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Commit fb465d95 authored by Carlos de Lannoy's avatar Carlos de Lannoy
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fix bug in 16S validtion w premade indices

parent e49000d7
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......@@ -363,7 +363,7 @@ def get_validate_parser():
for arg in (fast5_in, out_dir, target_16S, nb_folds, cores,
parameter_file, hdf_path):
parser.add_argument(arg[0], **arg[1])
parser.add_argument('--nn-dir', required=True, type=lambda x: check_input_path(x),
parser.add_argument('--nn-dir', required=False, type=lambda x: check_input_path(x), default=f'{__location__}/16S_db/',
help='Directory containing pre-made nns for single k-mers, to be used directly')
parser.add_argument('--ground-truth-16s', required=True, type=str, help='csv denoting which species reads belong to')
parser.add_argument('--index-files', type=lambda x: check_input_path(x),
......
......@@ -91,9 +91,11 @@ test_read_dir = parse_output_path(f'{args.out_dir}test_reads/', clean=True)
if args.index_files:
index_fn_list = sorted(os.listdir(args.index_files))
for fi, fn in enumerate(index_fn_list):
idx_df = pd.read_csv(f'{args.index_files}{fn}',index_col=0)
idx_df = pd.read_csv(f'{args.index_files}{fn}', index_col=0)
idx_df.loc[:, 'fn'] = args.fast5_in + idx_df.index
fast5_df.loc[:, f'fold_{fi}'] = idx_df.loc[fast5_df.index, 'fold']
copy(f'{args.index_files}{fn}', f'{read_index_dir}index_fold{fi}.csv')
idx_df.to_csv(f'{read_index_dir}index_fold{fi}.csv')
# copy(f'{args.index_files}{fn}', f'{read_index_dir}index_fold{fi}.csv')
for sp in species_list:
_ = parse_output_path(f'{test_read_dir}{sp}/fold_{fi}')
else:
......
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