def pipeline(task, wkname, conf=None): logindent(2) # Points to npr parameters according to task properties if not task: source_seqtype = "aa" if "aa" in GLOBALS["seqtypes"] else "nt" npr_conf = IterConfig(conf, wkname, len(GLOBALS["target_species"]), source_seqtype) cogconf, cogclass = npr_conf.cog_selector initial_task = cogclass(GLOBALS["target_species"], set(), source_seqtype, conf, cogconf) initial_task.main_tree = main_tree = None initial_task.threadid = generate_runid() initial_task.configid = initial_task.threadid initial_task.target_wkname = wkname # Register node db.add_node(initial_task.threadid, initial_task.nodeid, initial_task.cladeid, initial_task.targets, initial_task.outgroups) new_tasks = [initial_task] else: conf = GLOBALS[task.configid] npr_conf = IterConfig(conf, wkname, task.size, task.seqtype) new_tasks = process_task(task, wkname, npr_conf, conf['_nodeinfo']) process_new_tasks(task, new_tasks, conf) logindent(-2) return new_tasks
def pipeline(task, wkname, conf=None): logindent(2) if not task: # in this case, conf is expected source_seqtype = "aa" if "aa" in GLOBALS["seqtypes"] else "nt" all_seqs = GLOBALS["target_sequences"] initial_task = Msf(set(all_seqs), set(), seqtype=source_seqtype) initial_task.main_tree = None initial_task.threadid = generate_runid() initial_task.configid = initial_task.threadid initial_task.target_wkname = wkname # Register node db.add_node(initial_task.threadid, initial_task.nodeid, initial_task.cladeid, initial_task.target_seqs, initial_task.out_seqs) new_tasks = [initial_task] else: conf = GLOBALS[task.configid] npr_conf = IterConfig(conf, wkname, task.size, task.seqtype) new_tasks = process_task(task, wkname, npr_conf, conf["_nodeinfo"]) process_new_tasks(task, new_tasks, conf) logindent(-2) return new_tasks