polaris/loopScore.py

import torch
import cooler
import click
from torch import nn
from tqdm import tqdm
from torch.cuda.amp import autocast
from importlib_resources import files
from torch.utils.data import DataLoader
from polaris.utils.util_loop import bedpewriter
from polaris.model.polarisnet import polarisnet
from polaris.utils.util_data import centerPredCoolDataset

@click.command()
@click.option('-b','--batchsize', type=int, default=128, help='Batch size [128]')
@click.option('-C','--cpu', type=bool, default=False, help='Use CPU [False]')
@click.option('-G','--gpu', type=str, default=None, help='Comma-separated GPU indices [auto select]')
@click.option('-c','--chrom', type=str, default=None, help='Comma separated chroms [all autosomes]')
@click.option('-nw','--workers', type=int, default=16, help='Number of cpu threads [16]')
@click.option('-t','--threshold', type=float, default=0.5, help='Loop Score Threshold [0.5]')
@click.option('-s','--sparsity', type=float, default=0.9, help='Allowed sparsity of submatrices [0.9]')
@click.option('-md','--max_distance', type=int, default=3000000, help='Max distance (bp) between contact pairs [3000000]')
@click.option('-r','--resol',type=int,default=5000,help ='Resolution [5000]')
@click.option('--raw',type=bool,default=False,help ='Raw matrix or balanced matrix')
@click.option('-i','--input', type=str,required=True,help='Hi-C contact map path')
@click.option('-o','--output', type=str,required=True,help='.bedpe file path to save loop candidates')
def score(batchsize, cpu, gpu, chrom, workers, threshold, sparsity, max_distance, resol, input, output, raw, image=224):
    """Predict loop score for each pixel in the input contact map
    """
    print('\npolaris loop score START :) ')

    center_size = image // 2
    start_idx = (image - center_size) // 2
    end_idx = (image + center_size) // 2
    slice_obj_pred = (slice(None), slice(None), slice(start_idx, end_idx), slice(start_idx, end_idx))
    slice_obj_coord = (slice(None), slice(start_idx, end_idx), slice(start_idx, end_idx))
    
    loopwriter = bedpewriter(output,resol,max_distance)
    
    if cpu:
        assert gpu is None, "\033[91m QAQ The CPU and GPU modes cannot be used simultaneously. Please check the command. \033[0m\n"
        gpu = ['None']
        device = torch.device("cpu")
        print('Using CPU mode... (This may take significantly longer than using GPU mode.)')
    else:
        if torch.cuda.is_available():
            if gpu is not None:
                print("Using the specified GPU: " + gpu)
                gpu=[int(i) for i in gpu.split(',')]
                device = torch.device(f"cuda:{gpu[0]}")
            else:
                gpuIdx = torch.cuda.current_device()
                device = torch.device(gpuIdx)
                print("Automatically selected GPU: " + str(gpuIdx))
                gpu=[gpu]
        else:
            device = torch.device("cpu")
            gpu = ['None']
            cpu = True
            print('GPU is not available!')
            print('Using CPU mode... (This may take significantly longer than using GPU mode.)')
           

    coolfile = cooler.Cooler(input + '::/resolutions/' + str(resol))
    modelstate = str(files('polaris').joinpath('model/sft_loop.pt'))
    _modelstate = torch.load(modelstate, map_location=device.type)
    parameters = _modelstate['parameters']

    if chrom is None:
        chrom =coolfile.chromnames
    else:
        chrom = chrom.split(',')
        
    # for rmchr in ['chrMT','MT','chrM','M','Y','chrY','X','chrX','chrW','W','chrZ','Z']: # 'Y','chrY','X','chrX'
    #     if rmchr in chrom:
    #         chrom.remove(rmchr)    
                  
    print(f"Analysing chroms: {chrom}")
    
    model = polarisnet(
            image_size=parameters['image_size'], 
            in_channels=parameters['in_channels'], 
            out_channels=parameters['out_channels'],
            embed_dim=parameters['embed_dim'], 
            depths=parameters['depths'],
            channels=parameters['channels'], 
            num_heads=parameters['num_heads'], 
            drop=parameters['drop'], 
            drop_path=parameters['drop_path'], 
            pos_embed=parameters['pos_embed']
    ).to(device)
    model.load_state_dict(_modelstate['model_state_dict'])
    if not cpu and len(gpu) > 1:
        model = nn.DataParallel(model, device_ids=gpu) 
    model.eval()
        
    badc=[]
    chrom_ = tqdm(chrom, dynamic_ncols=True)
    for _chrom in chrom_:
        test_data = centerPredCoolDataset(coolfile,_chrom,max_distance_bin=max_distance//resol,w=image,step=center_size,s=sparsity,raw=raw)
        test_dataloader = DataLoader(test_data, batch_size=batchsize, shuffle=False,num_workers=workers,prefetch_factor=4,pin_memory=(gpu is not None))
        
        chrom_.desc = f"[Analyzing {_chrom} with {len(test_data)} submatrices]"
        
        if len(test_data) == 0:
            badc.append(_chrom)
            
        with torch.no_grad():
            for X in test_dataloader:
                bin_i,bin_j,targetX=X
                bin_i = bin_i*resol
                bin_j = bin_j*resol
                with autocast():
                    pred = torch.sigmoid(model(targetX.float().to(device)))[slice_obj_pred].flatten()
                    loop = torch.nonzero(pred>threshold).flatten().cpu()
                    prob = pred[loop].cpu().numpy().flatten().tolist()
                    frag1 = bin_i[slice_obj_coord].flatten().cpu().numpy()[loop].flatten().tolist()
                    frag2 = bin_j[slice_obj_coord].flatten().cpu().numpy()[loop].flatten().tolist()

                loopwriter.write(_chrom,frag1,frag2,prob)   
    
    if len(badc)==len(chrom):
        raise ValueError("polaris loop score FAILED :( \nThe '-s' value needs to be increased for more sparse data.")
    else:
        print(f'\npolaris loop score FINISHED :)\nLoopscore file saved at {output}')  
        if len(badc)>0:
            print(f"But the size of {badc} are too small or their contact matrix are too sparse.\nYou may need to check the data or run these chr respectively by increasing -s.")         
    
if __name__ == '__main__':
    score()