Add stdin support to the tskit CLI

python/CHANGELOG.rst

@@ -2,6 +2,11 @@
 [1.0.4] - 2026-XX-XX
 --------------------
 
+**Features**
+
+- CLI commands that load a tree sequence now accept ``-`` as the input path to
+  read from stdin. (:issue:`3468`)
+
 --------------------
 [1.0.3] - 2026-05-14
 --------------------

python/tests/test_cli.py

@@ -73,6 +73,11 @@ def capture_output(func, *args, **kwargs):
     return stdout_output, stderr_output
 
 
+class MockStdIn:
+    def __init__(self, buffer):
+        self.buffer = buffer
+
+
 class TestCli(unittest.TestCase):
     """
     Superclass of tests for the CLI needing temp files.
@@ -310,6 +315,16 @@ def test_vcf_allow_position_zero(self, flags, expected):
         assert args.tree_sequence == tree_sequence
         assert args.allow_position_zero == expected
 
+    def test_vcf_stdin_file(self):
+        parser = cli.get_tskit_parser()
+        args = parser.parse_args(["vcf", "-"])
+        assert args.tree_sequence == "-"
+
+    def test_vcf_requires_tree_sequence(self):
+        parser = cli.get_tskit_parser()
+        with pytest.raises(SystemExit):
+            parser.parse_args(["vcf"])
+
     def test_info_default_values(self):
         parser = cli.get_tskit_parser()
         cmd = "info"
@@ -560,6 +575,13 @@ def test_vcf(self):
         assert len(stderr) == 0
         self.verify_vcf(stdout)
 
+    def test_vcf_stdin(self):
+        with open(self._tree_sequence_file, "rb") as f:
+            with mock.patch("sys.stdin", MockStdIn(f)):
+                stdout, stderr = capture_output(cli.tskit_main, ["vcf", "-0", "-"])
+        assert len(stderr) == 0
+        self.verify_vcf(stdout)
+
     def verify_info(self, ts, output_info):
         assert str(ts) == output_info
 

python/tskit/cli.py

@@ -45,10 +45,15 @@ def sys_exit(message):
 
 
 def load_tree_sequence(path):
+    if path in [None, "-"]:
+        path = getattr(sys.stdin, "buffer", sys.stdin)
     try:
         return tskit.load(path)
-    except OSError as e:
-        sys_exit(f"Load error: {e}")
+    except (OSError, EOFError, tskit.FileFormatError) as e:
+        message = str(e)
+        if isinstance(e, EOFError) and len(message) == 0:
+            message = "End of file"
+        sys_exit(f"Load error: {message}")
 
 
 def run_info(args):
@@ -134,7 +139,10 @@ def run_vcf(args):
 
 
 def add_tree_sequence_argument(parser):
-    parser.add_argument("tree_sequence", help="The tskit tree sequence file")
+    parser.add_argument(
+        "tree_sequence",
+        help="The tskit tree sequence file, or '-' for stdin",
+    )
 
 
 def add_precision_argument(parser):