def check_masters(self, idle):
if time.time() - self.last_heartbeat_from_master > self.max_wait:
terminate = False
with helpers.ExclusiveConnect(self.hbdb_path) as cursor:
cursor.execute("SELECT * FROM heartbeat WHERE thread_type='master' "
"AND pulse>?", (time.time() - self.max_wait - cursor.lag,))
masters = cursor.fetchall()
if not masters:
terminate = True
self.last_heartbeat_from_master = time.time()
if terminate:
self.terminate("%s of master inactivity (spent %s%% time idle)" %
(br.pretty_time(self.max_wait), idle))
return
def check_masters(self, idle):
if time.time() - self.last_heartbeat_from_master > self.max_wait:
terminate = False
with helpers.ExclusiveConnect(self.hbdb_path) as cursor:
cursor.execute(
"SELECT * FROM heartbeat WHERE thread_type='master' "
"AND pulse>?",
(time.time() - self.max_wait - cursor.lag, ))
masters = cursor.fetchall()
if not masters:
terminate = True
self.last_heartbeat_from_master = time.time()
if terminate:
self.terminate(
"%s of master inactivity (spent %s%% time idle)" %
(br.pretty_time(self.max_wait), idle))
return
def total_elapsed(self, prefix="", postfix=""):
return "%s%s%s" % (prefix, br.pretty_time(round(time()) - self.start), postfix)
def split(self, prefix="", postfix=""):
split = round(time()) - self.split_time
self.split_time = round(time())
return "%s%s%s" % (prefix, br.pretty_time(split), postfix)
with open("./analysis/best_scheme.txt", "r") as ifile:
content = ifile.read()
content = re.findall(r"RaxML-style partition definitions\n(.*)", content, re.DOTALL)[0]
with open("./RAxML/partition.txt", "w") as ofile:
ofile.write(content)
shutil.copy("%s/%s.phy" % (new_dir, file_name), "./RAxML/")
with open("./RAxML/RAxML.sh", "w") as ofile:
model = "PROTGAMMAGTR" if alphabet == IUPAC.protein else "GTRGAMMA"
sh_output = "source /home/bondsr/.bashrc;\n"
sh_output += "/usr/lib64/openmpi/1.4-gcc/bin/mpirun -np 20 /home/kochbj/bin/bin/raxmlHPC-MPI " \
"-s !!!1!!!/%s/%s.phy -n %s -m %s -f d -p 12345 -N 20 -w !!!1!!!/%s/ML_trees/ " \
"-q !!!1!!!/%s/partition.txt;\n" % (file_name, file_name, file_name, model, file_name, file_name)
sh_output += "/usr/lib64/openmpi/1.4-gcc/bin/mpirun -np 20 /home/kochbj/bin/bin/raxmlHPC-MPI " \
"-s !!!1!!!/%s/%s.phy -n %s -m %s -f d -p 12345 -b 12345 -N 100 " \
"-w !!!1!!!/%s/bootstraps/ -q !!!1!!!/%s/partition.txt;\n" % (file_name, file_name, file_name, model, file_name, file_name)
sh_output += "/home/bondsr/bin/best_ML_tree.py !!!1!!!/%s/ML_trees/RAxML_info.%s;\n" % (file_name, file_name)
sh_output += "/home/bondsr/bin/raxmlHPC-PTHREADS-SSE3 -n %s -m %s -f b -p 12345 -T 2 " \
"-w !!!1!!!/%s/cons_tree/ -t !!!1!!!/%s/ML_trees/RAxML_best.%s " \
"-z !!!1!!!/%s/bootstraps/RAxML_bootstrap.%s;\n" % (file_name, model, file_name, file_name, file_name, file_name, file_name)
ofile.write(sh_output)
os.chdir(blocks_file_dir)
print("Job complete, it ran in %s" % br.pretty_time(round(clock()) - start_time))
def total_elapsed(self, prefix="", postfix=""):
return "%s%s%s" % (prefix, br.pretty_time(round(time()) - self.start),
postfix)
def split(self, prefix="", postfix=""):
split = round(time()) - self.split_time
self.split_time = round(time())
return "%s%s%s" % (prefix, br.pretty_time(split), postfix)
all_by_all_handle = open("%s/all_by_all.csv" % in_args.outdir, "a")
printer = br.DynamicPrint(quiet=in_args.quiet, log=in_args.log)
counter = 1
start_time = round(time())
for hit in blast_p_hits_handle:
counter += 1
if counter % 1000 == 0:
printer.write("\t--> formatting %s of %s hits" % (counter, total_hits))
if hit == "":
continue
data = hit.split("\t")
if data[0] == data[1]:
continue
if data[10] == '0.0':
data[10] = '1e-181'
try:
data[1] = total_hash_map[data[1]]
data[0] = total_hash_map[data[0]]
all_by_all_handle.write("%s" % "\t".join(data))
except KeyError:
print("Error:\t", data)
printer.write("\t--> formatting %s of %s hits" % (counter, total_hits))
print("\n\tDone formatting in %s" % br.pretty_time(round(time()) - start_time))
os.remove("%s/temp_blast_hits.csv" % in_args.outdir)