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# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from __future__ import absolute_import
import os
import re
import logging
log = logging.getLogger("main")
from ..master_task import ModelTesterTask
from ..master_job import Job
from ..utils import basename, PhyloTree, GLOBALS
__all__ = ["Prottest"]
class Prottest(ModelTesterTask):
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file,
constrain_tree, conf):
self.alg_phylip_file = alg_phylip_file
self.alg_fasta_file = alg_fasta_file
self.alg_basename = basename(self.alg_phylip_file)
self.conf = conf
self.lk_mode = self.conf["prottest"]["_lk_mode"]
if self.lk_mode == "raxml":
phyml_optimization = "n"
elif self.lk_mode == "phyml":
phyml_optimization = "lr"
else:
raise ValueError("Choose a valid lk_mode value (raxml or phyml)")
base_args = {
"--datatype": "aa",
"--input": self.alg_basename,
"--bootstrap": "0",
"-o": phyml_optimization,
"--model": None, # I will iterate over this value when
# creating jobs
"--quiet": ""
}
ModelTesterTask.__init__(self, nodeid, "mchooser", "Prottest",
base_args, conf["prottest"])
self.best_model = None
self.seqtype = "aa"
self.models = self.conf["prottest"]["_models"]
self.init()
self.post_init()
def post_init(self):
self.best_model_file = os.path.join(self.taskdir, "best_model.txt")
self.tree_file = None #os.path.join(self.taskdir, "final_tree.nw")
# Phyml cannot write the output in a different directory that
# the original alg file. So I use relative path to alg file
# for processes and I create a symlink for each of the
# instances.
for job in self.jobs:
fake_alg_file = os.path.join(job.jobdir, self.alg_basename)
if os.path.exists(fake_alg_file):
os.remove(fake_alg_file)
try: # Does not work on windows
os.symlink(self.alg_phylip_file, fake_alg_file)
except OSError:
log.warning("Unable to create symbolic links. Duplicating files instead")
shutil.copy(self.alg_phylip_file, fake_alg_file)
def load_jobs(self):
for m in self.models:
args = self.args.copy()
args["--model"] = m
job = Job(self.conf["app"]["phyml"], args,
parent_ids=[self.nodeid], jobname="phyml-bionj")
job.flag = "phyml"
self.jobs.append(job)
if self.lk_mode == "raxml":
raxml_args = {
"-f": "e",
"-s": self.alg_basename,
"-m": "PROTGAMMA%s" % m,
"-n": self.alg_basename+"."+m,
"-t": os.path.join(GLOBALS["tasks_dir"], job.jobid,
self.alg_basename+"_phyml_tree.txt")
}
raxml_job = Job(self.conf["app"]["raxml"], raxml_args,
parent_ids=[job.jobid], jobname="raxml-tree-optimize")
raxml_job.dependencies.add(job)
raxml_job.flag = "raxml"
raxml_job.model = m
self.jobs.append(raxml_job)
log.log(26, "Models to test %s", self.models)
def finish(self):
lks = []
if self.lk_mode == "phyml":
for job in [j for j in self.jobs if j.flag == "phyml"]:
tree_file = os.path.join(job.jobdir,
self.alg_basename+"_phyml_tree.txt")
stats_file = os.path.join(j.jobdir,
self.alg_basename+"_phyml_stats.txt")
tree = PhyloTree(tree_file)
m = re.search('Log-likelihood:\s+(-?\d+\.\d+)',
open(stats_file).read())
lk = float(m.groups()[0])
tree.add_feature("lk", lk)
tree.add_feature("model", job.args["--model"])
lks.append([float(tree.lk), tree.model, tree])
elif self.lk_mode == "raxml":
for job in [j for j in self.jobs if j.flag == "raxml"]:
lk = open(os.path.join(job.jobdir, "RAxML_log.%s"
%job.args["-n"])).readline().split()[1]
tree = PhyloTree(job.args["-t"])
tree.add_feature("lk", lk)
tree.add_feature("model", job.model)
lks.append([lk, tree.model, tree])
lks.sort()
lks.reverse()
# choose the model with higher likelihood
best_model = lks[-1][1]
best_tree = lks[-1][2]
open(self.best_model_file, "w").write(best_model)
if self.tree_file:
tree.write(self.tree_file)
ModelTesterTask.finish(self)
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