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from __future__ import absolute_import
# #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#############################################################
import os
import sys
import re
import shutil
import logging
log = logging.getLogger("main")
from ..master_task import TreeTask
from ..master_job import Job
from ..utils import (basename, Tree, OrderedDict, GLOBALS, DATATYPES, pjoin)
from .. import db
__all__ = ["FastTree"]
class FastTree(TreeTask):
def __init__(self, nodeid, alg_file, constrain_id, model, seqtype,
conf, confname, parts_id=None):
GLOBALS["citator"].add('fasttree')
self.confname = confname
self.conf = conf
self.alg_phylip_file = alg_file
self.constrain_tree = None
if constrain_id:
self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_alg)
self.alg_basename = basename(self.alg_phylip_file)
self.seqtype = seqtype
self.tree_file = ""
if model:
log.warning("FastTree does not support model selection")
self.model = None
self.lk = None
base_args = OrderedDict()
base_args["-nopr"] = ""
if self.seqtype == "nt":
base_args["-gtr -nt"] = ""
elif self.seqtype == "aa":
pass
else:
raise ValueError("Unknown seqtype %s" %self.seqtype)
TreeTask.__init__(self, nodeid, "tree", "FastTree", base_args,
self.conf[confname])
self.init()
def load_jobs(self):
args = self.args.copy()
try:
del args["-wag"]
except KeyError:
pass
if self.constrain_tree:
args["-constraints"] = pjoin(GLOBALS["input_dir"], self.constrain_tree)
args[pjoin(GLOBALS["input_dir"], self.alg_phylip_file)] = ""
appname = self.conf[self.confname]["_app"]
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.cores = self.conf["threading"][appname]
if self.constrain_tree:
job.add_input_file(self.constrain_tree)
job.add_input_file(self.alg_phylip_file)
self.jobs.append(job)
def finish(self):
job = self.jobs[-1]
t = Tree(job.stdout_file)
TreeTask.store_data(self, t.write(), {})
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