diff --git a/PanACoTA/subcommands/corepers.py b/PanACoTA/subcommands/corepers.py index 62756a8c677191fde6ca40deb986f175a6aaaebc..5104d1446fd42d8aabb027c413feaa49f1fe887a 100755 --- a/PanACoTA/subcommands/corepers.py +++ b/PanACoTA/subcommands/corepers.py @@ -144,6 +144,7 @@ def main(cmd, pangenome, tol, multi, mixed, outputdir, floor=False, verbose=0, q # Write persistent genome to file pers.write_persistent(fams, outputfile) logger.info("Persistent genome step done.") + return outputfile def get_info(tol, multi, mixed, floor): diff --git a/test/test_functional/test_corepers.py b/test/test_functional/test_corepers.py index 9d07b7999f5b76afe15585021d3f08d875b11567..6cb5b858bab57f5b790b0cfcb4cc117affd62f05 100755 --- a/test/test_functional/test_corepers.py +++ b/test/test_functional/test_corepers.py @@ -52,11 +52,11 @@ def test_main_default(capsys): multi = False mixed = False cmd = "cmd" - corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH) + out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_1.lst") + assert corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH) == out_pers # Check creation of binary file for pangenome, and remove it assert os.path.isfile(UPAN + ".bin") # Check presence of persistent genome, and its content, and remove it - out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_1.lst") exp_pers = os.path.join(EXP_PATH, "exp_coregenome.txt") assert os.path.isfile(out_pers) assert tutil.compare_order_content(out_pers, exp_pers) @@ -81,11 +81,11 @@ def test_main_pers(capsys): multi = False mixed = False cmd = "cmd" - corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH) + out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_0.99.lst") + assert corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH) == out_pers # Check creation of binary file for pangenome, and remove it assert os.path.isfile(UPAN + ".bin") # Check presence of persistent genome, and its content, and remove it - out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_0.99.lst") exp_pers = os.path.join(EXP_PATH, "exp_coregenome.txt") assert os.path.isfile(out_pers) assert tutil.compare_order_content(out_pers, exp_pers) @@ -117,11 +117,12 @@ def test_main_pers_floor_verbose2(capsys): floor = True cmd = "cmd" floor = True - corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH, floor=floor, verbose=2) + out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_F0.99.lst") + assert corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH, + floor=floor, verbose=2) == out_pers # Check creation of binary file for pangenome, and remove it assert os.path.isfile(UPAN + ".bin") # Check presence of persistent genome, and its content, and remove it - out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_F0.99.lst") exp_pers = os.path.join(EXP_PATH, "exp_pers-floor-strict.txt") assert os.path.isfile(out_pers) assert tutil.compare_order_content(out_pers, exp_pers) @@ -153,11 +154,12 @@ def test_main_pers_floor_mixed_debug(capsys): mixed = True floor = True cmd = "cmd" - corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH, floor=floor, verbose = 15) + out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_F0.99-mixed.lst") + assert corepers.main(cmd, UPAN, tol, multi, mixed, GENEPATH, + floor=floor, verbose = 15) == out_pers # Check creation of binary file for pangenome, and remove it assert os.path.isfile(UPAN + ".bin") # Check presence of persistent genome, and its content, and remove it - out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_F0.99-mixed.lst") exp_pers = os.path.join(EXP_PATH, "exp_pers-floor-mixed.txt") assert os.path.isfile(out_pers) assert tutil.compare_order_content(out_pers, exp_pers) @@ -191,11 +193,11 @@ def test_main_pers_floor_multi(capsys): floor = True cmd = "cmd" outdir = os.path.join(GENEPATH, "outdir") - corepers.main(cmd, UPAN, tol, multi, mixed, outdir, floor=floor) + out_pers = os.path.join(outdir, "PersGenome_pangenome.lst_F0.99-multi.lst") + assert corepers.main(cmd, UPAN, tol, multi, mixed, outdir, floor=floor) == out_pers # Check creation of binary file for pangenome, and remove it assert os.path.isfile(UPAN + ".bin") # Check presence of persistent genome, and its content, and remove it - out_pers = os.path.join(outdir, "PersGenome_pangenome.lst_F0.99-multi.lst") exp_pers = os.path.join(EXP_PATH, "exp_pers-floor-multi.txt") assert os.path.isfile(out_pers) assert tutil.compare_order_content(out_pers, exp_pers) @@ -237,9 +239,9 @@ def test_main_from_parse(capsys): corepers.main_from_parse(args) # Check creation of binary file for pangenome, and remove it + out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_1.lst") assert os.path.isfile(UPAN + ".bin") # Check presence of persistent genome, and its content, and remove it - out_pers = os.path.join(GENEPATH, "PersGenome_pangenome.lst_1.lst") exp_pers = os.path.join(EXP_PATH, "exp_coregenome.txt") assert os.path.isfile(out_pers) assert tutil.compare_order_content(out_pers, exp_pers)