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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 AlgTask
from ..master_job import Job
from ..utils import SeqGroup, OrderedDict
__all__ = ["Uhire"]
class Uhire(AlgTask):
def __init__(self, nodeid, multiseq_file, seqtype, conf):
# Initialize task
AlgTask.__init__(self, nodeid, "alg", "Usearch-Uhire",
OrderedDict(), conf["uhire"])
self.conf = conf
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.init()
self.alg_fasta_file = os.path.join(self.taskdir, "final_alg.fasta")
self.alg_phylip_file = os.path.join(self.taskdir, "final_alg.iphylip")
def load_jobs(self):
# split the original set of sequences in clusters.
uhire_args = {
"--clumpfasta": "./",
"--maxclump": "%s" %self.conf["uhire"]["_maxclump"],
"--usersort": "",
"--uhire": self.multiseq_file,
}
uhire_job = Job(self.conf["app"]["usearch"], uhire_args, "usearch-uhire",
parent_ids=[self.nodeid])
# Builds a muscle alignment for each of those clusters. (This
# is a special job to align all clumps independently. The
# whole shell command is used as job binary, so it is very
# important that there is no trailing lines at the end of the
# command.)
cmd = """
(mkdir clumpalgs/;
for fname in %s/clump.* %s/master;
do %s -in $fname -out clumpalgs/`basename $fname` -maxiters %s;
done;) """ %(
os.path.join("../",uhire_job.jobid),
os.path.join("../",uhire_job.jobid),
self.conf["app"]["muscle"],
self.conf["uhire"]["_muscle_maxiters"])
alg_job = Job(cmd, {}, "uhire_muscle_algs", parent_ids=[uhire_job.jobid])
alg_job.dependencies.add(uhire_job)
# Merge the cluster alignemnts into a single one
umerge_args = {
"--maxlen": self.conf["uhire"]["_max_seq_length"],
"--mergeclumps": "../%s/clumpalgs/" %alg_job.jobid,
"--output": "alg.fasta",
}
umerge_job = Job(self.conf["app"]["usearch"], umerge_args, "usearch-umerge",
parent_ids=[alg_job.jobid])
umerge_job.dependencies.add(alg_job)
# Add all jobs to the task queue queue
self.jobs.extend([uhire_job, alg_job, umerge_job])
def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
final_job = self.jobs[2]
alg = SeqGroup(os.path.join(final_job.jobdir, "alg.fasta"))
alg.write(outfile=self.alg_fasta_file, format="fasta")
alg.write(outfile=self.alg_phylip_file, format="iphylip_relaxed")
AlgTask.finish(self)
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