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e3814d7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | # This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# --------------------------------------------------------
# The all-in-one script to preprocess hic matrices.
# --------------------------------------------------------
import os
import argparse
from dataset_informations import *
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-c', '--cell-line', help='REQUIRED: Cell line for analysis[example:GM12878]',
required=True)
parser.add_argument('-hr', '--high-res', help='High resolution specified[default:10kb]',
default='10kb', choices=res_map.keys())
parser.add_argument('-dr', '--downsample-ratio', help='The ratio of downsampling[example:16]',
default=16, type=int)
parser.add_argument('-ds', '--downsample-seed', help = 'The seed of downsampling[default:0]',
default = 0, type=int)
args = parser.parse_args()
cell_line = args.cell_line
high_res = args.high_res
ratio = args.downsample_ratio
seed = args.downsample_seed
RAW2npz_command = f'python -m data_processing.RAWobserved2npz -c {cell_line} -hr {high_res}'
os.system(RAW2npz_command)
# downsample with seed 0
downsample_command = f'python -m data_processing.Downsample -c {cell_line} -hr {high_res} -lr {high_res}_d{ratio} -r {ratio} --seed {seed}'
os.system(downsample_command)
# transform the matrix with the default setting.
hr_transform_command = f'python -m data_processing.Transform -c {cell_line} -r {high_res} --cutoff 255'
lr_transform_command = f'python -m data_processing.Transform -c {cell_line} -r {high_res}_d{ratio}_seed{seed} --cutoff 100'
os.system(hr_transform_command)
os.system(lr_transform_command)
# Also transform the matrix with only HiC channel for calculating MSE.
hr_transform_command = f'python -m data_processing.Transform -c {cell_line} -r {high_res} --cutoff 255 -tn HiC'
lr_transform_command = f'python -m data_processing.Transform -c {cell_line} -r {high_res}_d{ratio}_seed{seed} --cutoff 100 -tn HiC'
os.system(hr_transform_command)
os.system(lr_transform_command)
for dataset in set_dict.keys():
generate_command = f'python -m data_processing.Generate -c {cell_line} -s {dataset} -hr {high_res} -lr {high_res}_d{ratio}_seed{seed}'
os.system(generate_command)
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