inftime = 0.0
secs = time()
for groupinfo in infernalorder:
group = groupinfo[0]
if group == "fasta_groups":
continue
secs = time()
skip = False
if exists(otufolder + group + "/R1hits.txt"):
skip = True
#only run infernal if there were more than 100 total sequences in group
if not skip:
currotufolder = otufolder + group
#create the cm file and calibrate it
cmfile = open(currotufolder + "/infernal_" + group + ".cm", 'w')
cmfile.write(cmbuild_from_file(currotufolder + "/bayesfold-aln.sto"))
cmfile.close()
cmfile = currotufolder + "/infernal_" + group + ".cm"
calibrate_file(cmfile, cpus=args.c)
#Run all rounds of selection through infernal at once
#make a pool of workers, one for each cpu available
manager = Manager()
lock = manager.Lock()
#calculate maximal amount of CPU power and theads we can use
procs = int(floor(args.c/args.r))
if procs == 0:
procs = 1
poolsize = args.r
if args.c < args.r:
poolsize = args.c
secs = time()
print "GROUP: " + group
logfile = open(otufolder + group + "/log.txt")
log = logfile.readlines()
logfile.close()
print ''.join(log)
seqs = int(log[1].split()[0])
skip = False
if exists(otufolder + group + "/R1hits.txt"):
skip = True
#only run infernal if there were more than 100 total sequences in group
if seqs > 99 and not skip:
currotufolder = otufolder + group
#create the cm file and calibrate it
cmfile = open(currotufolder + "/infernal_" + group + ".cm", 'w')
cmfile.write(cmbuild_from_file(currotufolder + "/locarnap-aln.sto"))
cmfile.close()
cmfile = currotufolder + "/infernal_" + group + ".cm"
calibrate_file(cmfile)
#Run all rounds of selection through infernal at once
#make a pool of workers, one for each cpu available
manager = Manager()
lock = manager.Lock()
#calculate maximal amount of CPU power and theads we can use
procs = int(floor(args.c/args.r))
if procs == 0:
procs = 1
poolsize = args.r
if args.c < args.r:
poolsize = args.c
