| import pickle | |
| from _bootstrap import use_project_root | |
| use_project_root() | |
| with open('conf/data/asPICKLE/data_filter.pickle', 'rb') as binary_reader: | |
| data_filter = pickle.load(binary_reader) | |
| # extract the complexes with antibody identity 98% from data_filter | |
| # 1. read the nanobody_seqs_98.fasta to get the PDB id of the complexes | |
| fasta_file_path = 'conf/data/asFASTA/nanobody_seqs_98.fasta' | |
| PDB = '' | |
| PDBs = [] | |
| with open(fasta_file_path, 'r') as file: | |
| lines = file.readlines() | |
| for line in lines: | |
| if line[0] == '>': | |
| PDB = line[1:] | |
| PDB = PDB.strip() | |
| PDBs.append(PDB) | |
| file.close() | |
| data_filter_nano_identiy98 = [] | |
| for item in data_filter: | |
| if item[0] in PDBs: | |
| data_filter_nano_identiy98.append(item) | |
| # Save data_filter_nano_identiy98 as pickle file | |
| with open('conf/data/asPICKLE/data_filter_nano_identiy98.pickle', 'wb') as binary_writer: | |
| pickle.dump(data_filter_nano_identiy98, binary_writer) | |
| # write the antigen sequences as FASTA file | |
| antigen_seqs_fasta = open("conf/data/asFASTA/antigen_seqs_after_nanobody_identiy98.fasta", "w") | |
| for item in data_filter_nano_identiy98: | |
| antigen_seqs_fasta.write(">" + item[0] + " \n") | |
| antigen_seqs_fasta.write(item[17] + " \n") | |