scripts/helper_scripts/make_pssm_input_dict.py

import argparse
import os
import sys

_PROJECT_ROOT = os.path.abspath(os.path.dirname(__file__))
while _PROJECT_ROOT and not os.path.isdir(os.path.join(_PROJECT_ROOT, "model")):
    _PARENT = os.path.dirname(_PROJECT_ROOT)
    if _PARENT == _PROJECT_ROOT:
        break
    _PROJECT_ROOT = _PARENT
_MODEL_ROOT = os.path.join(_PROJECT_ROOT, "model")
_ONESCIENCE_ROOT = os.environ.get("ONESCIENCE_ROOT")
for _path in (_MODEL_ROOT, _PROJECT_ROOT):
    if os.path.exists(_path) and _path not in sys.path:
        sys.path.insert(0, _path)
if _ONESCIENCE_ROOT:
    _ONESCIENCE_SRC = os.path.join(_ONESCIENCE_ROOT, "src")
    for _path in (_ONESCIENCE_SRC, _ONESCIENCE_ROOT):
        if os.path.exists(_path) and _path not in sys.path:
            sys.path.insert(0, _path)

def main(args):
    import json
    import numpy as np
    with open(args.jsonl_input_path, 'r') as json_file:
        json_list = list(json_file)
    
    my_dict = {}
    for json_str in json_list:
        result = json.loads(json_str)
        all_chain_list = [item[-1:] for item in list(result) if item[:9]=='seq_chain']
        path_to_PSSM = args.PSSM_input_path+"/"+result['name'] + ".npz"
        print(path_to_PSSM)
        pssm_input = np.load(path_to_PSSM)
        pssm_dict = {}
        for chain in all_chain_list:
            pssm_dict[chain] = {}
            pssm_dict[chain]['pssm_coef'] = pssm_input[chain+'_coef'].tolist() #[L] per position coefficient to trust PSSM; 0.0 - do not use it; 1.0 - just use PSSM only
            pssm_dict[chain]['pssm_bias'] = pssm_input[chain+'_bias'].tolist() #[L,21] probability (sums up to 1.0 over alphabet of size 21) from PSSM
            pssm_dict[chain]['pssm_log_odds'] = pssm_input[chain+'_odds'].tolist() #[L,21] log_odds ratios coming from PSSM; optional/not needed
        my_dict[result['name']] = pssm_dict
    
    #Write output to:    
    with open(args.output_path, 'w') as f:
        f.write(json.dumps(my_dict) + '\n')
    
if __name__ == "__main__":
    argparser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    argparser.add_argument("--PSSM_input_path", type=str, help="Path to PSSMs saved as npz files.")
    argparser.add_argument("--jsonl_input_path", type=str, help="Path where to load .jsonl dictionary of parsed pdbs.")
    argparser.add_argument("--output_path", type=str, help="Path where to save .jsonl dictionary with PSSM bias.")

    args = argparser.parse_args()
    main(args)