log.critical('Starting Apex for %s ...',file_name)
log.critical('moff Input file: %s XIC_tol %s XIC_win %4.4f moff_rtWin_peak %4.4f ' % (file_name, tol, h_rt_w, s_w))
if args.raw_list is None:
log.critical('RAW file from folder : %s' % loc_raw)
else:
log.critical('RAW file : %s' % args.raw_list)
log.critical('Output file in : %s', loc_output)
if 'matched' in df.columns:
log.critical('Apex module has detected mbr peptides')
#print 'Original input size', df.shape
name = os.path.basename(file_name).split('.')[0]
#multithreadlogs.LoggingInit_apex(os.path.join(loc_output, name + '__moff.log'))
moff.check_log_existence(os.path.join(loc_output, name + '__moff.log'))
myPool = multiprocessing.Pool(num_CPU)
start_time= time.time()
result = {}
offset = 0
for df_index in range(0,len(data_split)):
result[df_index] = myPool.apply_async(moff.apex_multithr,args = (data_split[df_index],name,raw_list, tol, h_rt_w, s_w, s_w_match, loc_raw, loc_output, offset ))
offset += len(data_split[df_index])
myPool.close()
myPool.join()
log.critical('...apex terminated')
if 'off' in args.mbr:
# put everython in mbr_loc
output_list_loc = []
if not (args.loc_in is None):
for item in os.listdir(args.loc_in):
# log.critical(item)
if os.path.isfile(os.path.join(args.loc_in, item)):
if os.path.join(args.loc_in, item).endswith('.' + args.ext):
output_list_loc.append(os.path.join(args.loc_in, item))
else:
output_list_loc = args.tsv_list
for c, file_name in enumerate(output_list_loc):
name = os.path.basename(file_name).split('.')[0]
moff.check_log_existence(os.path.join(
args.loc_out, name + '__moff.log'))
fh = logging.FileHandler(os.path.abspath(
os.path.join(args.loc_out, name + '__moff.log')), mode='a')
fh.setLevel(logging.DEBUG)
log.addHandler(fh)
log_file = os.path.join(args.loc_out, name + '__moff.log')
tol = args.tol
h_rt_w = args.xic_length
s_w = args.rt_peak_win
s_w_match = args.rt_peak_win_match
if args.tsv_list is not None:
# raw_list contains the current raws file provided by args.raw_list option
raw_list = args.raw_list[c]