From 42c439e1fab9fcd3791899f88667644a1051df9d Mon Sep 17 00:00:00 2001
From: Carlos de Lannoy <cvdelannoy@gmail.com>
Date: Tue, 3 May 2022 16:12:40 +0200
Subject: [PATCH] additional args for inference
---
argparse_dicts.py | 7 ++++++-
env.yaml | 2 +-
inference/run_inference.py | 11 ++++++++---
3 files changed, 15 insertions(+), 5 deletions(-)
diff --git a/argparse_dicts.py b/argparse_dicts.py
index 6d0b582..5f69749 100644
--- a/argparse_dicts.py
+++ b/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
diff --git a/env.yaml b/env.yaml
index 6bb80e4..24012f8 100755
--- a/env.yaml
+++ b/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
diff --git a/inference/run_inference.py b/inference/run_inference.py
index 74eacf6..353207f 100644
--- a/inference/run_inference.py
+++ b/inference/run_inference.py
@@ -1,4 +1,4 @@
-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)
-
--
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