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| import argparse | |
| 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) | |