additional args for inference

argparse_dicts.py

@@ -110,6 +110,11 @@ inference_mode = ('--inference-mode', {
     'help': 'Run inference [once] on fast5s available in folder, or [watch] folder indefinitely for new reads [default: watch]'
 })
 
+copy_reads = ('--copy-reads', {
+    'action': 'store_true',
+    'help': 'Copy reads to the output directory before starting processing'
+})
+
 # --- output ---
 out_dir = ('--out-dir', {
     'type': lambda x: parse_output_path(x),
@@ -289,7 +294,7 @@ def get_training_parser():
 
 def get_run_inference_parser():
     parser = argparse.ArgumentParser(description='Start up inference routine and watch a fast5 directory for reads.')
-    for arg in (fast5_in, out_dir, model, inference_mode, mem, batch_size):
+    for arg in (fast5_in, out_dir, model, inference_mode, mem, batch_size, copy_reads):
         parser.add_argument(arg[0], **arg[1])
     # parser.add_argument('--continuous-nn', action='store_true',help='Used RNN can handle continuous reads.')
     return parser

env.yaml

@@ -6,7 +6,7 @@ channels:
 dependencies:
   - python=3.8.10
   - matplotlib=3.5.1  # avoid issues with heatmaps
-  - tensorflow=2.4.1
+  - tensorflow-gpu=2.4.1
   - pandas=1.3.1
   - bokeh=2.3.3
   - snakemake=5.26.1

inference/run_inference.py

-import sys, signal, os, h5py
+import sys, signal, os, h5py, shutil
 from pathlib import Path
 from datetime import datetime
 import tensorflow as tf
@@ -94,7 +94,9 @@ def main(args):
         run_time = datetime.now() - start_time
         read_manager_process.terminate()
         read_manager_process.join()
-        print(f'runtime was {run_time.seconds} s')
+        with open(args.out_dir + 'run_stats.log', 'w') as fh:
+            fh.write(f'wall_time: {run_time.seconds}s')
+        print(f'wall time was {run_time.seconds} s')
         if abundance_mode:
             freq_array = abundance_array / max(abundance_array.sum(), 1)
             abundance_txt = 'kmer,abundance,frequency\n' + \
@@ -105,5 +107,8 @@ def main(args):
 if __name__ == '__main__':
     parser = get_run_inference_parser()
     args = parser.parse_args()
+    if args.copy_reads:
+        fast5_in_new = parse_output_path(args.out_dir + 'fast5_in/', clean=True)
+        shutil.copytree(args.fast5_in, fast5_in_new, dirs_exist_ok=True)
+        args.fast5_in = fast5_in_new
     main(args)
-