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, 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):
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):
# 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(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 __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()