def run_infernal(cmfile,
rnd,
seqs,
outfolder,
cpus=1,
score=0.0,
calibrate=False):
if exists("%s/R%ihits.fna" % (outfolder, rnd)):
return
if not exists(cmfile):
raise IOError("cmfile path provided does not exist: %s" % cmfile)
params = {
'--mid': True,
'--Fmid': 0.0002,
'--notrunc': True,
'--toponly': True,
'--cpu': cpus
} # '-g': True,
if calibrate:
calibrate_file(cmfile, cpus=cpus)
result = cmsearch_from_file(cmfile, seqs, RNA, cutoff=score, params=params)
with open("%s/R%ihits.fna" % (outfolder, rnd), 'w') as fout:
for hit in result:
fout.write(">%s score:%0.1f e-val:%f\n%s\n" %
(hit[0], hit[14], hit[15], seqs.getSeq(hit[0])))
if exists("%s/log.txt" % outfolder):
with open("%s/log.txt" % outfolder, 'a') as fout:
fout.write("Round %i: %i hits\n" % (rnd, len(result)))
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
pool = Pool(processes=poolsize)
extracpus = args.c - (procs*poolsize)
for i in range(args.r, 0, -1):
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
pool = Pool(processes=poolsize)
extracpus = args.c - (procs*poolsize)
for i in range(args.r, 0, -1):