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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 shutil
import sys
import re
import logging
log = logging.getLogger("main")
from ..master_task import TreeTask
from ..master_job import Job
from ..utils import basename, PhyloTree, OrderedDict, GLOBALS, DATATYPES
from .. import db
__all__ = ["Phyml"]
modelcodes = {
'JC' :'000000',
'K80' :'010010' ,
'TrNef' :'010020' ,
'TPM1' :'012210' ,
'TPM2' :'010212' ,
'TPM3' :'012012' ,
'TIM1ef':'012230' ,
'TIM2ef':'010232' ,
'TIM3ef':'012032' ,
'TVMef' :'012314' ,
'SYM' :'012345' ,
'F81' :'000000' ,
'HKY' :'010010' ,
'TrN' :'010020' ,
'TPM1uf':'012210' ,
'TPM2uf':'010212' ,
'TPM3uf':'012012' ,
'TIM1' :'012230' ,
'TIM2' :'010232' ,
'TIM3' :'012032' ,
'TVM' :'012314' ,
'GTR' :'012345',
}
class Phyml(TreeTask):
def __init__(self, nodeid, alg_phylip_file, constrain_id, model,
seqtype, conf, confname, parts_id=None):
GLOBALS["citator"].add('phyml')
base_args = OrderedDict({
"--model": "",
"--no_memory_check": "",
"--quiet": "",
"--constraint_tree": ""})
if model and model.startswith('pmodeltest-'):
model = model.replace('pmodeltest-', '')
self.fullmodel = model
# overwrites default options if model selection says so
if "+I" in model:
conf[confname]["-v"]=" e"
elif "!I" in model:
conf[confname]["-v"]=" 0"
if "+G" in model:
#conf[confname]["-c"]=" 4"
conf[confname]["-a"]="e"
elif "!G" in model:
conf[confname]["-c"]=" 1"
conf[confname].pop("-a", None)
if "+F" in model:
conf[confname]["-f"] = "m" if seqtype == "nt" else "e"
elif "!F" in model:
conf[confname]["-f"] = '0.25,0.25,0.25,0.25' if seqtype == "nt" else "m"
model = model.split("+")[0].split("!")[0]
if seqtype == "nt":
model = modelcodes[model]
elif not model:
model = conf[confname]["_aa_model"] if seqtype == "aa" else conf[confname]["_nt_model"]
self.fullmodel = ""
else:
self.fullmodel = model+"-prottest"
model= model # use the model as provided by prottest (older, simpler approach)
self.model = model
self.confname = confname
self.conf = conf
self.constrain_tree = None
if constrain_id:
self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_tree)
self.alg_phylip_file = alg_phylip_file
TreeTask.__init__(self, nodeid, "tree", "Phyml",
base_args, conf[confname])
self.seqtype = seqtype
self.lk = None
self.init()
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
args["--datatype"] = self.seqtype
args["--model"] = self.model
args["--input"] = self.alg_phylip_file
if self.constrain_tree:
args["--constraint_tree"] = self.constrain_tree
args["-u"] = self.constrain_tree
else:
del args["--constraint_tree"]
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.alg_phylip_file, job.jobdir)
if self.constrain_tree:
job.add_input_file(self.constrain_tree, job.jobdir)
job.jobname += "-"+self.fullmodel
self.jobs.append(job)
def finish(self):
lks = []
j = self.jobs[0]
tree_file = os.path.join(j.jobdir,
self.alg_phylip_file+"_phyml_tree.txt")
stats_file = os.path.join(j.jobdir,
self.alg_phylip_file+"_phyml_stats.txt")
m = re.search('Log-likelihood:\s+(-?\d+\.\d+)',
open(stats_file).read())
lk = float(m.groups()[0])
stats = {"lk": lk}
tree = PhyloTree(tree_file)
TreeTask.store_data(self, tree.write(), stats)
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