From 7de52b9f08125a5228e3e5eb2d310d3f2223f172 Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Fri, 8 Sep 2023 20:18:54 +0100 Subject: [PATCH] Add clade annotation to plotting test --- python/gubbins/tests/test_python_scripts.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/gubbins/tests/test_python_scripts.py b/python/gubbins/tests/test_python_scripts.py index ef1ef641..ba01b905 100644 --- a/python/gubbins/tests/test_python_scripts.py +++ b/python/gubbins/tests/test_python_scripts.py @@ -151,9 +151,10 @@ def test_recombination_counting_per_gene(self): anno_input = os.path.join(data_dir, "test_annotation.gff") markup_input = os.path.join(data_dir, "test_markup.csv") meta_input = os.path.join(data_dir, "test_epi.csv") + clades_input = os.path.join(data_dir, "test_clades.csv") fig_output = os.path.join(data_dir, "test_plot.pdf") plot_cmd = "plot_gubbins.R --tree " + tree_input + " --rec " + rec_input + " --markup " + markup_input + " --annotation " + anno_input \ - + " --meta " + meta_input + " --output " + fig_output + + " --meta " + meta_input + " --clades " + clades_input + " --output " + fig_output subprocess.check_call(plot_cmd, shell=True) os.remove(fig_output)