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)
def finish(self):
# Dump sequences into MSF
all_seqs = self.target_seqs | self.out_seqs
fasta = '\n'.join([">%s\n%s" % (n, db.get_seq(n, self.seqtype))
for n in all_seqs])
MsfTask.store_data(self, fasta)
def finish(self):
# Dump sequences into MSF
all_seqs = self.target_seqs | self.out_seqs
fasta = '\n'.join(
[">%s\n%s" % (n, db.get_seq(n, self.seqtype)) for n in all_seqs])
MsfTask.store_data(self, fasta)
