Tests for additional problematic sites

Author: jeromekelleher

sc2ts/cli.py

@@ -201,7 +201,7 @@ def initialise(ts, match_db, additional_problematic_sites, verbose, log_file):
     additional_problematic = []
     if additional_problematic_sites is not None:
         additional_problematic = (
-            np.loadtxt(additional_problematic_sites).astype(int).tolist()
+            np.loadtxt(additional_problematic_sites, ndmin=1).astype(int).tolist()
         )
         logger.info(
             f"Excluding additional {len(additional_problematic)} problematic sites"

tests/test_cli.py

@@ -1,4 +1,4 @@
-
+import numpy as np
 import click.testing as ct
 import pytest
 import tskit
@@ -7,8 +7,8 @@
 from sc2ts import __main__ as main
 from sc2ts import cli
 
-class TestInitialise:
 
+class TestInitialise:
     def test_defaults(self, tmp_path):
         ts_path = tmp_path / "trees.ts"
         match_db_path = tmp_path / "match.db"
@@ -24,3 +24,23 @@ def test_defaults(self, tmp_path):
         other_ts.tables.assert_equals(ts.tables)
         match_db = sc2ts.MatchDb(match_db_path)
         assert len(match_db) == 0
+
+    @pytest.mark.parametrize("additional", [[100], [100, 200]])
+    def test_additional_problematic_sites(self, tmp_path, additional):
+        ts_path = tmp_path / "trees.ts"
+        match_db_path = tmp_path / "match.db"
+        problematic_path = tmp_path / "additional_problematic.txt"
+        np.savetxt(problematic_path, additional)
+        runner = ct.CliRunner(mix_stderr=False)
+        result = runner.invoke(
+            cli.cli,
+            f"initialise {ts_path} {match_db_path} "
+            f"--additional-problematic-sites {problematic_path}",
+            catch_exceptions=False,
+        )
+        assert result.exit_code == 0
+        ts = tskit.load(ts_path)
+        other_ts = sc2ts.initial_ts(additional_problematic_sites=additional)
+        other_ts.tables.assert_equals(ts.tables)
+        match_db = sc2ts.MatchDb(match_db_path)
+        assert len(match_db) == 0