| import argparse |
| from dms_utils import deep_mutational_scan |
| from pathlib import Path |
| import numpy as np |
|
|
| import esm |
| from util import load_structure, extract_coords_from_structure |
| import biotite.structure |
| from collections import defaultdict |
|
|
|
|
| def get_native_seq(pdbfile, chain): |
| structure = load_structure(pdbfile, chain) |
| _ , native_seq = extract_coords_from_structure(structure) |
| return native_seq |
| |
| def write_dms_lib(args): |
| '''Writes a deep mutational scanning library, including the native/wildtype (wt) of the |
| indicated target chain in the structure to an output Fasta file''' |
|
|
| sequence = get_native_seq(args.pdbfile, args.chain) |
| Path(args.outpath).parent.mkdir(parents=True, exist_ok=True) |
| with open(args.dmspath, 'w') as f: |
| f.write('>wt\n') |
| f.write(sequence+'\n') |
| for pos, wt, mt in deep_mutational_scan(sequence): |
| assert(sequence[pos] == wt) |
| mut_seq = sequence[:pos] + mt + sequence[(pos + 1):] |
|
|
| f.write('>' + str(wt) + str(pos+1) + str(mt) + '\n') |
| f.write(mut_seq + '\n') |
|
|
|
|
| def main(): |
| parser = argparse.ArgumentParser( |
| description='Create a DMS library based on target chain in the structure.' |
| ) |
| parser.add_argument( |
| 'pdbfile', type=str, |
| help='input filepath, either .pdb or .cif', |
| ) |
| parser.add_argument( |
| '--dmspath', type=str, |
| help='output filepath for dms library', |
| ) |
| parser.add_argument( |
| '--chain', type=str, |
| help='chain id for the chain of interest', default='A', |
| ) |
|
|
| args = parser.parse_args() |
|
|
| if args.dmspath is None: |
| args.dmspath = f'predictions/{args.pdbfile[:-4]}-{args.chain}_dms.fasta' |
|
|
| write_dms_lib(args) |
|
|
| if __name__ == '__main__': |
| |
| main() |
|
|
