Added version number

README.md

@@ -6,7 +6,7 @@
 
 ### Prerequirements
 
-To be able to use `RiboDetector`, all you need to do is to install `Python 3.8` with `conda` and Python libraries: `tqdm`, `numpy`, `biopython`, `torch`, `onnxruntime` (if run on CPU mode) using `pip`, for example:
+To be able to use `RiboDetector`, all you need to do is to install `Python 3.8` (make sure you have version `3.8` because `3.7` cannot serialize a string larger than 4GiB) with `conda` and Python libraries: `tqdm`, `numpy`, `biopython`, `torch` or `onnxruntime` (if run on CPU mode) using `pip`, for example:
 
 ```shell
 conda create -n ribodetector python=3.8

data_loader/seq_encoder.py

@@ -1,4 +1,4 @@
-import itertools
+# import itertools
 import gzip
 from Bio.Seq import Seq
 from pathlib import Path

detect.py

@@ -11,6 +11,7 @@
 from parse_config import ConfigParser
 from torch.multiprocessing import Pool
 from torch.utils.data import DataLoader
+from utils.__version__ import __version__
 from argparse import RawTextHelpFormatter
 import data_loader.seq_encoder as SeqEncoder
 from data_loader.dataset import SeqData, PairedReadData
@@ -654,6 +655,8 @@ def separate_paired_reads(self, r1, r1_labels, r2, r2_labels):
                           'Not needed when free RAM >=5 * your_file_size (uncompressed, sum of paired ends)',
                           'When chunk_size=256, memory=16 it will load 256 * 16 * 1024 reads each chunk (use ~20 GB for 100bp paired end)'
                       ))
+    args.add_argument('-v', '--version', action='version',
+                      version='%(prog)s {version}'.format(version=__version__))
 
     if not isinstance(args, tuple):
         args = args.parse_args()

detect_cpu.py

@@ -6,9 +6,10 @@
 import onnxruntime
 import numpy as np
 from tqdm import tqdm
-import torch.multiprocessing as mp
+import multiprocessing as mp
 from collections import defaultdict
 from parse_config import ConfigParser
+from utils.__version__ import __version__
 
 from argparse import RawTextHelpFormatter
 import data_loader.seq_encoder as SeqEncoder
@@ -432,6 +433,9 @@ def listener(self, q_pbar):
                           'When chunk_size=1024 and threads=10, each process will load 1024 reads, in total consumming 10G memory'
                       ))
 
+    args.add_argument('-v', '--version', action='version',
+                      version='%(prog)s {version}'.format(version=__version__))
+
     if not isinstance(args, tuple):
         args = args.parse_args()
     if args.config is None: