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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 logging
import shutil
import importlib
log = logging.getLogger("main")
from ..master_task import AlgTask, Task
from ..master_job import Job
from ..utils import (SeqGroup, OrderedDict, checksum, pjoin,
GLOBALS, DATATYPES)
from ..apps import APP2CLASS, CLASS2MODULE
from .. import db
#from . import __init__ as task
__all__ = ["MetaAligner"]
def seq_reverser_job(multiseq_file, outfile, parent_ids, trimal_bin):
""" Returns a job reversing all sequences in MSF or MSA. """
reversion_args = {"-in": multiseq_file, "-out": outfile,
"-reverse": "", "-fasta": ""}
job = Job(trimal_bin, reversion_args, "TrimalAlgReverser",
parent_ids=parent_ids)
return job
class MCoffee(AlgTask):
def __init__(self, nodeid, seqtype, all_alg_files, conf, confname, parent_ids):
GLOBALS["citator"].add('mcoffee')
base_args = OrderedDict({
"-output": "fasta",
})
# Initialize task
self.confname = confname
self.conf = conf
AlgTask.__init__(self, nodeid, "alg", "Mcoffee",
base_args, self.conf[confname])
self.all_alg_files = all_alg_files
self.parent_ids = parent_ids
self.seqtype = seqtype
self.init()
def load_jobs(self):
args = self.args.copy()
args["-outfile"] = "mcoffee.fasta"
alg_paths = [pjoin(GLOBALS["input_dir"], algid)
for algid in self.all_alg_files]
args["-aln"] = ' '.join(alg_paths)
job = Job(self.conf["app"]["tcoffee"], args, parent_ids=self.parent_ids)
for key in self.all_alg_files:
job.add_input_file(key)
self.jobs.append(job)
def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
alg = SeqGroup(os.path.join(self.jobs[0].jobdir, "mcoffee.fasta"))
fasta = alg.write(format="fasta")
phylip = alg.write(format="iphylip_relaxed")
alg_list_string = '\n'.join([pjoin(GLOBALS["input_dir"],
aname) for aname in self.all_alg_files])
db.add_task_data(self.taskid, DATATYPES.alg_list, alg_list_string)
AlgTask.store_data(self, fasta, phylip)
def init_output_info(self):
self.alg_list_file = "%s.%s" %(self.taskid, DATATYPES.alg_list)
AlgTask.init_output_info(self)
class MetaAligner(AlgTask):
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
self.confname = confname
self.conf = conf
# Initialize task
AlgTask.__init__(self, nodeid, "alg", "Meta-Alg",
OrderedDict(), self.conf[self.confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.size = conf["_nodeinfo"][nodeid].get("size", 0)
self.all_alg_files = None
self.init()
#if self.conf[confname]["_alg_trimming"]:
# self.alg_list_file = pjoin(self.taskdir, "alg_list.txt")
# open(self.alg_list_file, "w").write("\n".join(self.all_alg_files))
# trim_job = self.jobs[-1]
# trim_job.args["-compareset"] = self.alg_list_file
# trim_job.args["-out"] = pjoin(self.taskdir, "final_trimmed_alg.fasta")
# trim_job.alg_fasta_file = trim_job.args["-out"]
# trim_job.alg_phylip_file = None
def load_jobs(self):
readal_bin = self.conf["app"]["readal"]
trimal_bin = self.conf["app"]["trimal"]
input_dir = GLOBALS["input_dir"]
multiseq_file = pjoin(input_dir, self.multiseq_file)
multiseq_file_r = pjoin(input_dir, self.multiseq_file+"_reversed")
first = seq_reverser_job(multiseq_file, multiseq_file_r,
[self.nodeid], readal_bin)
#print self.multiseq_file
first.add_input_file(self.multiseq_file)
self.jobs.append(first)
all_alg_names = []
mcoffee_parents = []
for aligner_name in self.conf[self.confname]["_aligners"]:
aligner_name = aligner_name[1:]
_classname = APP2CLASS[self.conf[aligner_name]["_app"]]
_module = importlib.import_module("ete3.tools.ete_build_lib.task", "ete3")
#_module = __import__(CLASS2MODULE[_classname], globals(), locals(), [], 0)
_aligner = getattr(_module, _classname)
# Normal alg
task1 = _aligner(self.nodeid, self.multiseq_file, self.seqtype,
self.conf, aligner_name)
task1.size = self.size
self.jobs.append(task1)
all_alg_names.append(task1.alg_fasta_file)
# Alg of the reverse
task2 = _aligner(self.nodeid, self.multiseq_file+"_reversed",
self.seqtype, self.conf, aligner_name)
task2.size = self.size
task2.dependencies.add(first)
self.jobs.append(task2)
# Restore reverse alg
reverse_out = pjoin(input_dir, task2.alg_fasta_file)
task3 = seq_reverser_job(reverse_out,
reverse_out+"_restored",
[task2.taskid], readal_bin)
task3.dependencies.add(task2)
task3.add_input_file(task2.alg_fasta_file)
all_alg_names.append(reverse_out+"_restored")
self.jobs.append(task3)
mcoffee_parents.extend([task1.taskid, task2.taskid])
# Combine signal from all algs using Mcoffee
mcoffee_task = MCoffee(self.nodeid, self.seqtype, all_alg_names,
self.conf, self.confname, parent_ids=mcoffee_parents)
# reversed algs are not actually saved into db, but it should
# be present since the reverser job is always executed
mcoffee_task.dependencies.update(list(self.jobs))
self.jobs.append(mcoffee_task)
if self.conf[self.confname]["_alg_trimming"]:
trimming_cutoff = 1.0 / len(all_alg_names)
targs = {}
targs["-forceselect"] = pjoin(input_dir, mcoffee_task.alg_fasta_file)
targs["-compareset"] = pjoin(input_dir, mcoffee_task.alg_list_file)
targs["-out"] = "mcoffee.trimmed.fasta"
targs["-fasta"] = ""
targs["-ct"] = trimming_cutoff
trim_job = Job(trimal_bin, targs, parent_ids=[mcoffee_task.taskid])
trim_job.jobname = "McoffeeTrimming"
trim_job.dependencies.add(mcoffee_task)
trim_job.alg_fasta_file = targs["-out"]
for key in all_alg_names:
trim_job.add_input_file(key)
trim_job.add_input_file(mcoffee_task.alg_fasta_file)
trim_job.add_input_file(mcoffee_task.alg_list_file)
self.jobs.append(trim_job)
def finish(self):
if self.conf[self.confname]["_alg_trimming"]:
# If trimming happened after mcoffee, let's save the
# resulting output
trim_job = self.jobs[-1]
alg = SeqGroup(pjoin(trim_job.jobdir, trim_job.alg_fasta_file))
fasta = alg.write(format="fasta")
phylip = alg.write(format="iphylip_relaxed")
AlgTask.store_data(self, fasta, phylip)
else:
# If no post trimming, output is just what Mcoffee
# produced, so we can recycle its data ids.
mc_task = self.jobs[-1]
fasta_id = db.get_dataid(mc_task.taskid, DATATYPES.alg_fasta)
phylip_id = db.get_dataid(mc_task.taskid, DATATYPES.alg_phylip)
db.register_task_data(self.taskid, DATATYPES.alg_fasta, fasta_id)
db.register_task_data(self.taskid, DATATYPES.alg_phylip, phylip_id)
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