def __init__(self, nodeid, alg_fasta_file, alg_phylip_file,
constrain_tree, conf, confname):
GLOBALS["citator"].add(PHYML_CITE)
self.alg_phylip_file = alg_phylip_file
self.alg_fasta_file = alg_fasta_file
self.confname = confname
self.conf = conf
self.lk_mode = conf[confname]["_lk_mode"]
if self.lk_mode == "raxml":
phyml_optimization = "n"
elif self.lk_mode == "phyml":
phyml_optimization = "lr"
else:
raise ValueError("Choose a valid lk_mode value (raxml or phyml)")
base_args = {
"--datatype": "aa",
"--input": self.alg_phylip_file,
"--bootstrap": "0",
"-o": phyml_optimization,
"--model": None, # I will iterate over this value when
# creating jobs
"--quiet": ""
}
self.models = conf[confname]["_models"]
task_name = "Prottest-[%s]" %','.join(self.models)
ModelTesterTask.__init__(self, nodeid, "mchooser", task_name,
base_args, conf[confname])
self.best_model = None
self.seqtype = "aa"
self.init()
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, conf):
GLOBALS["citator"].add(JMODELTEST_CITE)
self.conf = conf
base_args = {
'-d': alg_fasta_file,
}
args = self.conf["jmodeltest"]
if args.get("-t", "ML") == "ML":
task_type = "tree"
else:
task_type = "mchooser"
ModelTesterTask.__init__(self, nodeid, task_type, "Jmodeltest",
base_args, self.conf[confname])
# set app arguments and options
self.alg_fasta_file = alg_fasta_file
self.alg_phylip_file = alg_phylip_file
self.seqtype = "nt"
self.models = "see jmodeltest params"
self.init()
self.best_model_file = os.path.join(self.taskdir, "best_model.txt")
if task_type == "tree":
self.tree_file = os.path.join(self.taskdir, "final_tree.nw")
else:
self.tree_file = None
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file,
constrain_tree, conf):
self.alg_phylip_file = alg_phylip_file
self.alg_fasta_file = alg_fasta_file
self.alg_basename = basename(self.alg_phylip_file)
self.conf = conf
self.lk_mode = self.conf["prottest"]["_lk_mode"]
if self.lk_mode == "raxml":
phyml_optimization = "n"
elif self.lk_mode == "phyml":
phyml_optimization = "lr"
else:
raise ValueError("Choose a valid lk_mode value (raxml or phyml)")
base_args = {
"--datatype": "aa",
"--input": self.alg_basename,
"--bootstrap": "0",
"-o": phyml_optimization,
"--model": None, # I will iterate over this value when
# creating jobs
"--quiet": ""
}
ModelTesterTask.__init__(self, nodeid, "mchooser", "Prottest",
base_args, conf["prottest"])
self.best_model = None
self.seqtype = "aa"
self.models = self.conf["prottest"]["_models"]
self.init()
self.post_init()
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, constrain_tree,
conf, confname):
GLOBALS["citator"].add(PHYML_CITE)
self.alg_phylip_file = alg_phylip_file
self.alg_fasta_file = alg_fasta_file
self.confname = confname
self.conf = conf
self.lk_mode = conf[confname]["_lk_mode"]
if self.lk_mode == "raxml":
phyml_optimization = "n"
elif self.lk_mode == "phyml":
phyml_optimization = "lr"
else:
raise ValueError("Choose a valid lk_mode value (raxml or phyml)")
base_args = {
"--datatype": "aa",
"--input": self.alg_phylip_file,
"--bootstrap": "0",
"-o": phyml_optimization,
"--model": None, # I will iterate over this value when
# creating jobs
"--quiet": ""
}
self.models = conf[confname]["_models"]
task_name = "Prottest-[%s]" % ','.join(self.models)
ModelTesterTask.__init__(self, nodeid, "mchooser", task_name,
base_args, conf[confname])
self.best_model = None
self.seqtype = "aa"
self.init()
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, conf):
GLOBALS["citator"].add(JMODELTEST_CITE)
self.conf = conf
base_args = {
'-d': alg_fasta_file,
}
args = self.conf["jmodeltest"]
if args.get("-t", "ML") == "ML":
task_type = "tree"
else:
task_type = "mchooser"
ModelTesterTask.__init__(self, nodeid, task_type, "Jmodeltest",
base_args, self.conf[confname])
# set app arguments and options
self.alg_fasta_file = alg_fasta_file
self.alg_phylip_file = alg_phylip_file
self.seqtype = "nt"
self.models = "see jmodeltest params"
self.init()
self.best_model_file = os.path.join(self.taskdir, "best_model.txt")
if task_type == "tree":
self.tree_file = os.path.join(self.taskdir, "final_tree.nw")
else:
self.tree_file = None
def __init__(self, nodeid, alg_fasta_file, alg_phylip_file, constrain_tree,
conf):
self.alg_phylip_file = alg_phylip_file
self.alg_fasta_file = alg_fasta_file
self.alg_basename = basename(self.alg_phylip_file)
self.conf = conf
self.lk_mode = self.conf["prottest"]["_lk_mode"]
if self.lk_mode == "raxml":
phyml_optimization = "n"
elif self.lk_mode == "phyml":
phyml_optimization = "lr"
else:
raise ValueError("Choose a valid lk_mode value (raxml or phyml)")
base_args = {
"--datatype": "aa",
"--input": self.alg_basename,
"--bootstrap": "0",
"-o": phyml_optimization,
"--model": None, # I will iterate over this value when
# creating jobs
"--quiet": ""
}
ModelTesterTask.__init__(self, nodeid, "mchooser", "Prottest",
base_args, conf["prottest"])
self.best_model = None
self.seqtype = "aa"
self.models = self.conf["prottest"]["_models"]
self.init()
self.post_init()
