Func test tree module when not verbose

test/test_functional/test_tree.py

@@ -121,6 +121,43 @@ def test_main_quicktree(capsys):
     assert "END" in out
 
 
+def test_main_quicktree_notverbose(capsys):
+    """
+    Test that when giving the alignment file, running with quicktree, no bootstraps,
+    it creates expected files
+    """
+    outdir = GENEPATH
+    soft = "quicktree"
+    model = None
+    threads = 1
+    cmd = "cmd: test_main_quicktree"
+    tree.main(cmd, ALIGNMENT, outdir, soft, model, threads)
+    # Check output files
+    # stockholm alignments
+    stockholm = os.path.join(outdir, "exp_pers4genomes.grp.aln.stockholm")
+    assert os.path.isfile(stockholm)
+    # quicktree logfile
+    log_file = stockholm + ".quicktree.log"
+    assert os.path.isfile(log_file)
+    with open(log_file, "r") as logf:
+        assert logf.readlines() == []
+    # tree file
+    tree_file = stockholm + ".quicktree_tree.nwk"
+    assert os.path.isfile(tree_file)
+    assert tutils.is_tree_lengths(tree_file)
+    assert not tutils.is_tree_bootstrap(tree_file)
+    # log files
+    logs_base = os.path.join(outdir, "PanACoTA-tree-quicktree.log")
+    assert os.path.isfile(logs_base)
+    assert os.path.isfile(logs_base + ".details")
+    assert os.path.isfile(logs_base + ".err")
+    # Check logs
+    out, err = capsys.readouterr()
+    assert "Converting fasta alignment to stockholm format." in out
+    assert "Running Quicktree..." in out
+    assert "END" in out
+
+
 def test_main_fastme(capsys):
     """
     Test that when giving the alignment file, running with fastme, no bootstraps,