Add output to query, and clarify semantics of -l

tests/test_cli.py

@@ -122,3 +122,26 @@ def test_path_required(self):
     def test_list(self, vcz_path):
         result = run_vcztools(f"query -l {vcz_path}")
         assert list(result.splitlines()) == ["NA00001", "NA00002", "NA00003"]
+
+    def test_list_ignores_output(self, vcz_path, tmp_path):
+        output = tmp_path / "tmp.txt"
+        result = run_vcztools(f"query -l {vcz_path} -o {output}")
+        assert list(result.splitlines()) == ["NA00001", "NA00002", "NA00003"]
+        assert not output.exists()
+
+    def test_output(self, vcz_path, tmp_path):
+        output = tmp_path / "tmp.txt"
+        result = run_vcztools(f"query -f '%POS\n' {vcz_path} -o {output}")
+        assert list(result.splitlines()) == []
+        assert output.exists()
+
+
+def test_top_level():
+    runner = ct.CliRunner(mix_stderr=False)
+    result = runner.invoke(
+        cli.vcztools_main,
+        catch_exceptions=False,
+    )
+    assert result.exit_code == 0
+    assert len(result.stdout) > 0
+    assert len(result.stderr) == 0

vcztools/cli.py

@@ -34,6 +34,13 @@ def handle_broken_pipe(output):
 exclude = click.option(
     "-e", "--exclude", type=str, help="Filter expression to exclude variant sites."
 )
+output = click.option(
+    "-o",
+    "--output",
+    type=click.File("w"),
+    default="-",
+    help="File path to write output to (defaults to stdout '-').",
+)
 
 
 class NaturalOrderGroup(click.Group):
@@ -68,6 +75,7 @@ def index(path, nrecords, stats):
 
 @click.command
 @click.argument("path", type=click.Path())
+@output
 @click.option(
     "-l",
     "--list-samples",
@@ -83,27 +91,25 @@ def index(path, nrecords, stats):
 )
 @include
 @exclude
-def query(path, list_samples, format, include, exclude):
+def query(path, output, list_samples, format, include, exclude):
     if list_samples:
-        query_module.list_samples(path)
+        # bcftools query -l ignores the --output option and always writes to stdout
+        output = sys.stdout
+        with handle_broken_pipe(output):
+            query_module.list_samples(path, output)
         return
+
     if format is None:
         raise click.UsageError("Missing option -f / --format")
-
-    query_module.write_query(
-        path, query_format=format, include=include, exclude=exclude
-    )
+    with handle_broken_pipe(output):
+        query_module.write_query(
+            path, output, query_format=format, include=include, exclude=exclude
+        )
 
 
 @click.command
 @click.argument("path", type=click.Path())
-@click.option(
-    "-o",
-    "--output",
-    type=click.File("w"),
-    default="-",
-    help="File path to write output to (defaults to stdout '-').",
-)
+@output
 @click.option(
     "-h",
     "--header-only",

vcztools/query.py

@@ -9,15 +9,14 @@
 
 from vcztools import constants
 from vcztools.filter import FilterExpressionEvaluator, FilterExpressionParser
-from vcztools.utils import open_file_like, vcf_name_to_vcz_name
+from vcztools.utils import vcf_name_to_vcz_name
 
 
-def list_samples(vcz_path, output=None):
+def list_samples(vcz_path, output):
     root = zarr.open(vcz_path, mode="r")
 
-    with open_file_like(output) as output:
-        sample_ids = root["sample_id"][:]
-        print("\n".join(sample_ids), file=output)
+    sample_ids = root["sample_id"][:]
+    print("\n".join(sample_ids), file=output)
 
 
 class QueryFormatParser:
@@ -328,7 +327,7 @@ def generate(root) -> str:
 
 def write_query(
     vcz,
-    output=None,
+    output,
     *,
     query_format: str,
     include: Optional[str] = None,
@@ -342,6 +341,5 @@ def write_query(
     root = zarr.open(vcz, mode="r")
     generator = QueryFormatGenerator(query_format, include=include, exclude=exclude)
 
-    with open_file_like(output) as output:
-        for result in generator(root):
-            print(result, sep="", end="", file=output)
+    for result in generator(root):
+        print(result, sep="", end="", file=output)