diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py
index 51baddb41a538e7351288b023a3b5a7315d2e7ff..ad4ed1470688c5474d7aaed14ebb1ff4bc3ea71c 100755
--- a/PanACoTA/subcommands/annotate.py
+++ b/PanACoTA/subcommands/annotate.py
@@ -352,7 +352,7 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn
if not kept_genomes:
logger.info("No genome kept for annotation.")
- return 0
+ return "", 0
# Info on folder containing original sequences
if not from_info:
logger.info(f"-> Original sequences folder ('orig_name' column): {db_path} ")
@@ -372,7 +372,7 @@ def main(cmd, list_file, db_path, res_dir, name, date, l90=100, nbcont=999, cutn
# orig_name, to_annnote, gsize, nb_conts, L90
utils.write_genomes_info(genomes, [], list_file, res_dir, qc=True)
logger.info("QC only done.")
- return 0
+ return "", 0
# STEP 3. Rename genomes kept, ordered by decreasing quality
gfunc.rename_all_genomes(kept_genomes)
diff --git a/test/test_functional/test_annote.py b/test/test_functional/test_annote.py
index e4c3ca1c21d6124c2010968289cc6f30d02ca45c..40547be15f40ed35977c7100f1bb658c12cb05d1 100755
--- a/test/test_functional/test_annote.py
+++ b/test/test_functional/test_annote.py
@@ -126,8 +126,9 @@ def test_main_given_tmp_verbose3(capsys):
l90 = 10
date = "0417"
verbose = 3
- annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90,
- cutn=3, tmp_dir=tmpdir, verbose=verbose)
+ info_file = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-default.lst")
+ assert annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90,
+ cutn=3, tmp_dir=tmpdir, verbose=verbose) == (info_file, 3)
out, err = capsys.readouterr()
# Check that warnings are written to stderr
assert "WARNING" in err
@@ -164,7 +165,8 @@ def test_main_all_discard_nbcont(capsys):
nbcont = 0
cutn = 0
date = "0417"
- annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, nbcont=nbcont, cutn=cutn)
+ assert annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, nbcont=nbcont,
+ cutn=cutn) == ("", 0)
# check that there are the 2 concatenated genomes in tmppath.
# The third genome is listfile is composed of only 1 file, so no need to concatenate, nor
# to change the file as we do not use cutn
@@ -189,8 +191,8 @@ def test_main_qc():
date = "0417"
force = False
qc_only = True
- annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90=l90,
- cutn=cutn, qc_only=qc_only)
+ assert annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90=l90,
+ cutn=cutn, qc_only=qc_only) == ("", 0)
# Check files are here
lstfile = os.path.join(GENEPATH, "ALL-GENOMES-info-list_genomes-func-test-default.lst")
exp_lstfile = os.path.join(EXP_DIR, "exp_ALL-GENOMES-QC.lst")
@@ -223,13 +225,14 @@ def test_main_existresdirforce(capsys):
date = "0417"
l90 = 5
cutn = 3
- annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, force=True, l90=l90,
- prodigal_only=True, cutn = cutn, small=True)
+ info_file = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-default.lst")
+ assert annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, force=True, l90=l90,
+ prodigal_only=True, cutn = cutn, small=True) == (info_file, 4)
out, err = capsys.readouterr()
# Check that tmp files exist in the right folder
# -> 2 fna files created (concatenations)
- # -> + 3 files created (split 5N)
+ # -> + 4 files created (split 3N)
assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "A_H738.fasta-all.fna"))
assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "H299_H561.fasta-all.fna"))
assert len(glob.glob(os.path.join(GENEPATH, "tmp_files", '*.fna'))) == 6
@@ -296,14 +299,14 @@ def test_main_onexistingprokkadir(capsys):
list_file = os.path.join(TEST_DIR, "list_genomes-func-test-exist_dir.txt")
name = "ESCO"
date = "0417"
- annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, cutn=0, res_annot_dir=EXP_DIR,
- verbose=3)
+ lstout = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-exist_dir.lst")
+ lstexp = os.path.join(EXP_DIR, "exp_LSTINFO-func-annot_exists-prokkadir.lst")
+ assert annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, cutn=0,
+ res_annot_dir=EXP_DIR, verbose=3) == (lstout, 2)
out, err = capsys.readouterr()
# Check that tmp files folder is empty (prokka res are somewhere else)
assert len(os.listdir(os.path.join(GENEPATH, "tmp_files"))) == 0
# Test that result files are in result dir
- lstout = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-exist_dir.lst")
- lstexp = os.path.join(EXP_DIR, "exp_LSTINFO-func-annot_exists-prokkadir.lst")
assert os.path.isfile(lstout)
assert tutil.compare_order_content(lstout, lstexp)
logfile = os.path.join(GENEPATH,
@@ -335,14 +338,14 @@ def test_main_onexistingprodigaldir(capsys):
list_file = os.path.join(TEST_DIR, "list_genomes-func-test-exist_dir.txt")
name = "ESCO"
date = "0417"
- annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, cutn=0, res_annot_dir=EXP_DIR,
- verbose=3, prodigal_only=True)
+ lstout = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-exist_dir.lst")
+ lstexp = os.path.join(EXP_DIR, "exp_LSTINFO-func-annot_exists-prokkadir.lst")
+ assert annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, cutn=0,
+ res_annot_dir=EXP_DIR, verbose=3, prodigal_only=True) == (lstout, 2)
out, err = capsys.readouterr()
# Check that tmp files folder is empty (prokka res are somewhere else)
assert len(os.listdir(os.path.join(GENEPATH, "tmp_files"))) == 0
# Test that result files are in result dir
- lstout = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-exist_dir.lst")
- lstexp = os.path.join(EXP_DIR, "exp_LSTINFO-func-annot_exists-prokkadir.lst")
assert os.path.isfile(lstout)
assert tutil.compare_order_content(lstout, lstexp)
logfile = os.path.join(GENEPATH,
@@ -390,8 +393,9 @@ def test_main_existing_prokkadir_errorannot():
# # Run annotation
name = "ESCO"
date = "0417"
- annot.main("cmd", list_file, genome_path_used, GENEPATH, name, date, cutn=0,
- res_annot_dir=genome_path_used)
+ info_file = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-exist_dir.lst")
+ assert annot.main("cmd", list_file, genome_path_used, GENEPATH, name, date, cutn=0,
+ res_annot_dir=genome_path_used) == (info_file, 1)
# Check that only 1 genome was formated (the other one had problems with prokka)
prot_dir = os.path.join(GENEPATH, "Proteins")
@@ -515,8 +519,9 @@ def test_main_existing_prokkadir_errorformat():
# Run annotation
name = "ESCO"
date = "0417"
- annot.main("cmd", list_file, genome_path_used, GENEPATH, name, date, cutn=0,
- res_annot_dir=genome_path_used)
+ info_file = os.path.join(GENEPATH, "LSTINFO-list_genomes-func-test-exist_dir.lst")
+ assert annot.main("cmd", list_file, genome_path_used, GENEPATH, name, date, cutn=0,
+ res_annot_dir=genome_path_used) == (info_file, 1)
# Check that genome 1 is not formatted, while no error with prokka
logfile = os.path.join(GENEPATH,
@@ -547,8 +552,9 @@ def test_main_frominfo(capsys):
name = "TOTO"
date = "1205"
infofile = os.path.join(TEST_DIR, "lstinfo.lst")
- annot.main("cmd", listfile, dbpath, GENEPATH, name, date, from_info=infofile,
- prodigal_only=True, small=True)
+ out_infofile = os.path.join(GENEPATH, "LSTINFO-lstinfo.lst")
+ assert annot.main("cmd", listfile, dbpath, GENEPATH, name, date, from_info=infofile,
+ prodigal_only=True, small=True) == (out_infofile, 3)
out, err = capsys.readouterr()
# Check logs
assert ("Generating distribution of L90 and #contigs graphs.") in out