From 9e67ecf82f7ecb7244070dc31b818a09399beed0 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Fri, 23 Oct 2020 19:33:21 +0200 Subject: [PATCH] Func test tree module when not verbose --- test/test_functional/test_tree.py | 37 +++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/test/test_functional/test_tree.py b/test/test_functional/test_tree.py index 72758e21..df0b9867 100755 --- a/test/test_functional/test_tree.py +++ b/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, -- GitLab