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import os
import argparse
import json
from tqdm import tqdm
# conda install -c conda-forge -c bioconda foldseek
def get_foldseek_structure_seq(pdb_dir, rm_tmp=True):
# foldseek createdb INPUT_dir_with_structures tmp_db
# foldseek lndb tmp_db_h tmp_db_ss_h
# foldseek convert2fasta tmp_db_ss OUTPUT_3di.fasta
# use command to generate foldseek structure seq
os.makedirs("tmp_db", exist_ok=True)
os.system(f"foldseek createdb {pdb_dir} tmp_db/tmp_db")
os.system(f"foldseek lndb tmp_db/tmp_db_h tmp_db/tmp_db_ss_h")
os.system(f"foldseek convert2fasta tmp_db/tmp_db_ss tmp_db/tmp_db_ss.fasta")
results = []
# read fasta file
with open("tmp_db/tmp_db_ss.fasta", "r") as f:
for line in tqdm(f):
if line.startswith(">"):
name = line.split()[0][1:]
seq = next(f).strip()
results.append({"name":name.split('.')[0], "foldseek_seq":seq})
if rm_tmp:
os.system("rm -rf tmp_db")
return results
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("--pdb_dir", type=str, default=None)
parser.add_argument("--out_file", type=str, default=None)
parser.add_argument("--rm_tmp", type=bool, default=True)
args = parser.parse_args()
results = get_foldseek_structure_seq(args.pdb_dir, args.rm_tmp)
with open(args.out_file, "w") as f:
f.write("\n".join([json.dumps(r) for r in results])) |