = %s" % (option[0], option[1]))
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)
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
def read(results_file):
"""Parse a CODEML results file."""
results = {}
if not os.path.exists(results_file):
raise IOError("Results file does not exist.")
with open(results_file) as handle:
lines = handle.readlines()
(results, multi_models, multi_genes) = _parse_codeml.parse_basics(lines,
results)
results = _parse_codeml.parse_nssites(lines, results, multi_models,
multi_genes)
results = _parse_codeml.parse_pairwise(lines, results)
results = _parse_codeml.parse_distances(lines, results)
if len(results) == 0:
raise ValueError("Invalid results file")
return results
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