def __init__(self, target_sp, out_sp, seqtype, conf, confname):
self.seed = conf[confname]["_seed"]
self.missing_factor = float(conf[confname]["_species_missing_factor"])
node_id, clade_id = generate_node_ids(target_sp, out_sp)
# Initialize task
CogSelectorTask.__init__(self, node_id, "cog_selector", "Cog-Selector",
None, conf[confname])
# taskid does not depend on jobs, so I set it manually
self.cladeid = clade_id
self.seqtype = seqtype
self.targets = target_sp
self.outgroups = out_sp
self.init()
self.size = len(target_sp | out_sp)
self.cog_analysis = None
self.cogs = None
def __init__(self, target_sp, out_sp, seqtype, conf, confname):
self.missing_factor = float(conf[confname]["_species_missing_factor"])
self.max_missing_factor = float(conf[confname]["_max_species_missing_factor"])
self.cog_hard_limit = int(conf[confname]["_max_cogs"])
node_id, clade_id = generate_node_ids(target_sp, out_sp)
# Initialize task
CogSelectorTask.__init__(self, node_id, "cog_selector",
"MCL-COGs", None, conf[confname])
# taskid does not depend on jobs, so I set it manually
self.cladeid = clade_id
self.seqtype = seqtype
self.targets = target_sp
self.outgroups = out_sp
self.init()
self.size = len(target_sp | out_sp)
self.cog_analysis = None
self.cogs = None
def __init__(self, target_seqs, out_seqs, seqtype):
# Nodeid represents the whole group of sequences (used to
# compute task unique ids). Cladeid represents target
# sequences. Same cladeid with different outgroups would mean
# an independent set of tasks.
node_id, clade_id = generate_node_ids(target_seqs, out_seqs)
# Initialize task
MsfTask.__init__(self, node_id, "msf", "MSF")
# taskid does not depend on jobs, so I set it manually
self.taskid = node_id
self.init()
self.nodeid = node_id
self.cladeid = clade_id
self.seqtype = seqtype
self.target_seqs = target_seqs
self.out_seqs = out_seqs
if out_seqs & target_seqs:
log.error(out_seqs)
log.error(target_seqs)
raise DataError("Outgroup seqs included in target seqs.")
all_seqs = self.target_seqs | self.out_seqs
self.size = len(all_seqs)
def __init__(self, target_seqs, out_seqs, seqtype):
# Nodeid represents the whole group of sequences (used to
# compute task unique ids). Cladeid represents target
# sequences. Same cladeid with different outgroups would mean
# an independent set of tasks.
node_id, clade_id = generate_node_ids(target_seqs, out_seqs)
# Initialize task
MsfTask.__init__(self, node_id, "msf", "MSF")
# taskid does not depend on jobs, so I set it manually
self.taskid = node_id
self.init()
self.nodeid = node_id
self.cladeid = clade_id
self.seqtype = seqtype
self.target_seqs = target_seqs
self.out_seqs = out_seqs
if out_seqs & target_seqs:
log.error(out_seqs)
log.error(target_seqs)
raise DataError("Outgroup seqs included in target seqs.")
all_seqs = self.target_seqs | self.out_seqs
self.size = len(all_seqs)