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| import sys |
| import time |
| import numpy as np |
| import os |
| import argparse |
| from utils import * |
| from dataset_informations import * |
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| def data_down_parser(): |
| parser = argparse.ArgumentParser(description='Downsample data from high resolution data') |
| req_args = parser.add_argument_group('Required Arguments') |
| req_args.add_argument('-c', dest='cell_line', help='REQUIRED: Cell line for analysis[example:GM12878]', |
| required=True) |
| req_args.add_argument('-hr', dest='high_res', help='REQUIRED: High resolution specified[example:10kb]', |
| default='10kb', choices=res_map.keys(), required=True) |
| req_args.add_argument('-lr', dest='low_res', help='REQUIRED: Low resolution specified[example:10kb_d16]', |
| default='10kb_d16', required=True) |
| req_args.add_argument('-r', dest='ratio', help='REQUIRED: The ratio of downsampling[example:16]', |
| default=16, type=int, required=True) |
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| return parser |
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| def downsampling(matrix, down_ratio, verbose=False): |
| """ |
| Downsampling method. |
| """ |
| if verbose: print(f"[Downsampling] Matrix shape is {matrix.shape}") |
| tag_mat, tag_len = dense2tag(matrix) |
| sample_idx = np.random.choice(tag_len, tag_len // down_ratio) |
| sample_tag = tag_mat[sample_idx] |
| if verbose: print(f'[Downsampling] Sampling 1/{down_ratio} of {tag_len} reads') |
| down_mat = tag2dense(sample_tag, matrix.shape[0]) |
| return down_mat |
|
|
| def downsample(in_file, low_res, ratio, seed): |
| np.random.seed(args.seed) |
| data = np.load(in_file) |
| hic = data['hic'] |
| compact_idx = data['compact'] |
| norm = data['norm'] |
| down_hic = downsampling(hic, ratio, seed) |
| chr_name = os.path.basename(in_file).split('_')[0] |
| out_file = os.path.join(os.path.dirname(in_file), f'{chr_name}_{low_res}_seed{seed}.npz') |
| np.savez_compressed(out_file, hic=down_hic, compact=compact_idx, norm=norm, ratio=ratio) |
| print('Saving file:', out_file) |
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|
|
| if __name__ == '__main__': |
| parser = data_down_parser() |
| parser.add_argument('--seed', type=int, default=0) |
| args = parser.parse_args(sys.argv[1:]) |
|
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| cell_line = args.cell_line |
| high_res = args.high_res |
| low_res = args.low_res |
| ratio = args.ratio |
|
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| data_dir = os.path.join(root_dir, hic_matrix_dir, cell_line) |
| in_files = [os.path.join(data_dir, f) for f in os.listdir(data_dir) if f.find(f'{high_res}.npz') >= 0] |
| in_files = sorted(in_files) |
|
|
| print(f'Generating {low_res} files from {high_res} files by {ratio}x downsampling.') |
| start = time.time() |
| for file in in_files: |
| downsample(file, low_res, ratio, args.seed) |
| print(f'All downsampling processes done. Running cost is {(time.time()-start)/60:.1f} min.') |
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