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Capricorn / HiC_evaluation /batch_evaluation.py
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# 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 evaluate Capricorn and baselines.
# --------------------------------------------------------
import os
import argparse
from dataset_informations import *
# The setting used in our evaluation. You could add your personalized setting for the experiments.
# We removed some duplicated evaluation(e.g. Capricorn evaluation was repeated in many experiments, and we didn't rerun it many times.)
# Currently not include the submatrix comparison experiments. Please see submatrices_loop_calc.py for the experiments.
Evaluate_settings = {
'Example_GM12878':
{
'convert_to_cool' : False,
'run_HiCCUPS': False,
'run_Chromosight': True,
'run_Mustache': True,
'compare_MSE': False,
'compare_HiCCUPS': False,
'compare_Chromosight': True,
'compare_Mustache': True,
'dataset': 'test',
'cell_line': 'GM12878',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb_d16_seed0',
'multiple': 1,
'caption': 'hic',
'save_dir': 'results/example/LC/GM12878'
},
]
},
'Example_K562':
{
'convert_to_cool' : False,
'run_HiCCUPS': False,
'run_Chromosight': True,
'run_Mustache': True,
'compare_MSE': False,
'compare_HiCCUPS': False,
'compare_Chromosight': True,
'compare_Mustache': True,
'dataset': 'test',
'cell_line': 'K562',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb_d16_seed0',
'multiple': 1,
'caption': 'hic',
'save_dir': 'results/example/LC/K562'
},
]
},
'Main_GM12878':
{
'convert_to_cool' : True,
'run_HiCCUPS': True,
'run_Chromosight': True,
'run_Mustache': True,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': True,
'compare_Mustache': True,
'dataset': 'test',
'cell_line': 'GM12878',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': f'{root_dir}/mat/GM12878',
'res': '10kb_d16_seed0',
'multiple': 1,
'caption': 'hic',
'save_dir': 'results/main_results/LC/GM12878'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/GM12878_HiCARN_1_K562_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCARN_1/GM12878'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/GM12878_HiCARN_2_K562_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCARN_2/GM12878'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/GM12878_HiCSR_K562_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCSR/GM12878'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/GM12878_HiCNN_K562_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCNN/GM12878'
},
{
'data_dir': 'checkpoints/10_09_05_15_diffusion_3d_noaug_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/main_results/Capricorn/GM12878'
},
]
},
'Main_K562':
{
'convert_to_cool' : True,
'run_HiCCUPS': True,
'run_Chromosight': True,
'run_Mustache': True,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': True,
'compare_Mustache': True,
'dataset': 'test',
'cell_line': 'K562',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': f'{root_dir}/mat/K562',
'res': '10kb_d16_seed0',
'multiple': 1,
'caption': 'hic',
'save_dir': 'results/main_results/LC/K562'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/K562_HiCARN_1_GM12878_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCARN_1/K562'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/K562_HiCARN_2_GM12878_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCARN_2/K562'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/K562_HiCSR_GM12878_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCSR/K562'
},
{
'data_dir': '/data/liuyf/biocom/HiCARN/HiCARN/Datasets_NPZ/predict/K562_HiCNN_GM12878_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/main_results/HiCNN/K562'
},
{
'data_dir': 'checkpoints/10_09_05_15_diffusion_3d_noaug_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/main_results/Capricorn/K562'
},
]
},
'channel_ablation_GM12878':
{
'convert_to_cool' : False,
'run_HiCCUPS': True,
'run_Chromosight': False,
'run_Mustache': False,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': False,
'compare_Mustache': False,
'dataset': 'test',
'cell_line': 'GM12878',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': 'checkpoints/10_06_15_58_diffusion_2d_noaugmentation_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H/GM12878'
},
{
'data_dir': 'checkpoints/10_09_05_15_diffusion_3d_noaug_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F/GM12878'
},
{
'data_dir': 'checkpoints/01_05_08_17_Capricorn_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F-L/GM12878'
},
{
'data_dir': 'checkpoints/01_05_08_20_Capricorn_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F-T/GM12878'
},
{
'data_dir': 'checkpoints/01_08_19_23_Capricorn_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H+O/GM12878'
},
{
'data_dir': 'checkpoints/01_17_03_41_Capricorn_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F-O/GM12878'
},
{
'data_dir': 'checkpoints/01_17_03_43_Capricorn_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H+L/GM12878'
},
{
'data_dir': 'checkpoints/01_18_09_21_Capricorn_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H+T/GM12878'
}
]
},
'channel_ablation_K562':
{
'convert_to_cool' : False,
'run_HiCCUPS': True,
'run_Chromosight': False,
'run_Mustache': False,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': False,
'compare_Mustache': False,
'dataset': 'test',
'cell_line': 'K562',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': 'checkpoints/10_06_08_42_diffusion_2d_noaugmentation_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H/K562'
},
{
'data_dir': 'checkpoints/10_09_05_15_diffusion_3d_noaug_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F/K562'
},
{
'data_dir': 'checkpoints/01_05_08_18_Capricorn_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F-L/K562'
},
{
'data_dir': 'checkpoints/01_05_08_19_Capricorn_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F-T/K562'
},
{
'data_dir': 'checkpoints/01_08_19_22_Capricorn_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H+O/K562'
},
{
'data_dir': 'checkpoints/01_17_03_41_Capricorn_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/F-O/K562'
},
{
'data_dir': 'checkpoints/01_17_03_42_Capricorn_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H+L/K562'
},
{
'data_dir': 'checkpoints/01_18_09_20_Capricorn_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/channel_ablation_results/H+T/K562'
}
]
},
'crosschromosome_GM12878':
{
'convert_to_cool' : False,
'run_HiCCUPS': True,
'run_Chromosight': False,
'run_Mustache': False,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': False,
'compare_Mustache': False,
'dataset': 'test_crosschromosome',
'cell_line': 'GM12878',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': f'{root_dir}/mat/GM12878',
'res' : '10kb_d16_seed0',
'caption': 'hic',
'save_dir': 'results/crosschromosome_results/LC/GM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_1_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_1/GM12878_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_2_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_2/GM12878_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCSR_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCSR/GM12878_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCNN_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCNN/GM12878_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_1_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_1/GM12878_TrainGM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_2_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_2/GM12878_TrainGM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCSR_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCSR/GM12878_TrainGM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCNN_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCNN/GM12878_TrainGM12878'
},
{
'data_dir': 'checkpoints/10_14_14_49_diffusion_3dcrosschr_noaug_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/crosschromosome_results/Capricorn/GM12878_TrainK562'
},
{
'data_dir': 'checkpoints/10_14_14_49_diffusion_3dcrosschr_noaug_GM12878/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/crosschromosome_results/Capricorn/GM12878_TrainGM12878'
},
]
},
'crosschromosome_K562':
{
'convert_to_cool' : False,
'run_HiCCUPS': True,
'run_Chromosight': False,
'run_Mustache': False,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': False,
'compare_Mustache': False,
'dataset': 'test_crosschromosome',
'cell_line': 'K562',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': f'{root_dir}/mat/K562',
'res' : '10kb_d16_seed0',
'caption': 'hic',
'save_dir': 'results/crosschromosome_results/LC/K562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_1_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_1/K562_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_2_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_2/K562_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCSR_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCSR/K562_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCNN_K562_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCNN/K562_TrainK562'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_1_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_1/K562_TrainGM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_2_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCARN_2/K562_TrainGM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCSR_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCSR/K562_TrainGM12878'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCNN_GM12878_base_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/crosschromosome_results/HiCNN/K562_TrainGM12878'
},
{
'data_dir': 'checkpoints/10_14_14_49_diffusion_3dcrosschr_noaug_K562/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/crosschromosome_results/Capricorn/K562_TrainK562'
},
{
'data_dir': 'checkpoints/10_14_14_49_diffusion_3dcrosschr_noaug_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/crosschromosome_results/Capricorn/K562_TrainGM12878'
},
]
},
'IO_ablation_GM12878':
{
'convert_to_cool' : False,
'run_HiCCUPS': True,
'run_Chromosight': False,
'run_Mustache': False,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': False,
'compare_Mustache': False,
'dataset': 'test',
'cell_line': 'GM12878',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/GM12878',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_1_K562_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_1/GM12878_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_1_K562_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_1/GM12878_I'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_2_K562_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_2/GM12878_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCARN_2_K562_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_2/GM12878_I'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCSR_K562_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCSR/GM12878_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCSR_K562_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCSR/GM12878_I'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCNN_K562_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCNN/GM12878_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/GM12878_HiCNN_K562_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCNN/GM12878_I'
},
{
'data_dir': 'checkpoints/10_09_05_14_diffusion_3dto2d_noaug_K562/best_mse_0/predict/GM12878',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/IO_ablation_results/Capricorn/GM12878_I'
},
]
},
'IO_ablation_K562':
{
'convert_to_cool' : False,
'run_HiCCUPS': True,
'run_Chromosight': False,
'run_Mustache': False,
'compare_MSE': True,
'compare_HiCCUPS': True,
'compare_Chromosight': False,
'compare_Mustache': False,
'dataset': 'test',
'cell_line': 'K562',
'target_datas': {
'MSE': {
'data_dir' : f'{root_dir}/{multichannel_matrix_dir}/HiC/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'HiCCUPS': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Mustache': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
'Chromosight': {
'data_dir' : f'{root_dir}/{hic_matrix_dir}/K562',
'res': '10kb',
'multiple': 1,
'caption': 'hic'
},
},
'datas': [
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_1_GM12878_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_1/K562_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_1_GM12878_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_1/K562_I'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_2_GM12878_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_2/K562_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCARN_2_GM12878_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCARN_2/K562_I'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCSR_GM12878_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCSR/K562_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCSR_GM12878_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCSR/K562_I'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCNN_GM12878_multi_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCNN/K562_IO'
},
{
'data_dir': 'checkpoints/baseline_ckpts/K562_HiCNN_GM12878_3to2_fixed',
'res': '10kb',
'multiple': 255,
'caption': 'hicarn',
'save_dir': 'results/IO_ablation_results/HiCNN/K562_I'
},
{
'data_dir': 'checkpoints/10_09_05_14_diffusion_3dto2d_noaug_GM12878/best_mse_0/predict/K562',
'res': '10kb',
'multiple': 255,
'caption': 'hic',
'save_dir': 'results/IO_ablation_results/Capricorn/K562_I'
},
]
},
}
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-e', '--experiment', type=str, required=True)
parser.add_argument('-pt', '--prepare-target-results', action='store_true')
args = parser.parse_args()
setting = Evaluate_settings[args.experiment]
convert_to_cool = setting['convert_to_cool']
run_HiCCUPS = setting['run_HiCCUPS']
run_Chromosight = setting['run_Chromosight']
run_Mustache = setting['run_Mustache']
compare_MSE = setting['compare_MSE']
compare_HiCCUPS = setting['compare_HiCCUPS']
compare_Chromosight = setting['compare_Chromosight']
compare_Mustache = setting['compare_Mustache']
cell_line = setting['cell_line']
dataset = setting['dataset']
target_datas = setting['target_datas']
datas = setting['datas']
if args.prepare_target_results:
if run_HiCCUPS:
data = target_datas['HiCCUPS']
os.makedirs(f'{data["data_dir"]}/{data["res"]}', exist_ok=True)
# Don't use external norms. If want to use some external norm, manaully do this convertion for data.
command = f'python -m HiC_evaluation.HiCCUPS --data-dir {data["data_dir"]} --resolution {data["res"]} -c {cell_line} -s {dataset} --hic-caption {data["caption"]} --multiple {data["multiple"]} --external-norm-file NONE'
os.system(command)
if run_Chromosight:
data = target_datas['Mustache']
if convert_to_cool:
os.makedirs(f'{data["data_dir"]}/{data["res"]}', exist_ok=True)
# Don't use external norms. If want to use some external norm, manaully do this convertion for data.
command = f'python -m data_processing.npz2cool --data-dir {data["data_dir"]} --resolution {data["res"]} -c {cell_line} -s {dataset} --hic-caption {data["caption"]} --multiple {data["multiple"]} --external-norm-file NONE'
os.system(command)
command = f'chromosight detect --pattern=loops_small --min-dist 15000 --max-dist 2000000 {data["data_dir"]}/bound200_res{data["res"]}.cool {data["data_dir"]}/{data["res"]}/chromosight_small'
os.system(command)
if run_Mustache:
data = target_datas['Mustache']
if convert_to_cool:
os.makedirs(f'{data["data_dir"]}/{data["res"]}', exist_ok=True)
# Don't use external norms. If want to use some external norm, manaully do this convertion for data.
command = f'python -m data_processing.npz2cool --data-dir {data["data_dir"]} --resolution {data["res"]} -c {cell_line} -s {dataset} --hic-caption {data["caption"]} --multiple {data["multiple"]} --external-norm-file NONE'
os.system(command)
command = f'python -m HiC_evaluation.mustache -r 10kb -f {data["data_dir"]}/bound200_res{data["res"]}.cool -o {data["data_dir"]}/{data["res"]}/mustache.tsv'
os.system(command)
for data in datas:
if data['save_dir'] is not None:
os.makedirs(data['save_dir'], exist_ok=True)
#some baselines have a different otuput name format. Change them to the standard format.
command = f'rename 40kb 10kb {data["data_dir"]}/*'
os.system(command)
command = f'rename predict_c c {data["data_dir"]}/*'
os.system(command)
# prepare the output dir
os.makedirs(f'{data["data_dir"]}/{data["res"]}', exist_ok=True)
if compare_MSE:
target_data = target_datas['MSE']
# Never use multiple for MSE.
command = f'python -m HiC_evaluation.Image_Metrics -t {target_data["data_dir"]} -tr {target_data["res"]} -p {data["data_dir"]} -pr {data["res"]} -pc {data["caption"]} -c {cell_line} -s {dataset}'
if data["save_dir"] is not None:
command = command + f' -o {data["save_dir"]}/Image_metrics.tsv'
os.system(command)
if run_HiCCUPS:
# Don't use external norms. If want to use some external norm, manaully do this convertion for data.
command = f'python -m HiC_evaluation.HiCCUPS --data-dir {data["data_dir"]} --resolution {data["res"]} -c {cell_line} -s {dataset} --hic-caption {data["caption"]} --multiple {data["multiple"]} --external-norm-file NONE'
os.system(command)
if compare_HiCCUPS:
target_data = target_datas['HiCCUPS']
pred_file = f'{data["data_dir"]}/{data["res"]}/HiCCUPS/HiCCUPS_loop_annotation.bedpe'
target_file = f'{target_data["data_dir"]}/{target_data["res"]}/HiCCUPS/HiCCUPS_loop_annotation.bedpe'
command = f'python -m HiC_evaluation.bedpe_comparison -t {target_file} -p {pred_file} -d -s {dataset}'
if data["save_dir"] is not None:
command = command + f' -o {data["save_dir"]}/HiCCUPS.tsv'
os.system(command)
if convert_to_cool:
# Don't use external norms. If want to use some external norm, manaully do this convertion for data.
command = f'python -m data_processing.npz2cool --data-dir {data["data_dir"]} --resolution {data["res"]} -c {cell_line} -s {dataset} --hic-caption {data["caption"]} --multiple {data["multiple"]} --external-norm-file NONE'
os.system(command)
if run_Chromosight:
command = f'chromosight detect --pattern=loops_small --min-dist 15000 --max-dist 2000000 {data["data_dir"]}/bound200_{data["res"]}.cool {data["data_dir"]}/{data["res"]}/chromosight_small'
os.system(command)
if compare_Chromosight:
target_data = target_datas['Chromosight']
pred_file = f'{data["data_dir"]}/{data["res"]}/chromosight_small.tsv'
target_file = f'{target_data["data_dir"]}/{target_data["res"]}/chromosight_small.tsv'
command = f'python -m HiC_evaluation.bedpe_comparison -t {target_file} -p {pred_file} -d -s {dataset}'
if data["save_dir"] is not None:
command = command + f' -o {data["save_dir"]}/chromosight.tsv'
os.system(command)
if run_Mustache:
command = f'python -m HiC_evaluation.mustache -r 10kb -f {data["data_dir"]}/bound200_{data["res"]}.cool -o {data["data_dir"]}/{data["res"]}/mustache.tsv'
os.system(command)
if compare_Mustache:
target_data = target_datas['Mustache']
pred_file = f'{data["data_dir"]}/{data["res"]}/mustache.tsv'
target_file = f'{target_data["data_dir"]}/{target_data["res"]}/mustache.tsv'
command = f'python -m HiC_evaluation.bedpe_comparison -t {target_file} -p {pred_file} -d -s {dataset}'
if data["save_dir"] is not None:
command = command + f' -o {data["save_dir"]}/mustache.tsv'
os.system(command)