def app_wrapper(func, args):
global NCURSES
base_dir = GLOBALS.get("scratch_dir", GLOBALS["basedir"])
lock_file = pjoin(base_dir, "alive")
if not args.enable_ui:
NCURSES = False
if not pexist(lock_file) or args.clearall:
open(lock_file, "w").write(time.ctime())
else:
clear_env()
print >> sys.stderr, '\nThe same process seems to be running. Use --clearall or remove the lock file "alive" within the output dir'
sys.exit(-1)
try:
if NCURSES:
curses.wrapper(main, func, args)
else:
main(None, func, args)
except ConfigError, e:
if GLOBALS.get('_background_scheduler', None):
GLOBALS['_background_scheduler'].terminate()
print >> sys.stderr, "\nConfiguration Error:", e
clear_env()
sys.exit(-1)
def app_wrapper(func, args):
global NCURSES
base_dir = GLOBALS.get("scratch_dir", GLOBALS["basedir"])
lock_file = pjoin(base_dir, "alive")
if not args.enable_ui:
NCURSES = False
if not pexist(lock_file) or args.clearall:
open(lock_file, "w").write(time.ctime())
else:
clear_env()
print >>sys.stderr, '\nThe same process seems to be running. Use --clearall or remove the lock file "alive" within the output dir'
sys.exit(-1)
try:
if NCURSES:
curses.wrapper(main, func, args)
else:
main(None, func, args)
except ConfigError, e:
if GLOBALS.get('_background_scheduler', None):
GLOBALS['_background_scheduler'].terminate()
print >>sys.stderr, "\nConfiguration Error:", e
clear_env()
sys.exit(-1)
def thread_name(task):
tid = getattr(task, "threadid", None)
if hasattr(task, 'target_wkname'):
name = getattr(task, 'target_wkname')
else:
name = GLOBALS.get(tid, {}).get("_name", "?")
if GLOBALS.get('verbosity', 4) < 2:
if len(name)>23:
name = "%s...%s" %(name[:10], name[-10:])
return "@@13:%s@@1:" %name
def finish(self):
def euc_dist(x, y):
return len(x.symmetric_difference(y)) / float((len(x) + len(y)))
dataid = db.get_dataid(*self.task_tree_file.split("."))
ttree = PhyloTree(db.get_data(dataid))
mtree = self.main_tree
ttree.dist = 0
cladeid, target_seqs, out_seqs = db.get_node_info(
self.threadid, self.nodeid)
self.out_seqs = out_seqs
self.target_seqs = target_seqs
ttree_content = ttree.get_cached_content()
if mtree and not out_seqs:
mtree_content = mtree.get_cached_content()
log.log(24,
"Finding best scoring outgroup from previous iteration.")
for _n in mtree_content:
if _n.cladeid == cladeid:
orig_target = _n
target_left = set(
[_n.name for _n in mtree_content[orig_target.children[0]]])
target_right = set(
[_n.name for _n in mtree_content[orig_target.children[1]]])
partition_pairs = []
everything = set([_n.name for _n in ttree_content[ttree]])
for n, content in ttree_content.iteritems():
if n is ttree:
continue
left = set([_n.name for _n in content])
right = everything - left
d1 = euc_dist(left, target_left)
d2 = euc_dist(left, target_right)
best_match = min(d1, d2)
partition_pairs.append([best_match, left, right, n])
partition_pairs.sort()
self.outgroup_match_dist = partition_pairs[0][0]
#self.outgroup_match = '#'.join( ['|'.join(partition_pairs[0][1]),
# '|'.join(partition_pairs[0][2])] )
outgroup = partition_pairs[0][3]
ttree.set_outgroup(outgroup)
ttree.dist = orig_target.dist
ttree.support = orig_target.support
# Merge task and main trees
parent = orig_target.up
orig_target.detach()
parent.add_child(ttree)
elif mtree and out_seqs:
log.log(26, "Rooting tree using %d custom seqs" % len(out_seqs))
self.outgroup_match = '|'.join(out_seqs)
#log.log(22, "Out seqs: %s", len(out_seqs))
#log.log(22, "Target seqs: %s", target_seqs)
if len(out_seqs) > 1:
#first root to a single seqs outside the outgroup
#(should never fail and avoids random outgroup split
#problems in unrooted trees)
ttree.set_outgroup(ttree & list(target_seqs)[0])
# Now tries to get the outgroup node as a monophyletic clade
outgroup = ttree.get_common_ancestor(out_seqs)
if set(outgroup.get_leaf_names()) ^ out_seqs:
msg = "Monophyly of the selected outgroup could not be granted! Probably constrain tree failed."
#dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, out_seqs)
raise TaskError(self, msg)
else:
outgroup = ttree & list(out_seqs)[0]
ttree.set_outgroup(outgroup)
orig_target = self.main_tree.get_common_ancestor(target_seqs)
found_target = outgroup.get_sisters()[0]
ttree = ttree.get_common_ancestor(target_seqs)
outgroup.detach()
self.pre_iter_support = orig_target.support
# Use previous dist and support
ttree.dist = orig_target.dist
ttree.support = orig_target.support
parent = orig_target.up
orig_target.detach()
parent.add_child(ttree)
else:
# ROOTS FIRST ITERATION
log.log(24, "Getting outgroup for first NPR split")
# if early split is provided in the command line, it
# overrides config file
mainout = GLOBALS.get("first_split_outgroup", "midpoint")
if mainout.lower() == "midpoint":
log.log(26, "Rooting to midpoint.")
best_outgroup = ttree.get_midpoint_outgroup()
if best_outgroup:
ttree.set_outgroup(best_outgroup)
else:
log.warning("Midpoint outgroup could not be set!")
ttree.set_outgroup(ttree.iter_leaves().next())
else:
if mainout.startswith("~"):
# Lazy defined outgroup. Will trust in the common
# ancestor of two or more OTUs
strict_common_ancestor = False
outs = set(mainout[1:].split())
if len(outs) < 2:
raise TaskError(
self, "First split outgroup error: common "
"ancestor calculation requires at least two OTU names"
)
else:
strict_common_ancestor = True
outs = set(mainout.split())
if outs - target_seqs:
raise TaskError(
self,
"Unknown seqs cannot be used to set first split rooting:%s"
% (outs - target_seqs))
if len(outs) > 1:
anchor = list(set(target_seqs) - outs)[0]
ttree.set_outgroup(ttree & anchor)
common = ttree.get_common_ancestor(outs)
out_seqs = common.get_leaf_names()
if common is ttree:
msg = "First split outgroup could not be granted:%s" % out_seqs
#dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
raise TaskError(self, msg)
if strict_common_ancestor and set(out_seqs) ^ outs:
msg = "Monophyly of first split outgroup could not be granted:%s" % out_seqs
#dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
raise TaskError(self, msg)
log.log(
26, "@@8:First split rooting to %d seqs@@1:: %s" %
(len(out_seqs), out_seqs))
ttree.set_outgroup(common)
else:
single_out = outs.pop()
common = ttree.set_outgroup(single_out)
log.log(
26, "@@8:First split rooting to 1 seq@@1:: %s" %
(single_out))
self.main_tree = ttree
orig_target = ttree
tn = orig_target.copy()
self.pre_iter_task_tree = tn
self.rf = orig_target.robinson_foulds(ttree)
self.pre_iter_support = orig_target.support
# Reloads node2content of the rooted tree and generate cladeids
ttree_content = self.main_tree.get_cached_content()
for n, content in ttree_content.iteritems():
cid = generate_id([_n.name for _n in content])
n.add_feature("cladeid", cid)
#ttree.write(outfile=self.pruned_tree)
self.task_tree = ttree
sys.exit(-1)
try:
if NCURSES:
curses.wrapper(main, func, args)
else:
main(None, func, args)
except ConfigError, e:
if GLOBALS.get('_background_scheduler', None):
GLOBALS['_background_scheduler'].terminate()
print >> sys.stderr, "\nConfiguration Error:", e
clear_env()
sys.exit(-1)
except DataError, e:
if GLOBALS.get('_background_scheduler', None):
GLOBALS['_background_scheduler'].terminate()
print >> sys.stderr, "\nData Error:", e
clear_env()
sys.exit(-1)
except KeyboardInterrupt:
# Control-C is also grabbed by the back_launcher, so it is no necessary
# to terminate from here
print >> sys.stderr, "\nProgram was interrupted."
if args.monitor:
print >> sys.stderr, (
"VERY IMPORTANT !!!: Note that launched"
" jobs will keep running as you provided the --monitor flag")
clear_env()
sys.exit(-1)
def finish(self):
def euc_dist(x, y):
return len(x.symmetric_difference(y)) / float((len(x) + len(y)))
dataid = db.get_dataid(*self.task_tree_file.split("."))
ttree = PhyloTree(db.get_data(dataid))
mtree = self.main_tree
ttree.dist = 0
cladeid, target_seqs, out_seqs = db.get_node_info(self.threadid, self.nodeid)
self.out_seqs = out_seqs
self.target_seqs = target_seqs
ttree_content = ttree.get_cached_content()
if mtree and not out_seqs:
mtree_content = mtree.get_cached_content()
log.log(24, "Finding best scoring outgroup from previous iteration.")
for _n in mtree_content:
if _n.cladeid == cladeid:
orig_target = _n
target_left = set([_n.name for _n in mtree_content[orig_target.children[0]]])
target_right = set([_n.name for _n in mtree_content[orig_target.children[1]]])
partition_pairs = []
everything = set([_n.name for _n in ttree_content[ttree]])
for n, content in ttree_content.iteritems():
if n is ttree:
continue
left = set([_n.name for _n in content])
right = everything - left
d1 = euc_dist(left, target_left)
d2 = euc_dist(left, target_right)
best_match = min(d1, d2)
partition_pairs.append([best_match, left, right, n])
partition_pairs.sort()
self.outgroup_match_dist = partition_pairs[0][0]
#self.outgroup_match = '#'.join( ['|'.join(partition_pairs[0][1]),
# '|'.join(partition_pairs[0][2])] )
outgroup = partition_pairs[0][3]
ttree.set_outgroup(outgroup)
ttree.dist = orig_target.dist
ttree.support = orig_target.support
# Merge task and main trees
parent = orig_target.up
orig_target.detach()
parent.add_child(ttree)
elif mtree and out_seqs:
log.log(26, "Rooting tree using %d custom seqs" %
len(out_seqs))
self.outgroup_match = '|'.join(out_seqs)
#log.log(22, "Out seqs: %s", len(out_seqs))
#log.log(22, "Target seqs: %s", target_seqs)
if len(out_seqs) > 1:
#first root to a single seqs outside the outgroup
#(should never fail and avoids random outgroup split
#problems in unrooted trees)
ttree.set_outgroup(ttree & list(target_seqs)[0])
# Now tries to get the outgroup node as a monophyletic clade
outgroup = ttree.get_common_ancestor(out_seqs)
if set(outgroup.get_leaf_names()) ^ out_seqs:
msg = "Monophyly of the selected outgroup could not be granted! Probably constrain tree failed."
#dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, out_seqs)
raise TaskError(self, msg)
else:
outgroup = ttree & list(out_seqs)[0]
ttree.set_outgroup(outgroup)
orig_target = self.main_tree.get_common_ancestor(target_seqs)
found_target = outgroup.get_sisters()[0]
ttree = ttree.get_common_ancestor(target_seqs)
outgroup.detach()
self.pre_iter_support = orig_target.support
# Use previous dist and support
ttree.dist = orig_target.dist
ttree.support = orig_target.support
parent = orig_target.up
orig_target.detach()
parent.add_child(ttree)
else:
# ROOTS FIRST ITERATION
log.log(24, "Getting outgroup for first NPR split")
# if early split is provided in the command line, it
# overrides config file
mainout = GLOBALS.get("first_split_outgroup", "midpoint")
if mainout.lower() == "midpoint":
log.log(26, "Rooting to midpoint.")
best_outgroup = ttree.get_midpoint_outgroup()
if best_outgroup:
ttree.set_outgroup(best_outgroup)
else:
log.warning("Midpoint outgroup could not be set!")
ttree.set_outgroup(ttree.iter_leaves().next())
else:
if mainout.startswith("~"):
# Lazy defined outgroup. Will trust in the common
# ancestor of two or more OTUs
strict_common_ancestor = False
outs = set(mainout[1:].split())
if len(outs) < 2:
raise TaskError(self, "First split outgroup error: common "
"ancestor calculation requires at least two OTU names")
else:
strict_common_ancestor = True
outs = set(mainout.split())
if outs - target_seqs:
raise TaskError(self, "Unknown seqs cannot be used to set first split rooting:%s" %(outs - target_seqs))
if len(outs) > 1:
anchor = list(set(target_seqs) - outs)[0]
ttree.set_outgroup(ttree & anchor)
common = ttree.get_common_ancestor(outs)
out_seqs = common.get_leaf_names()
if common is ttree:
msg = "First split outgroup could not be granted:%s" %out_seqs
#dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
raise TaskError(self, msg)
if strict_common_ancestor and set(out_seqs) ^ outs:
msg = "Monophyly of first split outgroup could not be granted:%s" %out_seqs
#dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
raise TaskError(self, msg)
log.log(26, "@@8:First split rooting to %d seqs@@1:: %s" %(len(out_seqs),out_seqs))
ttree.set_outgroup(common)
else:
single_out = outs.pop()
common = ttree.set_outgroup(single_out)
log.log(26, "@@8:First split rooting to 1 seq@@1:: %s" %(single_out))
self.main_tree = ttree
orig_target = ttree
tn = orig_target.copy()
self.pre_iter_task_tree = tn
self.rf = orig_target.robinson_foulds(ttree)
self.pre_iter_support = orig_target.support
# Reloads node2content of the rooted tree and generate cladeids
ttree_content = self.main_tree.get_cached_content()
for n, content in ttree_content.iteritems():
cid = generate_id([_n.name for _n in content])
n.add_feature("cladeid", cid)
#ttree.write(outfile=self.pruned_tree)
self.task_tree = ttree
sys.exit(-1)
try:
if NCURSES:
curses.wrapper(main, func, args)
else:
main(None, func, args)
except ConfigError, e:
if GLOBALS.get('_background_scheduler', None):
GLOBALS['_background_scheduler'].terminate()
print >>sys.stderr, "\nConfiguration Error:", e
clear_env()
sys.exit(-1)
except DataError, e:
if GLOBALS.get('_background_scheduler', None):
GLOBALS['_background_scheduler'].terminate()
print >>sys.stderr, "\nData Error:", e
clear_env()
sys.exit(-1)
except KeyboardInterrupt:
# Control-C is also grabbed by the back_launcher, so it is no necessary
# to terminate from here
print >>sys.stderr, "\nProgram was interrupted."
if args.monitor:
print >>sys.stderr, ("VERY IMPORTANT !!!: Note that launched"
" jobs will keep running as you provided the --monitor flag")
clear_env()
sys.exit(-1)
except: