diff options
| -rw-r--r-- | pyhegp/pyhegp.py | 22 |
1 files changed, 14 insertions, 8 deletions
diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py index 3133c25..15610a3 100644 --- a/pyhegp/pyhegp.py +++ b/pyhegp/pyhegp.py @@ -1,5 +1,5 @@ ### pyhegp --- Homomorphic encryption of genotypes and phenotypes -### Copyright © 2025 Arun Isaac <arunisaac@systemreboot.net> +### Copyright © 2025–2026 Arun Isaac <arunisaac@systemreboot.net> ### ### This file is part of pyhegp. ### @@ -26,7 +26,7 @@ import numpy as np import pandas as pd from scipy.stats import special_ortho_group -from pyhegp.serialization import Summary, read_summary, write_summary, read_genotype, read_phenotype, write_genotype, write_phenotype, write_key, is_genotype_metadata_column +from pyhegp.serialization import Summary, read_summary, write_summary, read_genotype, read_phenotype, write_genotype, write_phenotype, read_key, write_key, is_genotype_metadata_column Stats = namedtuple("Stats", "n mean std") @@ -197,11 +197,14 @@ def pool_command(pooled_summary_file, summary_files): @click.argument("phenotype-file", type=click.File("r"), required=False) @click.option("--summary", "-s", "summary_file", type=click.File("rb"), help="Summary statistics file") -@click.option("--key", "-k", "key_file", type=click.File("w"), +@click.option("--key-in", "key_input_file", type=click.File("rb"), + help="Input key") +@click.option("--key-out", "-k", "key_output_file", type=click.File("w"), help="Output key") @click.option("--force", "-f", is_flag=True, help="Overwrite output files even if they exist") -def encrypt_command(genotype_file, phenotype_file, summary_file, key_file, force): +def encrypt_command(genotype_file, phenotype_file, summary_file, + key_input_file, key_output_file, force): def write_ciphertext(plaintext_path, writer): ciphertext_path = Path(plaintext_path + ".hegp") if ciphertext_path.exists() and not force: @@ -215,10 +218,13 @@ def encrypt_command(genotype_file, phenotype_file, summary_file, key_file, force summary = read_summary(summary_file) else: summary = genotype_summary(genotype) - key = random_key(np.random.default_rng(), - len(drop_metadata_columns(genotype).columns)) - if key_file: - write_key(key_file, key) + if key_input_file: + key = read_key(key_input_file) + else: + key = random_key(np.random.default_rng(), + len(drop_metadata_columns(genotype).columns)) + if key_output_file: + write_key(key_output_file, key) encrypted_genotype = encrypt_genotype(genotype, key, summary) if len(encrypted_genotype) < len(genotype): |