option_parser.add_option('-l', '--log_dir')
(options, args) = option_parser.parse_args()
# check that we get the qiime-required arguments
if len(args) == 2:
jobs_list_file = args[0]
job_id = args[1]
elif len(args) == 0:
raise ValueError, "Didn't get the right command line arguments"
# make a directory for holding LSF log files
if options.log_dir == None:
log_dir = os.path.join(os.environ['HOME'], 'qiime_parallel_logs')
else:
log_dir = options.log_dir
if not os.path.exists(log_dir):
os.mkdir(log_dir, 0755)
# submit the jobs
jobs_handle = open(jobs_list_file, 'r')
job_ids = []
logs = []
for (i, line) in enumerate(jobs_handle):
datetimestamp = datetime.datetime.now().strftime('%Y%m%d_%H%M%S')
log = os.path.join(log_dir, 'job_%i_%s.log' % (i, datetimestamp))
job_id = lsf.submit_to_LSF(options.queue, log, line.strip())
job_ids.append(job_id)
logs.append(log)
jobs_handle.close()
option_parser.add_option('-l','--log_dir')
(options,args) = option_parser.parse_args()
# check that we get the qiime-required arguments
if len(args) == 2:
jobs_list_file = args[0]
job_id = args[1]
elif len(args) == 0:
raise ValueError, "Didn't get the right command line arguments"
# make a directory for holding LSF log files
if options.log_dir == None:
log_dir = os.path.join(os.environ['HOME'],'qiime_parallel_logs')
else:
log_dir = options.log_dir
if not os.path.exists(log_dir):
os.mkdir(log_dir,0755)
# submit the jobs
jobs_handle = open(jobs_list_file,'r')
job_ids = []
logs = []
for (i,line) in enumerate(jobs_handle):
datetimestamp = datetime.datetime.now().strftime('%Y%m%d_%H%M%S')
log = os.path.join( log_dir, 'job_%i_%s.log' % (i,datetimestamp) )
job_id = lsf.submit_to_LSF(options.queue,log,line.strip())
job_ids.append(job_id)
logs.append(log)
jobs_handle.close()
cmd += ' | align_vdj.py' + locus_options # 6. VDJ CLASSIFICATION
cmd += ' | translate_chains.py' # 7. TRANSLATION
# submit cmd to LSF for each part
log("Submitting jobs to LSF...")
jobIDs = []
logfiles = []
outnames = []
for part in parts:
partID = part.split('.')[-1]
partoutname = join(work_dir, 'parts/aligned.imgt.' + partID)
outnames.append(partoutname)
curr_cmd = 'cat %s | ' + cmd + ' > %s'
curr_cmd = curr_cmd % (part, partoutname)
logfile = join(work_dir, 'logs/alignment.log.' + partID)
jobID = lsf.submit_to_LSF(short_queue, logfile, curr_cmd)
logfiles.append(logfile)
jobIDs.append(jobID)
log("finished\n")
log("Waiting for LSF jobs...")
lsf.wait_for_LSF_jobs(jobIDs, logfiles)
log("finished\n")
# 8. CONCAT PARTS
log("Concatenating pieces...")
aligned_file = join(work_dir, basename + '.aligned.imgt')
cmd = 'find %s -name "aligned.imgt.*" | xargs cat > %s' % (join(
work_dir, 'parts'), aligned_file)
p = subprocess.Popen(cmd, shell=True)
p.wait()
cmd += ' | align_vdj.py' + locus_options # 6. VDJ CLASSIFICATION
cmd += ' | translate_chains.py' # 7. TRANSLATION
# submit cmd to LSF for each part
log("Submitting jobs to LSF...")
jobIDs = []
logfiles = []
outnames = []
for part in parts:
partID = part.split('.')[-1]
partoutname = join(work_dir,'parts/aligned.imgt.'+partID)
outnames.append(partoutname)
curr_cmd = 'cat %s | ' + cmd + ' > %s'
curr_cmd = curr_cmd % (part,partoutname)
logfile = join(work_dir,'logs/alignment.log.'+partID)
jobID = lsf.submit_to_LSF(short_queue,logfile,curr_cmd)
logfiles.append(logfile)
jobIDs.append(jobID)
log("finished\n")
log("Waiting for LSF jobs...")
lsf.wait_for_LSF_jobs(jobIDs,logfiles)
log("finished\n")
# 8. CONCAT PARTS
log("Concatenating pieces...")
aligned_file = join(work_dir,basename+'.aligned.imgt')
cmd = 'find %s -name "aligned.imgt.*" | xargs cat > %s' % (join(work_dir,'parts'),aligned_file)
p = subprocess.Popen(cmd,shell=True)
