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WIP: Enable reading config files output by atacworks #231

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WIP: Enable reading config files output by atacworks #231

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6 changes: 3 additions & 3 deletions scripts/cmd_args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,8 @@ def add_common_options(parser):

"""
# Pre-processing
parser.add('--config', required=False,
is_config_file=True, help='config file path')
parser.add('--genome', required=True, type=str,
help='chromosome sizes file for the genome. Sizes \
files for human genome 19 (hg19) and human \
Expand Down Expand Up @@ -142,7 +144,7 @@ def add_common_options(parser):
help="checkpoint path to load the model from for\
inference or resume training")
# dist-env args
parser.add('--gpu_idx', required=False, type=int,
parser.add('--gpu_idx', required=False, type=type_or_none_fn(int),
help='GPU ID to use. ID can be known from nvidia-smi; \
preempted by --distributed which uses all \
available gpus ')
Expand Down Expand Up @@ -241,8 +243,6 @@ def add_inference_options(parser):

"""
add_common_options(parser)
parser.add('--config', required=False,
is_config_file=True, help='config file path')
parser.add('--regions', required=True, type=type_or_none_fn(str),
help='atacworks denoising is done on whole genome by \
default. You can optionally specify a list of \
Expand Down
8 changes: 7 additions & 1 deletion scripts/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -584,7 +584,13 @@ def main():
# Save config parameters
dst_config_path = os.path.join(args.out_home,
args.mode + "_config.yaml")
save_config(dst_config_path, args)
# args object is manipulated in the code, we want to save the original
# unchanged args object.
args_org = parse_args(root_dir)
# Delete mode from args object, as mode is registered as an argument instead of
# a subparser
del args.mode
save_config(dst_config_path, args_org)


if __name__ == '__main__':
Expand Down