| import argparse |
| import json |
| import os |
|
|
|
|
| def main(args): |
| db_path = os.path.join(args.output_db_path, f"{args.output_db_name}.db") |
| index_path = os.path.join( |
| args.output_db_path, f"{args.output_db_name}.index" |
| ) |
| db_fp = open(db_path, "wb") |
| index = {} |
| db_offset = 0 |
| for chain_alignment_dir in os.listdir(args.alignment_dir): |
| cad_path = os.path.join(args.alignment_dir, chain_alignment_dir) |
| for f in os.listdir(cad_path): |
| f_path = os.path.join(cad_path, f) |
| with open(f_path, "rb") as fp: |
| file_bytes = fp.read() |
|
|
| l = len(file_bytes) |
| file_list = index.setdefault(chain_alignment_dir, []) |
| file_list.append((f, db_offset, l)) |
| |
| db_fp.write(file_bytes) |
| db_offset += l |
|
|
| db_fp.close() |
|
|
| with open(index_path, "w") as fp: |
| json.dump(index, fp) |
| |
|
|
|
|
| if __name__ == "__main__": |
| parser = argparse.ArgumentParser() |
| parser.add_argument( |
| "alignment_dir", type=str, |
| help="""Path to precomputed alignment directory, with one subdirectory |
| per chain.""" |
| ) |
| parser.add_argument("output_db_path", type=str) |
| parser.add_argument("output_db_name", type=str) |
|
|
| args = parser.parse_args() |
|
|
| main(args) |
|
|
