diff --git a/test/test_functional/test_annote-parser.py b/test/test_functional/test_annote-parser.py index 4f7a29bb95b8791689697bbe880b630e557626c7..de6c182bc0be6c89eeba9fb7f067b36214efb391 100755 --- a/test/test_functional/test_annote-parser.py +++ b/test/test_functional/test_annote-parser.py @@ -46,10 +46,21 @@ def test_parser_noarg(capsys): with pytest.raises(SystemExit): annot.parse(parser, "".split()) _, err = capsys.readouterr() - assert "[-d DB_PATH] -r RES_PATH [-l LIST_FILE] [-n NAME] [-Q]" in err - assert "[--info FROM_INFO] [--prodigal] [--small] [--l90 L90]" in err - assert "[--nbcont NBCONT] [--cutn CUTN] [--date DATE] [--tmp TMPDIR]" in err - assert "[--annot_dir ANNOTDIR] [-F] [--threads THREADS] [-v]" in err + assert "[-d DB_PATH]" in err + assert "-r RES_PATH " in err + assert "[-l LIST_FILE] [-n NAME] [-Q]" in err + assert "[--info FROM_INFO]" in err + assert "[--prodigal]" in err + assert "[--small]" in err + assert "[--l90 L90]" in err + assert "[--nbcont NBCONT]" in err + assert "[--cutn CUTN]" in err + assert "[--date DATE]" in err + assert "[--tmp TMPDIR]" in err + assert "[--annot_dir ANNOTDIR]" in err + assert "[-F]" in err + assert "[--threads THREADS]" in err + assert "[-v]" in err assert "[-q] [-h]" in err assert "the following arguments are required: -r" in err @@ -285,6 +296,7 @@ def test_parser_info_cutn(capsys): "PanACoTA will use the given sequences as is. It will not cut them. So, you cannot " "use both --cutn and --info.") in err + def test_info_and_lstfile(capsys): """ Test that there is an error message if user gives both -l infofile and --info LSTINFO @@ -353,8 +365,8 @@ def test_parser_small_noprodigal(capsys): with pytest.raises(SystemExit): annot.parse(parser, "-r respath -n name --small".split()) _, err = capsys.readouterr() - assert("You cannot use --small option with prokka. " - "Either use prodigal, or remove this option") in err + assert ("You cannot use --small option with prokka. " + "Either use prodigal, or remove this option") in err def test_parser_filter(capsys): @@ -376,11 +388,10 @@ def test_parser_filter(capsys): assert not options.force assert options.qc_only stdout, _ = capsys.readouterr() - assert(" !! Your genomes will be filtered, and only the ones with 'L90' <= 10 and 'number of contigs' < 999 " - "will be kept. If you want to change those thresholds, use '--l90' and '--nbcont' options.") in stdout - assert("! Your genomes will be split when sequence contains at least 5'N' in a row. " - "If you want to change this threshold, see --cutn option.") in stdout - + assert (" !! Your genomes will be filtered, and only the ones with 'L90' <= 10 and 'number of contigs' < 999 " + "will be kept. If you want to change those thresholds, use '--l90' and '--nbcont' options.") in stdout + assert ("! Your genomes will be split when sequence contains at least 5'N' in a row. " + "If you want to change this threshold, see --cutn option.") in stdout def test_parser_nosplit(capsys): diff --git a/test/test_functional/test_pangenome-parser.py b/test/test_functional/test_pangenome-parser.py index a14b349a1caafefdde5c6502758078d55fe68150..1f87175b582a13c6d0c1c131f55ce96a1ce8651f 100755 --- a/test/test_functional/test_pangenome-parser.py +++ b/test/test_functional/test_pangenome-parser.py @@ -29,7 +29,8 @@ def test_parser_noarg(capsys): assert " -o OUTDIR" in err assert "[-f OUTFILE]" in err assert " [-c {0,1,2}]" in err - assert "[-s SPEDIR] [--threads THREADS] [-v]" in err + assert "[-s SPEDIR]" in err + assert "[--threads THREADS]" in err assert "[-q] [-h]" in err assert "the following arguments are required: -l, -n, -d, -o" in err @@ -111,7 +112,8 @@ def test_thread_too_many(capsys): parser = argparse.ArgumentParser(description="Do pangenome", add_help=False) pangenome.build_parser(parser) with pytest.raises(SystemExit): - pangenome.parse(parser, f"-l lstinfo -n TEST4 -d dbpath -o od --threads {nb_cpu*10}".split()) + pangenome.parse( + parser, f"-l lstinfo -n TEST4 -d dbpath -o od --threads {nb_cpu*10}".split()) _, err = capsys.readouterr() assert ("You have {} threads on your computer, you cannot ask for more: " "invalid value: {}").format(nb_cpu, nb_cpu*10) in err diff --git a/test/test_functional/test_tree-parser.py b/test/test_functional/test_tree-parser.py index 74f99d54dc523da622dd8e6b82c5d3d12b3fb808..431e3e46259c3d73201dfd3c723cadb758a44891 100755 --- a/test/test_functional/test_tree-parser.py +++ b/test/test_functional/test_tree-parser.py @@ -23,13 +23,15 @@ def test_parser_noarg(capsys): _, err = capsys.readouterr() assert "usage: " in err assert "-a ALIGNMENT -o OUTDIR" in err - assert "[-s {fasttree,fastme,quicktree,iqtree,iqtree2}] [-b BOOT]" in err - assert "[--threads THREADS] [-m MODEL]" in err + assert "[-s {fasttree,fastme,quicktree,iqtree,iqtree2}]" in err + assert "[-b BOOT]" in err + assert "[--threads THREADS]" in err + assert "[-m MODEL]" in err assert "--mem MEMORY" in err assert "-B" in err assert "-M" in err assert "[-v]" in err - assert "[-q] [-h]" in err + assert "[-q]" in err assert "the following arguments are required: -a, -o" in err