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from __future__ import absolute_import
import os
import shutil
import sys
import re
import logging
log = logging.getLogger("main")
from ..master_task import TreeTask
from ..errors import TaskError,ConfigError
from ..master_job import Job
from ..utils import basename, PhyloTree, OrderedDict, GLOBALS, DATATYPES
from .. import db
__all__ = ["IQTree"]
class IQTree(TreeTask):
def __init__(self, nodeid, alg_phylip_file, constrain_id, model,
seqtype, conf, confname, parts_id=None):
GLOBALS["citator"].add('iqtree')
if constrain_id:
raise ConfigError("IQTree does not support topology constraints")
base_args = {}
if "-st" not in conf[confname]:
base_args["-st"] = "AA" if seqtype == "aa" else "DNA"
else:
if conf[confname]["-st"].startswith("CODON"):
if seqtype == "aa" or "aa" not in GLOBALS["seqtypes"]:
raise ConfigError("IQTREE CODON models require a codon alignment.\nProvide nucleotide sequences with '-n' and set '--nt-switch-thr 0.0' to ensure codon alignments.")
if model:
raise TaskError('External model selection not yet supported for IQTree')
else:
if "-m" in conf[confname]:
model = conf[confname]["-m"]
elif conf[confname].get("-st", "").startswith("CODON"):
model = "defaultCODON"
elif seqtype == "aa":
model = "WAG"
elif seqtype == "nt":
model = "HKY"
self.model = model
self.confname = confname
self.conf = conf
self.constrain_tree = None
self.alg_phylip_file = alg_phylip_file
self.seqtype = seqtype
self.lk = None
TreeTask.__init__(self, nodeid, "tree", "IQTree",
base_args, conf[confname])
self.init()
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
args['-s'] = self.alg_phylip_file
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.alg_phylip_file, job.jobdir)
job.jobname += "-"+self.model.replace(' ', '')
self.jobs.append(job)
def finish(self):
j = self.jobs[0]
tree_file = os.path.join(j.jobdir,
self.alg_phylip_file+".treefile")
stats_file = os.path.join(j.jobdir,
self.alg_phylip_file+".iqtree")
m = re.search('Log-likelihood of the tree:\s+(-?\d+\.\d+)',
open(stats_file).read())
lk = float(m.groups()[0])
stats = {"lk": lk}
tree = PhyloTree(tree_file)
self.store_data(tree.write(), stats)
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