diff --git a/test/test_unit/test_pangenome/test_mmseq_func.py b/test/test_unit/test_pangenome/test_mmseq_func.py index 225e2694ed1faabb0ed65096c3338f8ccccb393b..0ea678feb2f0afd9e03c1e92deca470753dfefbd 100755 --- a/test/test_unit/test_pangenome/test_mmseq_func.py +++ b/test/test_unit/test_pangenome/test_mmseq_func.py @@ -50,6 +50,7 @@ def setup_teardown_module(): os.remove(f) print("teardown") + # Clusters expected for the given databank (ref: [members] EXP_CLUSTERS = {"GEN2.1017.00001.i0002_00004": ["GEN2.1017.00001.i0002_00004", "GEN4.1111.00001.i0001_00002", @@ -232,7 +233,6 @@ def test_create_mmseqdb_not_all_exist(caplog): assert caplog.records[8].levelname == "DETAIL" - def test_do_mmseqdb_existok(caplog): """ Check that, when trying to run create_mmseqs_db while all output files already exist, @@ -250,12 +250,12 @@ def test_do_mmseqdb_existok(caplog): # Check files created/existing for file in [filename + ext for ext in outext]: assert os.path.isfile(file) - assert ("Creating database") in caplog.text + # assert ("Creating database") in caplog.text assert ("mmseqs database " "test/data/pangenome/generated_by_unit-tests/test_create_mmseqsdb_exist.msdb " "already exists. The program will use it.") in caplog.text - assert caplog.records[0].levelname == "INFO" - assert caplog.records[1].levelname == "WARNING" + # assert caplog.records[0].levelname == "INFO" + assert caplog.records[0].levelname == "WARNING" def test_do_mmseqdb_quiet(caplog): @@ -412,7 +412,7 @@ def test_mmseq2pan_givenout(): break assert found exp_pan = os.path.join(PATH_EXP_FILES, "exp_pangenome-4genomes.lst") - #Check that families written in output file are as expected + # Check that families written in output file are as expected with open(exp_pan, "r") as ep, open(outfile, "r") as pan: lines_exp = [] lines_out = [] @@ -593,7 +593,7 @@ def test_do_pangenome_justdone_panexists(caplog): -> removes mmseqs_clust to rerun it -> check content of generated panfile """ - caplog.set_level(15) # set level to detail + caplog.set_level(15) # set level to detail outdir = os.path.join(GENEPATH, "test_do_pangenome_outdir_exist") prt_bank = "exp_EXEM.All.prt" mmseqdb = os.path.join(PATH_TEST_FILES, "mmseq_db") @@ -626,7 +626,7 @@ def test_do_pangenome_justdone_panexists(caplog): found = True break assert found - # Check content of output pangenome file. Should contain families, and not empty + # Check content of output pangenome file. Should contain families, and not empty # as it was before running do_pangenome exp_pan = os.path.join(PATH_EXP_FILES, "exp_pangenome-4genomes.lst") with open(exp_pan, "r") as ep, open(panfile, "r") as pan: @@ -947,7 +947,7 @@ def test_run_all_pangenome_panexists_wrong(caplog): open(panfile_out, "w").close() with pytest.raises(SystemExit): mmseqs.run_all_pangenome(min_id, clust_mode, outdir, prt_path, - threads, panfile=panfile, quiet=quiet) + threads, panfile=panfile, quiet=quiet) # check that tmp dir was created and not empty tmp_dir = os.path.join(outdir, "tmp_exp_EXEM.All.prt_0.8-mode1")