if __name__ == "__main__":
tic = time()
parser = argparse.ArgumentParser(description="Find 'hit' Keio knockout strains that alter worm behaviour")
parser.add_argument('-j', '--json', help="Path to JSON parameters file",
default=JSON_PARAMETERS_PATH, type=str)
parser.add_argument('--features_path', help="Path to feature summaries file",
default=None, type=str)
parser.add_argument('--metadata_path', help="Path to metadata file",
default=None, type=str)
args = parser.parse_args()
FEATURES_PATH = args.features_path
METADATA_PATH = args.metadata_path
args = load_json(args.json)
if FEATURES_PATH is None:
FEATURES_PATH = Path(args.save_dir) / 'features.csv'
if METADATA_PATH is None:
METADATA_PATH = Path(args.save_dir) / 'metadata.csv'
# load feature summaries and metadata
features = pd.read_csv(FEATURES_PATH)
metadata = pd.read_csv(METADATA_PATH, dtype={'comments':str, 'source_plate_id':str})
# subset for desired imaging dates
if args.dates is not None:
assert type(args.dates) == list
metadata = metadata.loc[metadata['date_yyyymmdd'].astype(str).isin(args.dates)]
features = features.reindex(metadata.index)
window_summary_paths = list(window_dir.rglob(pattern))
window_feats = [f for f in window_summary_paths if 'features' in str(f)]
window_feats.sort(key=find_window)
window_files = [f for f in window_summary_paths if 'filenames' in str(f)]
window_files.sort(key=find_window)
assert all(find_window(f[0]) == find_window(f[1]) for f in zip(window_feats, window_files))
return window_feats, window_files
#%% Main
if __name__ == "__main__":
tic = time()
args = load_json(JSON_PARAMETERS_PATH)
strain_list = read_list_from_file(STRAIN_LIST_PATH)
window_dir = Path(args.project_dir) / 'Results'
window_date_dir = window_dir / str(DATE)
window_feats, window_files = find_window_summaries((window_date_dir if DATE is not None
else window_dir), pattern='*_window_*')
window_list = [find_window(p) for p in window_feats]
for w in tqdm(window_list):
compiled_feat_path = window_dir / 'features_summary_compiled_window_{}.csv'.format(str(w))
compiled_file_path = window_dir / 'filenames_summary_compiled_window_{}.csv'.format(str(w))