def load_jobs(self):
# Only one Muscle job is necessary to run this task
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
args["-in"] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
args["-out"] = "alg.fasta"
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.multiseq_file)
self.jobs.append(job)
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
# Mafft redirects resulting alg to std.output. The order of
# arguments is important, input file must be the last
# one.
args[""] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.multiseq_file)
job.cores = self.conf["threading"][appname]
self.jobs.append(job)
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
GLOBALS["citator"].add(MAFFT_CITE)
self.confname = confname
self.conf = conf
# Initialize task
AlgTask.__init__(self, nodeid, "alg", "Mafft",
OrderedDict(), self.conf[confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.init()
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()
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 __init__(self, nodeid, seqtype, all_alg_files, conf, confname, parent_ids):
GLOBALS["citator"].add(MCOFFEE_CITE)
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 __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
GLOBALS["citator"].add(DIALIGN_CITE)
# fixed options for running this task
base_args = OrderedDict({
'': None,
})
# Initialize task
self.confname = confname
self.conf = conf
AlgTask.__init__(self, nodeid, "alg", "DialignTX", base_args,
self.conf[self.confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.init()
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
GLOBALS["citator"].add(MUSCLE_CITE)
# fixed Muscle options
base_args = OrderedDict({
'-in': None,
'-out': None,
})
self.confname = confname
self.conf = conf
# Initialize task
AlgTask.__init__(self, nodeid, "alg", "Muscle",
base_args, self.conf[confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.init()
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
args["--model"] = self.model
args["--datatype"] = self.seqtype
args["--input"] = self.alg_phylip_file
if self.constrain_tree:
args["--constraint_tree"] = self.constrain_tree
args["-u"] = self.constrain_tree
else:
del args["--constraint_tree"]
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.alg_phylip_file, job.jobdir)
if self.constrain_tree:
job.add_input_file(self.constrain_tree, job.jobdir)
job.jobname += "-" + self.model
self.jobs.append(job)
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
GLOBALS["citator"].add(CLUSTALO_CITE)
base_args = OrderedDict({
'-i': None,
'-o': None,
'--outfmt': "fa",
})
self.confname = confname
self.conf = conf
# Initialize task
AlgTask.__init__(self, nodeid, "alg", "Clustal-Omega", base_args,
self.conf[self.confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.init()
def __init__(self,
nodeid,
alg_file,
constrain_id,
model,
seqtype,
conf,
confname,
parts_id=None):
GLOBALS["citator"].add(FASTTREE_CITE)
self.confname = confname
self.conf = conf
self.alg_phylip_file = alg_file
self.constrain_tree = None
if constrain_id:
self.constrain_tree = db.get_dataid(constrain_id,
DATATYPES.constrain_alg)
self.alg_basename = basename(self.alg_phylip_file)
self.seqtype = seqtype
self.tree_file = ""
if model:
log.warning("FastTree does not support model selection")
self.model = None
self.lk = None
base_args = OrderedDict()
base_args["-nopr"] = ""
if self.seqtype == "nt":
base_args["-gtr -nt"] = ""
elif self.seqtype == "aa":
pass
else:
raise ValueError("Unknown seqtype %s" % self.seqtype)
TreeTask.__init__(self, nodeid, "tree", "FastTree", base_args,
self.conf[confname])
self.init()
def __init__(self,
nodeid,
alg_phylip_file,
constrain_id,
model,
seqtype,
conf,
confname,
parts_id=None):
GLOBALS["citator"].add(PHYML_CITE)
base_args = OrderedDict({
"--model": "",
"--no_memory_check": "",
"--quiet": "",
"--constraint_tree": ""
})
self.confname = confname
self.conf = conf
self.constrain_tree = None
if constrain_id:
self.constrain_tree = db.get_dataid(constrain_id,
DATATYPES.constrain_tree)
self.alg_phylip_file = alg_phylip_file
TreeTask.__init__(self, nodeid, "tree", "Phyml", base_args,
conf[confname])
if seqtype == "aa":
self.model = model or conf[confname]["_aa_model"]
elif seqtype == "nt":
self.model = model or conf[confname]["_nt_model"]
self.seqtype = seqtype
self.lk = None
self.init()
def __init__(self,
nodeid,
alg_file,
constrain_id,
model,
seqtype,
conf,
confname,
parts_id=None):
GLOBALS["citator"].add(RAXML_CITE)
base_args = OrderedDict()
self.bootstrap = conf[confname].get("_bootstrap", None)
model = model or conf[confname]["_aa_model"]
self.confname = confname
self.conf = conf
self.alg_phylip_file = alg_file
try:
self.constrain_tree = db.get_dataid(constrain_id,
DATATYPES.constrain_tree)
except ValueError:
self.constrain_tree = None
self.partitions_file = parts_id
TreeTask.__init__(self, nodeid, "tree", "RaxML", base_args,
conf[confname])
max_cores = GLOBALS["_max_cores"]
appname = conf[confname]["_app"]
if max_cores > 1:
threads = conf["threading"].get("raxml-pthreads")
if threads > 1:
appname = appname.replace("raxml", "raxml-pthreads")
raxml_bin = conf["app"][appname]
else:
appname = appname.replace("raxml-pthreads", "raxml")
threads = 1
raxml_bin = conf["app"][appname]
self.raxml_bin = raxml_bin
self.threads = threads
self.seqtype = seqtype
# Process raxml options
method = conf[confname].get("_method", "GAMMA").upper()
if seqtype.lower() == "aa":
self.model_string = 'PROT%s%s' % (method, model.upper())
self.model = model
elif seqtype.lower() == "nt":
self.model_string = 'GTR%s' % method
self.model = "GTR"
else:
raise ValueError("Unknown seqtype %s", seqtype)
#inv = conf[confname].get("pinv", "").upper()
#freq = conf[confname].get("ebf", "").upper()
self.init()
def load_jobs(self):
args = OrderedDict(self.args)
args["-s"] = pjoin(GLOBALS["input_dir"], self.alg_phylip_file)
args["-m"] = self.model_string
args["-n"] = self.alg_phylip_file
if self.constrain_tree:
log.log(24, "Using constrain tree %s" % self.constrain_tree)
args["-g"] = pjoin(GLOBALS["input_dir"], self.constrain_tree)
if self.partitions_file:
log.log(24, "Using alg partitions %s" % self.partitions_file)
args['-q'] = pjoin(GLOBALS["input_dir"], self.partitions_file)
tree_job = Job(self.raxml_bin, args, parent_ids=[self.nodeid])
tree_job.jobname += "-" + self.model_string
tree_job.cores = self.threads
# Register input files necessary to run the job
tree_job.add_input_file(self.alg_phylip_file)
if self.constrain_tree:
tree_job.add_input_file(self.constrain_tree)
if self.partitions_file:
tree_job.add_input_file(self.partitions_file)
self.jobs.append(tree_job)
self.out_tree_file = os.path.join(
tree_job.jobdir, "RAxML_bestTree." + self.alg_phylip_file)
if self.bootstrap == "alrt":
alrt_args = tree_job.args.copy()
if self.constrain_tree:
del alrt_args["-g"]
if self.partitions_file:
alrt_args["-q"] = args['-q']
alrt_args["-f"] = "J"
alrt_args["-t"] = self.out_tree_file
alrt_job = Job(self.raxml_bin,
alrt_args,
parent_ids=[tree_job.jobid])
alrt_job.jobname += "-alrt"
alrt_job.dependencies.add(tree_job)
alrt_job.cores = self.threads
# Register necessary input files
alrt_job.add_input_file(self.alg_phylip_file)
if self.partitions_file:
alrt_job.add_input_file(self.partitions_file)
self.jobs.append(alrt_job)
self.alrt_job = alrt_job
elif self.bootstrap == "alrt_phyml":
alrt_args = {
"-o": "n",
"-i": self.alg_phylip_file,
"--bootstrap": "-2",
"-d": self.seqtype,
"-u": self.out_tree_file,
"--model": self.model,
"--quiet": "",
"--no_memory_check": "",
}
#if self.constrain_tree:
# alrt_args["--constraint_tree"] = self.constrain_tree
alrt_job = Job(self.conf["app"]["phyml"],
alrt_args,
parent_ids=[tree_job.jobid])
alrt_job.add_input_file(self.alg_phylip_file, alrt_job.jobdir)
alrt_job.jobname += "-alrt"
alrt_job.dependencies.add(tree_job)
alrt_job.add_input_file(self.alg_phylip_file)
self.jobs.append(alrt_job)
self.alrt_job = alrt_job
else:
# Bootstrap calculation
boot_args = tree_job.args.copy()
boot_args["-n"] = "bootstraps." + boot_args["-n"]
boot_args["-N"] = int(self.bootstrap)
boot_args["-b"] = 31416
boot_job = Job(self.raxml_bin,
boot_args,
parent_ids=[tree_job.jobid])
boot_job.jobname += "-%d-bootstraps" % (boot_args['-N'])
boot_job.dependencies.add(tree_job)
boot_job.cores = self.threads
# Register necessary input files
boot_job.add_input_file(self.alg_phylip_file)
if self.constrain_tree:
boot_job.add_input_file(self.constrain_tree)
if self.partitions_file:
boot_job.add_input_file(self.partitions_file)
self.jobs.append(boot_job)
# Bootstrap drawing on top of best tree
bootd_args = tree_job.args.copy()
if self.constrain_tree:
del bootd_args["-g"]
if self.partitions_file:
del bootd_args["-q"]
bootd_args["-n"] = "bootstrapped." + tree_job.args["-n"]
bootd_args["-f"] = "b"
bootd_args["-t"] = self.out_tree_file
bootd_args["-z"] = pjoin(boot_job.jobdir,
"RAxML_bootstrap." + boot_job.args["-n"])
bootd_job = Job(self.raxml_bin,
bootd_args,
parent_ids=[tree_job.jobid])
bootd_job.jobname += "-bootstrapped"
bootd_job.dependencies.add(boot_job)
bootd_job.cores = self.threads
self.jobs.append(bootd_job)
self.boot_job = boot_job
self.bootd_job = bootd_job
