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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 logging
log = logging.getLogger("main")
from ..master_task import MsfTask
from ..master_job import Job
from ..utils import (PhyloTree, SeqGroup, md5, generate_node_ids,
hascontent, pjoin, DATATYPES)
from ..errors import DataError
from .. import db
__all__ = ["Msf"]
class Msf(MsfTask):
def __init__(self, target_seqs, out_seqs, seqtype):
# Nodeid represents the whole group of sequences (used to
# compute task unique ids). Cladeid represents target
# sequences. Same cladeid with different outgroups would mean
# an independent set of tasks.
node_id, clade_id = generate_node_ids(target_seqs, out_seqs)
# Initialize task
MsfTask.__init__(self, node_id, "msf", "MSF")
# taskid does not depend on jobs, so I set it manually
self.taskid = node_id
self.init()
self.nodeid = node_id
self.cladeid = clade_id
self.seqtype = seqtype
self.target_seqs = target_seqs
self.out_seqs = out_seqs
if out_seqs & target_seqs:
log.error(out_seqs)
log.error(target_seqs)
raise DataError("Outgroup seqs included in target seqs.")
all_seqs = self.target_seqs | self.out_seqs
self.size = len(all_seqs)
def finish(self):
# Dump sequences into MSF
all_seqs = self.target_seqs | self.out_seqs
fasta = '\n'.join([">%s\n%s" % (n, db.get_seq(n, self.seqtype))
for n in all_seqs])
MsfTask.store_data(self, fasta)
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