def setup_hmm_search(args):
host = 'localhost'
idmap = None
if args.usemem:
scantype = 'mem'
else:
scantype = 'disk'
connecting_to_server = False
# If searching against a predefined database name
if args.db in EGGNOG_DATABASES:
dbpath, port = get_db_info(args.db)
print dbpath
db_present = [
pexists(dbpath + "." + ext)
for ext in 'h3f h3i h3m h3p idmap'.split()
]
if False in db_present:
print db_present
print colorify(
'Database %s not present. Use download_eggnog_database.py to fetch it'
% (args.db), 'red')
raise ValueError('Database not found')
if not args.no_refine:
if not pexists(pjoin(get_data_path(), 'OG_fasta')):
print colorify(
'Database data/OG_fasta/ not present. Use download_eggnog_database.py to fetch it',
'red')
raise ValueError('Database not found')
if scantype == 'mem':
idmap_file = dbpath + '.idmap'
end_port = 53200
# If searching against a custom hmm database
elif os.path.isfile(args.db + '.h3f'):
dbpath = args.db
if scantype == 'mem':
idmap_file = args.db + ".idmap"
if not pexists(idmap_file):
if generate_idmap(args.db):
idmap_file = args.db + ".idmap"
print >> sys.stderr, "idmap succesfully created!"
else:
raise ValueError("idmap could not be created!")
port = 53000
end_port = 53200
else:
idmap_file = None
port = None
# If searching against a emapper hmm server
elif ":" in args.db:
dbname, host, port = map(str.strip, args.db.split(":"))
scantype = 'mem'
port = int(port)
if dbname in EGGNOG_DATABASES:
dbfile, port = get_db_info(dbname)
args.db = dbname
else:
dbfile = dbname
idmap_file = dbfile + '.idmap'
if not pexists(idmap_file):
raise ValueError("idmap file not found: %s" % idmap_file)
dbpath = host
if not server_functional(host, port, args.dbtype):
print colorify(
"eggnog-mapper server not found at %s:%s" % (host, port),
'red')
exit(1)
connecting_to_server = True
else:
raise ValueError('Invalid database name/server')
# If memory based searches requested, start server
if scantype == "mem" and not connecting_to_server:
master_db, worker_db = None, None
for try_port in range(port, end_port, 2):
print colorify(
"Loading server at localhost, port %s-%s" %
(try_port, try_port + 1), 'lblue')
dbpath, master_db, worker_db = load_server(dbpath, try_port,
try_port + 1, args.cpu)
port = try_port
ready = False
for _ in xrange(TIMEOUT_LOAD_SERVER):
print "Waiting for server to become ready...", host, try_port
time.sleep(1)
if not master_db.is_alive() or not worker_db.is_alive():
master_db.terminate()
master_db.join()
worker_db.terminate()
worker_db.join()
break
elif server_functional(host, port, args.dbtype):
ready = True
break
if ready:
dbpath = host
break
elif scantype == "mem":
print colorify("DB Server already running or not needed!", 'yellow')
dbpath = host
# Preload seqid map to translate hits from hmmpgmd
if scantype == "mem":
print colorify("Reading idmap %s" % idmap_file, color='lblue')
idmap = {}
for _lnum, _line in enumerate(open(idmap_file)):
if not _line.strip():
continue
try:
_seqid, _seqname = map(str, _line.strip().split(' '))
except ValueError:
if _lnum == 0:
# idmap generated by esl_reformat has info line at beginning
continue
else:
raise
_seqid = int(_seqid)
idmap[_seqid] = [_seqname]
print len(idmap), "names loaded"
# If server mode, just listen for connections and exit when interrupted
if args.servermode:
while True:
print colorify(
"Server ready listening at %s:%s and using %d CPU cores" %
(host, port, args.cpu), 'green')
print colorify(
"Use `emapper.py -d %s:%s:%s (...)` to search against this server"
% (args.db, host, port), 'lblue')
time.sleep(10)
raise emapperException()
else:
return host, port, dbpath, scantype, idmap
def setup_hmm_search(args):
host = 'localhost'
idmap = None
if args.usemem:
scantype = 'mem'
else:
scantype = 'disk'
connecting_to_server = False
# If searching against a predefined database name
if args.db in EGGNOG_DATABASES:
dbpath, port = get_db_info(args.db)
db_present = [pexists(dbpath + "." + ext)
for ext in 'h3f h3i h3m h3p idmap'.split()]
if False in db_present:
print db_present
print colorify('Database %s not present. Use download_eggnog_database.py to fetch it' % (args.db), 'red')
raise ValueError('Database not found')
if not args.no_refine:
if not pexists(pjoin(DATA_PATH, 'OG_fasta')):
print colorify('Database data/OG_fasta/ not present. Use download_eggnog_database.py to fetch it', 'red')
raise ValueError('Database not found')
if scantype == 'mem':
idmap_file = dbpath + '.idmap'
end_port = 53200
# If searching against a custom hmm database
elif os.path.isfile(args.db + '.h3f'):
dbpath = args.db
if scantype == 'mem':
idmap_file = args.db + ".idmap"
if not pexists(idmap_file):
if generate_idmap(args.db):
idmap_file = args.db + ".idmap"
print >>sys.stderr, "idmap succesfully created!"
else:
raise ValueError("idmap could not be created!")
port = 53000
end_port = 53200
else:
idmap_file = None
port = None
# If searching against a emapper hmm server
elif ":" in args.db:
dbname, host, port = map(str.strip, args.db.split(":"))
scantype = 'mem'
port = int(port)
if dbname in EGGNOG_DATABASES:
dbfile, port = get_db_info(dbname)
args.db = dbname
else:
dbfile = dbname
idmap_file = dbfile + '.idmap'
if not pexists(idmap_file):
raise ValueError("idmap file not found: %s" % idmap_file)
dbpath = host
if not server_functional(host, port, args.dbtype):
print colorify("eggnog-mapper server not found at %s:%s" % (host, port), 'red')
exit(1)
connecting_to_server = True
else:
raise ValueError('Invalid database name/server')
# If memory based searches requested, start server
if scantype == "mem" and not connecting_to_server:
master_db, worker_db = None, None
for try_port in range(port, end_port, 2):
print colorify("Loading server at localhost, port %s-%s" %
(try_port, try_port + 1), 'lblue')
dbpath, master_db, worker_db = load_server(
dbpath, try_port, try_port + 1, args.cpu)
port = try_port
ready = False
for _ in xrange(TIMEOUT_LOAD_SERVER):
print "Waiting for server to become ready...", host, try_port
time.sleep(1)
if not master_db.is_alive() or not worker_db.is_alive():
master_db.terminate()
master_db.join()
worker_db.terminate()
worker_db.join()
break
elif server_functional(host, port, args.dbtype):
ready = True
break
if ready:
dbpath = host
break
elif scantype == "mem":
print colorify("DB Server already running or not needed!", 'yellow')
dbpath = host
# Preload seqid map to translate hits from hmmpgmd
if scantype == "mem":
print colorify("Reading idmap %s" % idmap_file, color='lblue')
idmap = {}
for _lnum, _line in enumerate(open(idmap_file)):
if not _line.strip():
continue
try:
_seqid, _seqname = map(str, _line.strip().split(' '))
except ValueError:
if _lnum == 0:
# idmap generated by esl_reformat has info line at beginning
continue
else:
raise
_seqid = int(_seqid)
idmap[_seqid] = [_seqname]
print len(idmap), "names loaded"
# If server mode, just listen for connections and exit when interrupted
if args.servermode:
while True:
print colorify("Server ready listening at %s:%s and using %d CPU cores" % (host, port, args.cpu), 'green')
print colorify("Use `emapper.py -d %s:%s:%s (...)` to search against this server" % (args.db, host, port), 'lblue')
time.sleep(10)
raise emapperException()
else:
return host, port, dbpath, scantype, idmap