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| import argparse |
| import os |
| import numpy as np |
| from dataset_informations import * |
| from tqdm import tqdm |
| from data_processing.Read_npz import read_npz |
| from data_processing.Read_external_norm import read_singlechromosome_norm |
|
|
| import cooler |
| import pandas as pd |
|
|
| if __name__ == '__main__': |
| parser = argparse.ArgumentParser() |
| parser.add_argument('--data-dir', type=str, required = True) |
| parser.add_argument('--hic-caption', type=str, default = 'hic') |
| parser.add_argument('--external-norm-file', type=str, |
| default = f'{root_dir}/{RAW_dir}/#(CELLLINE)/10kb_resolution_intrachromosomal/#(CHR)/MAPQGE30/#(CHR)_10kb.KRnorm') |
| parser.add_argument('--resolution', type=str, default='10kb') |
|
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| parser.add_argument('--bound', type=int, default=200) |
| parser.add_argument('--multiple', type=int, default=255) |
|
|
| parser.add_argument('-c', '--cell-line', default='GM12878') |
| parser.add_argument('-s', '--dataset', default='test', choices=['train', 'valid', 'test', 'train1', 'valid1', 'test1'], ) |
| args = parser.parse_args() |
|
|
| data_dir = args.data_dir |
| hic_caption = args.hic_caption |
| external_norm_file = args.external_norm_file |
| res = args.resolution |
| cell_line = args.cell_line |
| dataset = args.dataset |
| bound = args.bound |
| multiple = args.multiple |
| resolution = res_map[res.split('_')[0]] |
|
|
| chr_list = set_dict[dataset] |
| abandon_chromosome = abandon_chromosome_dict.get(cell_line, []) |
|
|
| bins = {"chrom": [], "start": [], "end": []} |
| reads = {"bin1_id": [], "bin2_id": [], "count": []} |
| for n in tqdm(chr_list): |
| if n in abandon_chromosome: |
| continue |
|
|
| in_file = os.path.join(data_dir, f'chr{n}_{res}.npz') |
|
|
| matrix, compact_idx, norm = read_npz(in_file, hic_caption = hic_caption, bound = bound, multiple=multiple, include_additional_channels=False) |
|
|
| if external_norm_file != 'NONE': |
| if '#(CHR)' in external_norm_file: |
| norm = read_singlechromosome_norm(external_norm_file, n, cell_line) |
| else: |
| raise NotImplementedError |
| |
| s = len(bins['chrom']) |
|
|
| for i in range(matrix.shape[0]): |
| bins['chrom'].append(f'chr{n}') |
| bins['start'].append(i*resolution) |
| bins['end'].append((i+1)*resolution) |
|
|
| for i in tqdm(range(matrix.shape[0]), leave=False): |
| for j in range(i, min(i+bound, matrix.shape[1])): |
| RAW = float(matrix[i][j])*norm[i]*norm[j] |
| if RAW > 0: |
| reads['bin1_id'].append(s+i) |
| reads["bin2_id"].append(s+j) |
| reads["count"].append(matrix[i][j]) |
|
|
| cool_file = os.path.join(data_dir, f"bound{bound}_{res}.cool") |
| cooler.create_cooler(cool_file, bins=pd.DataFrame.from_dict(bins), pixels=pd.DataFrame.from_dict(reads), dtypes={'count': float}) |
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