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| author | Arun Isaac | 2025-09-02 21:35:29 +0100 |
|---|---|---|
| committer | Arun Isaac | 2025-09-02 22:32:03 +0100 |
| commit | 5d0eca109a50e2349a35571577b14589cb5b75a9 (patch) | |
| tree | ba6dc7ceacdac66e962f5527a7e7e41c197e2102 | |
| parent | 831f3da094834547fd9a2d357a8006c065a85289 (diff) | |
| download | pyhegp-5d0eca109a50e2349a35571577b14589cb5b75a9.tar.gz pyhegp-5d0eca109a50e2349a35571577b14589cb5b75a9.tar.lz pyhegp-5d0eca109a50e2349a35571577b14589cb5b75a9.zip | |
Rename cat subcommand to cat-genotype.
A cat-phenotype subcommand is coming. Hence rename this.
| -rw-r--r-- | README.md | 2 | ||||
| -rw-r--r-- | pyhegp/pyhegp.py | 4 | ||||
| -rw-r--r-- | tests/test_pyhegp.py | 2 |
3 files changed, 4 insertions, 4 deletions
diff --git a/README.md b/README.md index ee7057f..2b3ab5d 100644 --- a/README.md +++ b/README.md @@ -87,7 +87,7 @@ pyhegp encrypt -s complete-summary genotype.tsv ``` Finally, the data owners share the encrypted data `genotype.tsv.hegp` with the broker who concatenates it and shares it with all parties. ``` -pyhegp cat -o complete-genotype.tsv.hegp genotype1.tsv.hegp genotype2.tsv.hegp ... +pyhegp cat-genotype -o complete-genotype.tsv.hegp genotype1.tsv.hegp genotype2.tsv.hegp ... ``` Note that all data sharing is carried out-of-band and is outside the scope of `pyhegp`. diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py index 98e904c..8217040 100644 --- a/pyhegp/pyhegp.py +++ b/pyhegp/pyhegp.py @@ -187,13 +187,13 @@ def encrypt_command(genotype_file, summary_file, key_file): with ciphertext_path.open("w") as ciphertext_file: write_genotype(ciphertext_file, encrypted_genotype) -@main.command("cat") +@main.command("cat-genotype") @click.option("--output", "-o", "output_file", type=click.File("wb"), default="-", help="output file") @click.argument("ciphertext-files", type=click.File("rb"), nargs=-1) -def cat_command(output_file, ciphertext_files): +def cat_genotype_command(output_file, ciphertext_files): write_genotype(output_file, cat_genotype([read_genotype(file) for file in ciphertext_files])) diff --git a/tests/test_pyhegp.py b/tests/test_pyhegp.py index 88f13ef..d34c331 100644 --- a/tests/test_pyhegp.py +++ b/tests/test_pyhegp.py @@ -221,7 +221,7 @@ def test_joint_workflow(tmp_path): assert ciphertext.exists() complete_ciphertext = tmp_path / "complete-genotype.tsv.hegp" result = runner.invoke( - main, ["cat", + main, ["cat-genotype", "-o", complete_ciphertext, *(str(tmp_path / f"genotype{i}.tsv.hegp") for i in range(4))]) assert result.exit_code == 0 |