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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 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, GLOBALS, DATATYPES)
from .. import db
__all__ = ["DummyTree"]
class DummyTree(TreeTask):
def __init__(self, nodeid, alg_file, constrain_id, model, seqtype,
conf, confname, parts_id=None):
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 = ""
self.model = None
self.lk = None
TreeTask.__init__(self, nodeid, "tree", "DummyTree", {}, {})
self.init()
def load_jobs(self):
pass
def finish(self):
node_info = self.conf["_nodeinfo"][self.nodeid]
target_seqs = node_info.get("target_seqs", set())
out_seqs = node_info.get("out_seqs", set())
all_seqs = list(target_seqs | out_seqs)
newick = "(%s, (%s));" %(all_seqs[0], ','.join(all_seqs[1:]))
TreeTask.store_data(self, newick, {})
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