TEST: Make sure error is raised on bad input

ukbparse/tests/test_main.py

@@ -1338,3 +1338,76 @@ def test_main_indexes():
             expdf.columns    = expcols
 
             assert np.all(df[expcols] == expdf[expcols])
+
+
+@patch_logging
+def test_main_bad_inputs():
+
+    data = tw.dedent("""
+    eid,col1
+    1,10
+    2,20
+    3,30
+    4,40
+    5,50
+    """)
+
+    badfile1 = tw.dedent("""
+    a
+    1
+    2
+    3
+    """)
+
+    badfile2 = tw.dedent("""
+    1
+    a
+    3
+    """)
+
+    with tempdir():
+        with open('data.txt',     'wt') as f: f.write(data)
+        with open('badfile1.txt', 'wt') as f: f.write(badfile1)
+        with open('badfile2.txt', 'wt') as f: f.write(badfile2)
+
+        with pytest.raises(Exception):
+            main.main('out.tsv nofile')
+
+        with pytest.raises(Exception):
+            main.main('-v foo out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-v 1,foo,3 out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-v 1:foo:3 out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-v nofile out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-v badfile1.txt sout.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-v badfile2.txt sout.tsv data.txt')
+
+        with pytest.raises(Exception):
+            main.main('-s foo out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-s 1,foo,3 out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-s 1:foo:3 out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-s nofile out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-s badfile1.txt sout.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-s badfile2.txt sout.tsv data.txt')
+
+        with pytest.raises(Exception):
+            main.main('-ex foo out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-ex 1,foo,3 out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-ex 1:foo:3 out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-ex nofile out.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-ex badfile1.txt sout.tsv data.txt')
+        with pytest.raises(Exception):
+            main.main('-ex badfile2.txt sout.tsv data.txt')