def process_job(job, session):
if log:
log.info("Processing job %d by worker %d" % (job.id, os.getpid()))
#log.info("Job: %s, %d, %d, %s, %s" % (job.alphabet, job.n, job.p, H, dist))
result = _rna.doAll(job.rna_data.encode("ascii"),job.wlen,job.wshift,job.gap,job.start,job.end,job.seed)
sres = []
for a in result:
if a.score>=20:
sres += [{"start":a.start,"end":a.end,"score":a.score}]
job.result=json.dumps(sres)
job.finish_time = datetime.datetime.now()
if len(job.error_string)>0:
job.status = ST_ERROR
else:
job.status = ST_DONE
session.commit()
log.info("Worker %d has finished job %d" % (os.getpid(), job.id))
_ = "Test 2. Check for module working"
sys.stderr.write(_ + " (please wait, it takes some time)... ")
f = gzip.open(RESOURCE_PATH+"/in.txt.gz", "r")
SS = f.read().strip()
f.close()
sfrom=0
end=-1
seed=4
dist=50
wlen=3000
wshift=1000
minscore=19
try:
res = _rna.doAll(SS,wlen,wshift,0.25,sfrom,10000,seed)
except:
failed[1] = True
if failed[1]:
sys.stderr.write("FAILED\n")
sys.exit(30)
else: sys.stderr.write("PASSED\n")
_ = "Test 3. Check for result correctness"
sys.stderr.write(_ + "... ")
result_data = str()
csvfile = StringIO.StringIO(result_data)
writer = csv.writer(csvfile, dialect="excel")
if args.wlen:
wlen=args.wlen;
if args.wshift:
wshift=args.wshift;
if args.minscore:
minscore=args.minscore;
try:
sequences = bioformats.read_sequences_from_file(args.FILE)
except bioformats.BioFormatException as e:
sys.stderr.write("Error: "+e.text+"\n")
sys.exit(1)
if not sequences:
sys.stderr.write("Error: file does not contain any sequence\n")
sys.exit(2)
name, seq = sequences[0]
res = _rna.doAll(seq.encode('ascii'),wlen,wshift,minscore,sfrom,10000,seed)
import csv
writer = csv.writer(sys.stdout, dialect="excel")
writer.writerow(["start", "end", "score"])
for a in res:
writer.writerow([a.start, a.end, a.score])
