def annotate_node(t, final_task):
cladeid2node = {}
# Annotate cladeid in the whole tree
for n in t.traverse():
if n.is_leaf():
n.add_feature("realname", db.get_seq_name(n.name))
#n.name = n.realname
if hasattr(n, "cladeid"):
cladeid2node[n.cladeid] = n
alltasks = GLOBALS[final_task.configid]["_nodeinfo"][final_task.nodeid]["tasks"]
npr_iter = get_iternumber(final_task.threadid)
n = cladeid2node[t.cladeid]
n.add_features(size=final_task.size)
for task in alltasks:
params = ["%s %s" %(k,v) for k,v in six.iteritems(task.args)
if not k.startswith("_")]
params = " ".join(params)
if task.ttype == "msf":
n.add_features(msf_outseqs=task.out_seqs,
msf_file=task.multiseq_file)
elif task.ttype == "acleaner":
n.add_features(clean_alg_mean_ident=task.mean_ident,
clean_alg_std_ident=task.std_ident,
clean_alg_max_ident=task.max_ident,
clean_alg_min_ident=task.min_ident,
clean_alg_type=task.tname,
clean_alg_cmd=params,
clean_alg_path=task.clean_alg_fasta_file)
elif task.ttype == "alg":
n.add_features(alg_mean_ident=task.mean_ident,
alg_std_ident=task.std_ident,
alg_max_ident=task.max_ident,
alg_min_ident=task.min_ident,
alg_type=task.tname,
alg_cmd=params,
alg_path=task.alg_fasta_file)
elif task.ttype == "tree":
n.add_features(tree_model=task.model,
tree_seqtype=task.seqtype,
tree_type=task.tname,
tree_cmd=params,
tree_path=task.tree_file,
tree_constrain=task.constrain_tree,
npr_iter=npr_iter)
elif task.ttype == "mchooser":
n.add_features(modeltester_models=task.models,
modeltester_type=task.tname,
modeltester_params=params,
modeltester_bestmodel=task.best_model,
)
elif task.ttype == "treemerger":
n.add_features(treemerger_type=task.tname,
treemerger_rf="RF=%s [%s]" %(task.rf[0], task.rf[1]),
treemerger_out_match_dist = task.outgroup_match_dist,
treemerger_out_match = task.outgroup_match,
)
def annotate_node(t, final_task):
cladeid2node = {}
# Annotate cladeid in the whole tree
for n in t.traverse():
if n.is_leaf():
n.add_feature("realname", db.get_seq_name(n.name))
#n.name = n.realname
if hasattr(n, "cladeid"):
cladeid2node[n.cladeid] = n
alltasks = GLOBALS[final_task.configid]["_nodeinfo"][
final_task.nodeid]["tasks"]
npr_iter = get_iternumber(final_task.threadid)
n = cladeid2node[t.cladeid]
n.add_features(size=final_task.size)
for task in alltasks:
params = [
"%s %s" % (k, v) for k, v in six.iteritems(task.args)
if not k.startswith("_")
]
params = " ".join(params)
if task.ttype == "tree":
n.add_features(tree_model=task.model,
tree_seqtype=task.seqtype,
tree_type=task.tname,
tree_cmd=params,
tree_file=rpath(task.tree_file),
tree_constrain=task.constrain_tree,
npr_iter=npr_iter)
elif task.ttype == "treemerger":
n.add_features(treemerger_type=task.tname,
treemerger_rf="RF=%s [%s]" %
(task.rf[0], task.rf[1]),
treemerger_out_match_dist=task.outgroup_match_dist,
treemerger_out_match=task.outgroup_match)
elif task.ttype == "concat_alg":
n.add_features(concatalg_cogs="%d" % task.used_cogs,
alg_path=task.alg_fasta_file)
def annotate_node(t, final_task):
cladeid2node = {}
# Annotate cladeid in the whole tree
for n in t.traverse():
if n.is_leaf():
n.add_feature("realname", db.get_seq_name(n.name))
#n.name = n.realname
if hasattr(n, "cladeid"):
cladeid2node[n.cladeid] = n
alltasks = GLOBALS[final_task.configid]["_nodeinfo"][final_task.nodeid]["tasks"]
npr_iter = get_iternumber(final_task.threadid)
n = cladeid2node[t.cladeid]
n.add_features(size=final_task.size)
for task in alltasks:
params = ["%s %s" %(k,v) for k,v in six.iteritems(task.args)
if not k.startswith("_")]
params = " ".join(params)
if task.ttype == "tree":
n.add_features(tree_model=task.model,
tree_seqtype=task.seqtype,
tree_type=task.tname,
tree_cmd=params,
tree_file=rpath(task.tree_file),
tree_constrain=task.constrain_tree,
npr_iter=npr_iter)
elif task.ttype == "treemerger":
n.add_features(treemerger_type=task.tname,
treemerger_rf="RF=%s [%s]" %(task.rf[0], task.rf[1]),
treemerger_out_match_dist = task.outgroup_match_dist,
treemerger_out_match = task.outgroup_match)
elif task.ttype == "concat_alg":
n.add_features(concatalg_cogs="%d"%task.used_cogs,
alg_path=task.alg_fasta_file)
def schedule(workflow_task_processor, pending_tasks, schedule_time, execution,
debug, norender):
# Adjust debug mode
if debug == "all":
log.setLevel(10)
pending_tasks = set(pending_tasks)
## ===================================
## INITIALIZE BASIC VARS
execution, run_detached = execution
thread2tasks = defaultdict(list)
for task in pending_tasks:
thread2tasks[task.configid].append(task)
expected_threads = set(thread2tasks.keys())
past_threads = {}
thread_errors = defaultdict(list)
## END OF VARS AND SHORTCUTS
## ===================================
cores_total = GLOBALS["_max_cores"]
if cores_total > 0:
job_queue = Queue()
back_launcher = Process(target=background_job_launcher,
args=(job_queue, run_detached,
GLOBALS["launch_time"], cores_total))
back_launcher.start()
else:
job_queue = None
back_launcher = None
GLOBALS["_background_scheduler"] = back_launcher
GLOBALS["_job_queue"] = job_queue
# Captures Ctrl-C for debuging DEBUG
#signal.signal(signal.SIGINT, control_c)
last_report_time = None
BUG = set()
try:
# Enters into task scheduling
while pending_tasks:
wtime = schedule_time
# ask SGE for running jobs
if execution == "sge":
#sgeid2jobs = db.get_sge_tasks()
#qstat_jobs = sge.qstat()
pass
else:
qstat_jobs = None
# Show summary of pending tasks per thread
thread2tasks = defaultdict(list)
for task in pending_tasks:
thread2tasks[task.configid].append(task)
set_logindent(0)
log.log(28, "@@13: Updating tasks status:@@1: (%s)" % (ctime()))
info_lines = []
for tid, tlist in six.iteritems(thread2tasks):
threadname = GLOBALS[tid]["_name"]
sizelist = ["%s" % getattr(_ts, "size", "?") for _ts in tlist]
info = "Thread @@13:%s@@1:: pending tasks: @@8:%s@@1: of sizes: %s" % (
threadname, len(tlist), ', '.join(sizelist))
info_lines.append(info)
for line in info_lines:
log.log(28, line)
if GLOBALS["email"] and last_report_time is None:
last_report_time = time()
send_mail(GLOBALS["email"], "Your NPR process has started",
'\n'.join(info_lines))
## ================================
## CHECK AND UPDATE CURRENT TASKS
checked_tasks = set()
check_start_time = time()
to_add_tasks = set()
GLOBALS["cached_status"] = {}
for task in sorted(pending_tasks, sort_tasks):
# Avoids endless periods without new job submissions
elapsed_time = time() - check_start_time
#if not back_launcher and pending_tasks and \
# elapsed_time > schedule_time * 2:
# log.log(26, "@@8:Interrupting task checks to schedule new jobs@@1:")
# db.commit()
# wtime = launch_jobs(sorted(pending_tasks, sort_tasks),
# execution, run_detached)
# check_start_time = time()
# Enter debuging mode if necessary
if debug and log.level > 10 and task.taskid.startswith(debug):
log.setLevel(10)
log.debug("ENTERING IN DEBUGGING MODE")
thread2tasks[task.configid].append(task)
# Update tasks and job statuses
if task.taskid not in checked_tasks:
try:
show_task_info(task)
task.status = task.get_status(qstat_jobs)
db.dataconn.commit()
if back_launcher and task.status not in set("DE"):
for j, cmd in task.iter_waiting_jobs():
j.status = "Q"
GLOBALS["cached_status"][j.jobid] = "Q"
if j.jobid not in BUG:
if not os.path.exists(j.jobdir):
os.makedirs(j.jobdir)
for ifile, outpath in six.iteritems(
j.input_files):
try:
_tid, _did = ifile.split(".")
_did = int(_did)
except (IndexError, ValueError):
dataid = ifile
else:
dataid = db.get_dataid(_tid, _did)
if not outpath:
outfile = pjoin(
GLOBALS["input_dir"], ifile)
else:
outfile = pjoin(outpath, ifile)
if not os.path.exists(outfile):
open(outfile, "w").write(
db.get_data(dataid))
log.log(
24, " @@8:Queueing @@1: %s from %s" %
(j, task))
if execution:
job_queue.put([
j.jobid, j.cores, cmd,
j.status_file
])
BUG.add(j.jobid)
update_task_states_recursively(task)
db.commit()
checked_tasks.add(task.taskid)
except TaskError as e:
log.error("Errors found in %s" % task)
import traceback
traceback.print_exc()
if GLOBALS["email"]:
threadname = GLOBALS[task.configid]["_name"]
send_mail(
GLOBALS["email"],
"Errors found in %s!" % threadname,
'\n'.join(map(str, [task, e.value, e.msg])))
pending_tasks.discard(task)
thread_errors[task.configid].append(
[task, e.value, e.msg])
continue
else:
# Set temporary Queued state to avoids launching
# jobs from clones
task.status = "Q"
if log.level < 24:
show_task_info(task)
if task.status == "D":
#db.commit()
show_task_info(task)
logindent(3)
# Log commands of every task
if 'cmd_log_file' not in GLOBALS[task.configid]:
GLOBALS[task.configid]['cmd_log_file'] = pjoin(
GLOBALS[task.configid]["_outpath"], "cmd.log")
O = open(GLOBALS[task.configid]['cmd_log_file'], "w")
O.close()
cmd_lines = get_cmd_log(task)
CMD_LOG = open(GLOBALS[task.configid]['cmd_log_file'], "a")
print(task, file=CMD_LOG)
for c in cmd_lines:
print(' ' + '\t'.join(map(str, c)), file=CMD_LOG)
CMD_LOG.close()
#
try:
#wkname = GLOBALS[task.configid]['_name']
create_tasks = workflow_task_processor(
task, task.target_wkname)
except TaskError as e:
log.error("Errors found in %s" % task)
pending_tasks.discard(task)
thread_errors[task.configid].append(
[task, e.value, e.msg])
continue
else:
logindent(-3)
to_add_tasks.update(create_tasks)
pending_tasks.discard(task)
elif task.status == "E":
log.error("task contains errors: %s " % task)
log.error("Errors found in %s")
pending_tasks.discard(task)
thread_errors[task.configid].append(
[task, None, "Found (E) task status"])
#db.commit()
#if not back_launcher:
# wtime = launch_jobs(sorted(pending_tasks, sort_tasks),
# execution, run_detached)
# Update global task list with recently added jobs to be check
# during next cycle
pending_tasks.update(to_add_tasks)
## END CHECK AND UPDATE CURRENT TASKS
## ================================
if wtime:
set_logindent(0)
log.log(28, "@@13:Waiting %s seconds@@1:" % wtime)
sleep(wtime)
else:
sleep(schedule_time)
# Dump / show ended threads
error_lines = []
for configid, etasks in six.iteritems(thread_errors):
error_lines.append("Thread @@10:%s@@1: contains errors:" %\
(GLOBALS[configid]["_name"]))
for error in etasks:
error_lines.append(" ** %s" % error[0])
e_obj = error[1] if error[1] else error[0]
error_path = e_obj.jobdir if isjob(e_obj) else e_obj.taskid
if e_obj is not error[0]:
error_lines.append(" -> %s" % e_obj)
error_lines.append(" -> %s" % error_path)
error_lines.append(" -> %s" % error[2])
for eline in error_lines:
log.error(eline)
pending_threads = set([ts.configid for ts in pending_tasks])
finished_threads = expected_threads - (pending_threads
| set(thread_errors.keys()))
just_finished_lines = []
finished_lines = []
for configid in finished_threads:
# configid is the the same as threadid in master tasks
final_tree_file = pjoin(GLOBALS[configid]["_outpath"],
GLOBALS["inputname"] + ".final_tree")
threadname = GLOBALS[configid]["_name"]
if configid in past_threads:
log.log(28, "Done thread @@12:%s@@1: in %d iteration(s)",
threadname, past_threads[configid])
finished_lines.append("Finished %s in %d iteration(s)" %
(threadname, past_threads[configid]))
else:
log.log(28, "Assembling final tree...")
main_tree, treeiters = assembly_tree(configid)
past_threads[configid] = treeiters - 1
log.log(28, "Done thread @@12:%s@@1: in %d iteration(s)",
threadname, past_threads[configid])
log.log(
28, "Writing final tree for @@13:%s@@1:\n %s\n %s",
threadname, final_tree_file + ".nw",
final_tree_file + ".nwx (newick extended)")
main_tree.write(outfile=final_tree_file + ".nw")
main_tree.write(outfile=final_tree_file + ".nwx",
features=[],
format_root_node=True)
if hasattr(main_tree, "alg_path"):
log.log(
28,
"Writing root node alignment @@13:%s@@1:\n %s",
threadname, final_tree_file + ".fa")
alg = SeqGroup(get_stored_data(main_tree.alg_path))
OUT = open(final_tree_file + ".fa", "w")
for name, seq, comments in alg:
realname = db.get_seq_name(name)
print(">%s\n%s" % (realname, seq), file=OUT)
OUT.close()
if hasattr(main_tree, "clean_alg_path"):
log.log(
28,
"Writing root node trimmed alignment @@13:%s@@1:\n %s",
threadname, final_tree_file + ".trimmed.fa")
alg = SeqGroup(
get_stored_data(main_tree.clean_alg_path))
OUT = open(final_tree_file + ".trimmed.fa", "w")
for name, seq, comments in alg:
realname = db.get_seq_name(name)
print(">%s\n%s" % (realname, seq), file=OUT)
OUT.close()
if norender == False:
log.log(
28, "Generating tree image for @@13:%s@@1:\n %s",
threadname, final_tree_file + ".png")
for lf in main_tree:
lf.add_feature("sequence",
alg.get_seq(lf.safename))
try:
from ete3.tools.phylobuild_lib.visualize import draw_tree
draw_tree(main_tree, GLOBALS[configid],
final_tree_file + ".png")
except Exception as e:
log.warning(
'@@8:something went wrong when generating the tree image. Try manually :(@@1:'
)
if DEBUG:
import traceback, sys
traceback.print_exc(file=sys.stdout)
just_finished_lines.append(
"Finished %s in %d iteration(s)" %
(threadname, past_threads[configid]))
if GLOBALS["email"]:
if not pending_tasks:
all_lines = finished_lines + just_finished_lines + error_lines
send_mail(GLOBALS["email"], "Your NPR process has ended",
'\n'.join(all_lines))
elif GLOBALS["email_report_time"] and time() - last_report_time >= \
GLOBALS["email_report_time"]:
all_lines = info_lines + error_lines + just_finished_lines
send_mail(GLOBALS["email"], "Your NPR report",
'\n'.join(all_lines))
last_report_time = time()
elif just_finished_lines:
send_mail(GLOBALS["email"], "Finished threads!",
'\n'.join(just_finished_lines))
log.log(26, "")
except:
raise
if thread_errors:
log.error("Done with ERRORS")
else:
log.log(28, "Done")
return thread_errors
def annotate_node(t, final_task):
cladeid2node = {}
# Annotate cladeid in the whole tree
for n in t.traverse():
if n.is_leaf():
n.add_feature("realname", db.get_seq_name(n.name))
#n.name = n.realname
if hasattr(n, "cladeid"):
cladeid2node[n.cladeid] = n
alltasks = GLOBALS[final_task.configid]["_nodeinfo"][
final_task.nodeid]["tasks"]
npr_iter = get_iternumber(final_task.threadid)
n = cladeid2node[t.cladeid]
n.add_features(size=final_task.size)
for task in alltasks:
params = [
"%s %s" % (k, v) for k, v in six.iteritems(task.args)
if not k.startswith("_")
]
params = " ".join(params)
if task.ttype == "msf":
n.add_features(msf_outseqs=task.out_seqs,
msf_file=task.multiseq_file)
elif task.ttype == "acleaner":
n.add_features(clean_alg_mean_ident=task.mean_ident,
clean_alg_std_ident=task.std_ident,
clean_alg_max_ident=task.max_ident,
clean_alg_min_ident=task.min_ident,
clean_alg_type=task.tname,
clean_alg_cmd=params,
clean_alg_path=task.clean_alg_fasta_file)
elif task.ttype == "alg":
n.add_features(alg_mean_ident=task.mean_ident,
alg_std_ident=task.std_ident,
alg_max_ident=task.max_ident,
alg_min_ident=task.min_ident,
alg_type=task.tname,
alg_cmd=params,
alg_path=task.alg_fasta_file)
elif task.ttype == "tree":
n.add_features(tree_model=task.model,
tree_seqtype=task.seqtype,
tree_type=task.tname,
tree_cmd=params,
tree_path=task.tree_file,
tree_constrain=task.constrain_tree,
npr_iter=npr_iter)
elif task.ttype == "mchooser":
n.add_features(
modeltester_models=task.models,
modeltester_type=task.tname,
modeltester_params=params,
modeltester_bestmodel=task.best_model,
)
elif task.ttype == "treemerger":
n.add_features(
treemerger_type=task.tname,
treemerger_rf="RF=%s [%s]" % (task.rf[0], task.rf[1]),
treemerger_out_match_dist=task.outgroup_match_dist,
treemerger_out_match=task.outgroup_match,
)
def get_concatenated_alg(alg_filenames, models=None,
sp_field=0, sp_delimiter="_",
kill_thr=0.0,
keep_species=set()):
# Concat alg container
concat = SeqGroup()
# Used to store different model partitions
concat.id2partition = {}
if not models:
models = ["None"]*len(alg_filenames)
else:
if len(models) != len(alg_filenames):
raise ValueError("Different number of algs and model names was found!")
expected_total_length = 0
# Check algs and gets the whole set of species
alg_objects = []
sp2alg = defaultdict(list)
for algfile, matrix in zip(alg_filenames, models):
alg = SeqGroup(algfile, "fasta")
alg_objects.append(alg)
lenseq = None
browsed_species = set()
alg.sp2seq = {}
# Set best matrix for this alignment
alg.matrix = matrix
# Change seq names to contain only species names
for i, seq in six.iteritems(alg.id2seq):
name = db.get_seq_name(alg.id2name[i])
taxid = get_species_code(name, splitter=sp_delimiter, field=sp_field)
if lenseq is not None and len(seq) != lenseq:
raise Exception("Inconsistent alignment when concatenating: Unequal length")
elif lenseq is None:
lenseq = len(seq)
alg.seqlength = len(seq)
expected_total_length += len(seq)
if taxid in browsed_species:
raise Exception("Inconsistent alignment when concatenating: Repeated species")
browsed_species.add(taxid) # Check no duplicated species in the same alg
sp2alg[taxid].append(alg) # Records all species seen in all algs.
alg.sp2seq[taxid] = seq
valid_species = [sp for sp in six.iterkeys(sp2alg) \
if sp in keep_species or \
len(sp2alg[sp])/float(len(alg_objects)) > kill_thr]
log.info("%d out of %d will be kept (missing factor threshold=%g, %d species forced to kept)" %\
(len(valid_species), len(sp2alg), kill_thr, len(keep_species)))
def sort_single_algs(alg1, alg2):
r = cmp(alg1.matrix, alg2.matrix)
if r == 0:
return cmp(sorted(alg1.id2name.values()),
sorted(alg2.id2name.values()))
else:
return r
sorted_algs = sorted(alg_objects, sort_single_algs)
concat_alg_lengths = [alg.seqlength for alg in sorted_algs]
model2win = {}
model2size = {}
for alg in sorted_algs:
model2size[alg.matrix] = model2size.get(alg.matrix, 0) + alg.seqlength
# Create concat alg
concat.id2seq = defaultdict(list)
for sp in sorted(valid_species):
log.log(20, "Concatenating sequences of [%s]" %sp)
for alg in sorted_algs:
seq = alg.sp2seq.get(sp, "-" * alg.seqlength)
concat.id2seq[sp].append(seq)
#current_seq = concat.id2seq.get(sp, "")
#concat.id2seq[sp] = current_seq + seq.strip()
concat.id2name[sp] = sp
concat.name2id[sp] = sp
concat.id2comment[sp] = [""]
concat.id2seq[sp] = ''.join(concat.id2seq[sp])
current_pos = 0
partitions = []
for model in sorted(model2size.keys()):
size = model2size[model]
part = "%s, %s = %d-%d" % (model, model+"_genes", \
current_pos + 1,\
current_pos + size)
current_pos += size
partitions.append(part)
# Basic Checks
seq_sizes = [len(seq) for seq in list(concat.id2seq.values())]
if len(set(seq_sizes)) != 1:
raise Exception("Concatenated alignment is not consistent: unequal seq length ")
if seq_sizes[0] != expected_total_length:
raise Exception("The size of concatenated alg is not what expected")
return concat, partitions, sp2alg, valid_species, concat_alg_lengths
def schedule(workflow_task_processor, pending_tasks, schedule_time, execution, debug, norender):
# Adjust debug mode
if debug == "all":
log.setLevel(10)
pending_tasks = set(pending_tasks)
## ===================================
## INITIALIZE BASIC VARS
execution, run_detached = execution
thread2tasks = defaultdict(list)
for task in pending_tasks:
thread2tasks[task.configid].append(task)
expected_threads = set(thread2tasks.keys())
past_threads = {}
thread_errors = defaultdict(list)
## END OF VARS AND SHORTCUTS
## ===================================
cores_total = GLOBALS["_max_cores"]
if cores_total > 0:
job_queue = Queue()
back_launcher = Process(target=background_job_launcher,
args=(job_queue, run_detached,
GLOBALS["launch_time"], cores_total))
back_launcher.start()
else:
job_queue = None
back_launcher = None
GLOBALS["_background_scheduler"] = back_launcher
GLOBALS["_job_queue"] = job_queue
# Captures Ctrl-C for debuging DEBUG
#signal.signal(signal.SIGINT, control_c)
last_report_time = None
BUG = set()
try:
# Enters into task scheduling
while pending_tasks:
wtime = schedule_time
# ask SGE for running jobs
if execution == "sge":
#sgeid2jobs = db.get_sge_tasks()
#qstat_jobs = sge.qstat()
pass
else:
qstat_jobs = None
# Show summary of pending tasks per thread
thread2tasks = defaultdict(list)
for task in pending_tasks:
thread2tasks[task.configid].append(task)
set_logindent(0)
log.log(28, "@@13: Updating tasks status:@@1: (%s)" % (ctime()))
info_lines = []
for tid, tlist in six.iteritems(thread2tasks):
threadname = GLOBALS[tid]["_name"]
sizelist = ["%s" %getattr(_ts, "size", "?") for _ts in tlist]
info = "Thread @@13:%s@@1:: pending tasks: @@8:%s@@1: of sizes: %s" %(
threadname, len(tlist), ', '.join(sizelist))
info_lines.append(info)
for line in info_lines:
log.log(28, line)
if GLOBALS["email"] and last_report_time is None:
last_report_time = time()
send_mail(GLOBALS["email"], "Your NPR process has started", '\n'.join(info_lines))
## ================================
## CHECK AND UPDATE CURRENT TASKS
checked_tasks = set()
check_start_time = time()
to_add_tasks = set()
GLOBALS["cached_status"] = {}
for task in sorted(pending_tasks, sort_tasks):
# Avoids endless periods without new job submissions
elapsed_time = time() - check_start_time
#if not back_launcher and pending_tasks and \
# elapsed_time > schedule_time * 2:
# log.log(26, "@@8:Interrupting task checks to schedule new jobs@@1:")
# db.commit()
# wtime = launch_jobs(sorted(pending_tasks, sort_tasks),
# execution, run_detached)
# check_start_time = time()
# Enter debuging mode if necessary
if debug and log.level > 10 and task.taskid.startswith(debug):
log.setLevel(10)
log.debug("ENTERING IN DEBUGGING MODE")
thread2tasks[task.configid].append(task)
# Update tasks and job statuses
if task.taskid not in checked_tasks:
try:
show_task_info(task)
task.status = task.get_status(qstat_jobs)
db.dataconn.commit()
if back_launcher and task.status not in set("DE"):
for j, cmd in task.iter_waiting_jobs():
j.status = "Q"
GLOBALS["cached_status"][j.jobid] = "Q"
if j.jobid not in BUG:
if not os.path.exists(j.jobdir):
os.makedirs(j.jobdir)
for ifile, outpath in six.iteritems(j.input_files):
try:
_tid, _did = ifile.split(".")
_did = int(_did)
except (IndexError, ValueError):
dataid = ifile
else:
dataid = db.get_dataid(_tid, _did)
if not outpath:
outfile = pjoin(GLOBALS["input_dir"], ifile)
else:
outfile = pjoin(outpath, ifile)
if not os.path.exists(outfile):
open(outfile, "w").write(db.get_data(dataid))
log.log(24, " @@8:Queueing @@1: %s from %s" %(j, task))
if execution:
job_queue.put([j.jobid, j.cores, cmd, j.status_file])
BUG.add(j.jobid)
update_task_states_recursively(task)
db.commit()
checked_tasks.add(task.taskid)
except TaskError as e:
log.error("Errors found in %s" %task)
import traceback
traceback.print_exc()
if GLOBALS["email"]:
threadname = GLOBALS[task.configid]["_name"]
send_mail(GLOBALS["email"], "Errors found in %s!" %threadname,
'\n'.join(map(str, [task, e.value, e.msg])))
pending_tasks.discard(task)
thread_errors[task.configid].append([task, e.value, e.msg])
continue
else:
# Set temporary Queued state to avoids launching
# jobs from clones
task.status = "Q"
if log.level < 24:
show_task_info(task)
if task.status == "D":
#db.commit()
show_task_info(task)
logindent(3)
# Log commands of every task
if 'cmd_log_file' not in GLOBALS[task.configid]:
GLOBALS[task.configid]['cmd_log_file'] = pjoin(GLOBALS[task.configid]["_outpath"], "cmd.log")
O = open(GLOBALS[task.configid]['cmd_log_file'], "w")
O.close()
cmd_lines = get_cmd_log(task)
CMD_LOG = open(GLOBALS[task.configid]['cmd_log_file'], "a")
print(task, file=CMD_LOG)
for c in cmd_lines:
print(' '+'\t'.join(map(str, c)), file=CMD_LOG)
CMD_LOG.close()
#
try:
#wkname = GLOBALS[task.configid]['_name']
create_tasks = workflow_task_processor(task, task.target_wkname)
except TaskError as e:
log.error("Errors found in %s" %task)
pending_tasks.discard(task)
thread_errors[task.configid].append([task, e.value, e.msg])
continue
else:
logindent(-3)
to_add_tasks.update(create_tasks)
pending_tasks.discard(task)
elif task.status == "E":
log.error("task contains errors: %s " %task)
log.error("Errors found in %s")
pending_tasks.discard(task)
thread_errors[task.configid].append([task, None, "Found (E) task status"])
#db.commit()
#if not back_launcher:
# wtime = launch_jobs(sorted(pending_tasks, sort_tasks),
# execution, run_detached)
# Update global task list with recently added jobs to be check
# during next cycle
pending_tasks.update(to_add_tasks)
## END CHECK AND UPDATE CURRENT TASKS
## ================================
if wtime:
set_logindent(0)
log.log(28, "@@13:Waiting %s seconds@@1:" %wtime)
sleep(wtime)
else:
sleep(schedule_time)
# Dump / show ended threads
error_lines = []
for configid, etasks in six.iteritems(thread_errors):
error_lines.append("Thread @@10:%s@@1: contains errors:" %\
(GLOBALS[configid]["_name"]))
for error in etasks:
error_lines.append(" ** %s" %error[0])
e_obj = error[1] if error[1] else error[0]
error_path = e_obj.jobdir if isjob(e_obj) else e_obj.taskid
if e_obj is not error[0]:
error_lines.append(" -> %s" %e_obj)
error_lines.append(" -> %s" %error_path)
error_lines.append(" -> %s" %error[2])
for eline in error_lines:
log.error(eline)
pending_threads = set([ts.configid for ts in pending_tasks])
finished_threads = expected_threads - (pending_threads | set(thread_errors.keys()))
just_finished_lines = []
finished_lines = []
for configid in finished_threads:
# configid is the the same as threadid in master tasks
final_tree_file = pjoin(GLOBALS[configid]["_outpath"],
GLOBALS["inputname"] + ".final_tree")
threadname = GLOBALS[configid]["_name"]
if configid in past_threads:
log.log(28, "Done thread @@12:%s@@1: in %d iteration(s)",
threadname, past_threads[configid])
finished_lines.append("Finished %s in %d iteration(s)" %(
threadname, past_threads[configid]))
else:
log.log(28, "Assembling final tree...")
main_tree, treeiters = assembly_tree(configid)
past_threads[configid] = treeiters - 1
log.log(28, "Done thread @@12:%s@@1: in %d iteration(s)",
threadname, past_threads[configid])
log.log(28, "Writing final tree for @@13:%s@@1:\n %s\n %s",
threadname, final_tree_file+".nw",
final_tree_file+".nwx (newick extended)")
main_tree.write(outfile=final_tree_file+".nw")
main_tree.write(outfile=final_tree_file+ ".nwx", features=[],
format_root_node=True)
if hasattr(main_tree, "alg_path"):
log.log(28, "Writing root node alignment @@13:%s@@1:\n %s",
threadname, final_tree_file+".fa")
alg = SeqGroup(get_stored_data(main_tree.alg_path))
OUT = open(final_tree_file+".fa", "w")
for name, seq, comments in alg:
realname = db.get_seq_name(name)
print(">%s\n%s" %(realname, seq), file=OUT)
OUT.close()
if hasattr(main_tree, "clean_alg_path"):
log.log(28, "Writing root node trimmed alignment @@13:%s@@1:\n %s",
threadname, final_tree_file+".trimmed.fa")
alg = SeqGroup(get_stored_data(main_tree.clean_alg_path))
OUT = open(final_tree_file+".trimmed.fa", "w")
for name, seq, comments in alg:
realname = db.get_seq_name(name)
print(">%s\n%s" %(realname, seq), file=OUT)
OUT.close()
if norender == False:
log.log(28, "Generating tree image for @@13:%s@@1:\n %s",
threadname, final_tree_file+".png")
for lf in main_tree:
lf.add_feature("sequence", alg.get_seq(lf.safename))
try:
from ete3.tools.phylobuild_lib.visualize import draw_tree
draw_tree(main_tree, GLOBALS[configid], final_tree_file+".png")
except Exception as e:
log.warning('@@8:something went wrong when generating the tree image. Try manually :(@@1:')
if DEBUG:
import traceback, sys
traceback.print_exc(file=sys.stdout)
just_finished_lines.append("Finished %s in %d iteration(s)" %(
threadname, past_threads[configid]))
if GLOBALS["email"]:
if not pending_tasks:
all_lines = finished_lines + just_finished_lines + error_lines
send_mail(GLOBALS["email"], "Your NPR process has ended", '\n'.join(all_lines))
elif GLOBALS["email_report_time"] and time() - last_report_time >= \
GLOBALS["email_report_time"]:
all_lines = info_lines + error_lines + just_finished_lines
send_mail(GLOBALS["email"], "Your NPR report", '\n'.join(all_lines))
last_report_time = time()
elif just_finished_lines:
send_mail(GLOBALS["email"], "Finished threads!",
'\n'.join(just_finished_lines))
log.log(26, "")
except:
raise
if thread_errors:
log.error("Done with ERRORS")
else:
log.log(28, "Done")
return thread_errors
def get_concatenated_alg(alg_filenames,
models=None,
sp_field=0,
sp_delimiter="_",
kill_thr=0.0,
keep_species=set()):
# Concat alg container
concat = SeqGroup()
# Used to store different model partitions
concat.id2partition = {}
if not models:
models = ["None"] * len(alg_filenames)
else:
if len(models) != len(alg_filenames):
raise ValueError(
"Different number of algs and model names was found!")
expected_total_length = 0
# Check algs and gets the whole set of species
alg_objects = []
sp2alg = defaultdict(list)
for algfile, matrix in zip(alg_filenames, models):
alg = SeqGroup(algfile, "fasta")
alg_objects.append(alg)
lenseq = None
browsed_species = set()
alg.sp2seq = {}
# Set best matrix for this alignment
alg.matrix = matrix
# Change seq names to contain only species names
for i, seq in six.iteritems(alg.id2seq):
name = db.get_seq_name(alg.id2name[i])
taxid = get_species_code(name,
splitter=sp_delimiter,
field=sp_field)
if lenseq is not None and len(seq) != lenseq:
raise Exception(
"Inconsistent alignment when concatenating: Unequal length"
)
elif lenseq is None:
lenseq = len(seq)
alg.seqlength = len(seq)
expected_total_length += len(seq)
if taxid in browsed_species:
raise Exception(
"Inconsistent alignment when concatenating: Repeated species"
)
browsed_species.add(
taxid) # Check no duplicated species in the same alg
sp2alg[taxid].append(alg) # Records all species seen in all algs.
alg.sp2seq[taxid] = seq
valid_species = [sp for sp in six.iterkeys(sp2alg) \
if sp in keep_species or \
len(sp2alg[sp])/float(len(alg_objects)) > kill_thr]
log.info("%d out of %d will be kept (missing factor threshold=%g, %d species forced to kept)" %\
(len(valid_species), len(sp2alg), kill_thr, len(keep_species)))
def sort_single_algs(alg1, alg2):
r = cmp(alg1.matrix, alg2.matrix)
if r == 0:
return cmp(sorted(alg1.id2name.values()),
sorted(alg2.id2name.values()))
else:
return r
sorted_algs = sorted(alg_objects, sort_single_algs)
concat_alg_lengths = [alg.seqlength for alg in sorted_algs]
model2win = {}
model2size = {}
for alg in sorted_algs:
model2size[alg.matrix] = model2size.get(alg.matrix, 0) + alg.seqlength
# Create concat alg
concat.id2seq = defaultdict(list)
for sp in sorted(valid_species):
log.log(20, "Concatenating sequences of [%s]" % sp)
for alg in sorted_algs:
seq = alg.sp2seq.get(sp, "-" * alg.seqlength)
concat.id2seq[sp].append(seq)
#current_seq = concat.id2seq.get(sp, "")
#concat.id2seq[sp] = current_seq + seq.strip()
concat.id2name[sp] = sp
concat.name2id[sp] = sp
concat.id2comment[sp] = [""]
concat.id2seq[sp] = ''.join(concat.id2seq[sp])
current_pos = 0
partitions = []
for model in sorted(model2size.keys()):
size = model2size[model]
part = "%s, %s = %d-%d" % (model, model+"_genes", \
current_pos + 1,\
current_pos + size)
current_pos += size
partitions.append(part)
# Basic Checks
seq_sizes = [len(seq) for seq in list(concat.id2seq.values())]
if len(set(seq_sizes)) != 1:
raise Exception(
"Concatenated alignment is not consistent: unequal seq length ")
if seq_sizes[0] != expected_total_length:
raise Exception("The size of concatenated alg is not what expected")
return concat, partitions, sp2alg, valid_species, concat_alg_lengths