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from __future__ import absolute_import
import os
import logging
log = logging.getLogger("main")
from ..master_task import AlgTask
from ..master_job import Job
from ..utils import (SeqGroup, OrderedDict, pjoin,
GLOBALS, DATATYPES)
from .. import db
__all__ = ["TCoffee"]
class TCoffee(AlgTask):
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
self.confname = confname
self.conf = conf
# Initialize task
task_name = "TCoffee(-%s)" %conf["-mode"] if "-mode" in conf else "TCoffee"
AlgTask.__init__(self, nodeid, "alg", task_name,
OrderedDict(), self.conf[self.confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.size = conf["_nodeinfo"][nodeid].get("size", 0)
self.init()
def load_jobs(self):
args = OrderedDict()
args[""] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
for k, v in self.args.items():
args[k] = v
args["-outfile"] = "mcoffee.fasta"
job = Job(self.conf["app"]["tcoffee"], args, parent_ids=[self.nodeid])
job.add_input_file(self.multiseq_file)
job.cores = self.conf["threading"]["tcoffee"]
self.jobs.append(job)
def finish(self):
alg = SeqGroup(os.path.join(self.jobs[0].jobdir, "mcoffee.fasta"))
fasta = alg.write(format="fasta")
phylip = alg.write(format="iphylip_relaxed")
AlgTask.store_data(self, fasta, phylip)
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