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(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_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 __init__(self, nodeid, alg_file, constrain_id, model, seqtype,
conf, confname, parts_id=None):
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 = ""
self.model = None
self.lk = None
TreeTask.__init__(self, nodeid, "tree", "DummyTree", {}, {})
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):
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 = ""
self.model = None
self.lk = None
TreeTask.__init__(self, nodeid, "tree", "DummyTree", {}, {})
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()