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| author | Arun Isaac | 2026-08-14 22:09:21 +0100 |
|---|---|---|
| committer | Arun Isaac | 2026-08-15 20:53:15 +0100 |
| commit | a7806b70c6d651acfdbbaeaa986b4bd28f1d685a (patch) | |
| tree | c2f18c4ddfbb1564b19593815d994929dfdee2d7 | |
| parent | bc371f2374156b7f6593ef0287bfb52b478ed92e (diff) | |
| download | domagi-a7806b70c6d651acfdbbaeaa986b4bd28f1d685a.tar.gz domagi-a7806b70c6d651acfdbbaeaa986b4bd28f1d685a.tar.lz domagi-a7806b70c6d651acfdbbaeaa986b4bd28f1d685a.zip | |
Add domagi overlap --paths.
| -rw-r--r-- | doc/domagi-overlap.dbk | 5 | ||||
| -rw-r--r-- | domagi/domagi.py | 8 | ||||
| -rw-r--r-- | tests/test_domagi.py | 17 |
3 files changed, 29 insertions, 1 deletions
diff --git a/doc/domagi-overlap.dbk b/doc/domagi-overlap.dbk index e8e40e7..657e664 100644 --- a/doc/domagi-overlap.dbk +++ b/doc/domagi-overlap.dbk @@ -13,6 +13,11 @@ <term><option>--path=<replaceable>PATH</replaceable></option></term> <listitem><para>Find paths touched by <replaceable>PATH</replaceable>. This argument may be specified more than once to find paths touched by more than one path.</para></listitem> </varlistentry> + <varlistentry> + <term><option>-R <replaceable>FILE</replaceable></option></term> + <term><option>--paths=<replaceable>FILE</replaceable></option></term> + <listitem><para>Find paths touched by paths listed in <replaceable>FILE</replaceable>, one per line.</para></listitem> + </varlistentry> <xi:include href="threads-argument.dbk" /> <xi:include href="help-option.dbk" /> </variablelist> diff --git a/domagi/domagi.py b/domagi/domagi.py index faa7429..77d28b9 100644 --- a/domagi/domagi.py +++ b/domagi/domagi.py @@ -267,9 +267,15 @@ def matrix(con, threads): multiple=True, metavar="PATH", help="find paths touched by PATH") +@click.option("-R", "--paths", "paths_file", + type=click.File(), + metavar="FILE", + help="find paths touched by paths listed in FILE") @common_options -def overlap(con, paths, threads): +def overlap(con, paths, paths_file, threads): set_duckdb_threads(con, threads) + if paths_file: + paths = [line.rstrip() for line in paths_file.readlines()] (con.execute(read_sql("overlap.sql"), [paths]) .fetchdf() .to_csv(sys.stdout, sep="\t", index=False)) diff --git a/tests/test_domagi.py b/tests/test_domagi.py index d678a3f..757d1ec 100644 --- a/tests/test_domagi.py +++ b/tests/test_domagi.py @@ -214,6 +214,23 @@ def test_domagi_overlap(tmp_path, test_data_file, expected_output): .sort_values(by=["#path", "path.touched"], ignore_index=True), check_dtype=False) + # Test passing in the paths through a file. + paths_file = tmp_path / "paths" + with open(paths_file, "w") as file: + for path in paths: + print(path, file=file) + result = runner.invoke(main, ["overlap", + "--db", duckdb_path, + "--paths", paths_file]) + assert result.exit_code == 0 + assert_frame_equal(pd.read_csv(expected_output, sep="\t") + .sort_values(by=["#path", "path.touched"], + ignore_index=True), + pd.read_csv(io.StringIO(result.stdout), + sep="\t") + .sort_values(by=["#path", "path.touched"], + ignore_index=True), + check_dtype=False) @pytest.mark.parametrize("test_data_file, expected_output", [(Path("test-data/test1.gfa"), |