diff --git a/PanACoTA/annotate_module/genome_seq_functions.py b/PanACoTA/annotate_module/genome_seq_functions.py
index 269f660251a727206e9baf50475fa08b86c661d6..e09697e5d1def7dd205ecb44634059a30369bdc8 100755
--- a/PanACoTA/annotate_module/genome_seq_functions.py
+++ b/PanACoTA/annotate_module/genome_seq_functions.py
@@ -188,7 +188,7 @@ def analyse_genome(genome, dbpath, tmp_path, cut, pat, genomes, soft, logger):
if line.startswith(">"):
# If not first contig, write info to output file (if needed)
if cur_seq != "":
- num = format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes,
+ num = format_contig(cut, pat, cur_seq, cur_contig_name, genome, contig_sizes,
gresf, num, logger)
# If problem while formatting contig, return False -> genome ignored
if num == -1:
@@ -205,7 +205,7 @@ def analyse_genome(genome, dbpath, tmp_path, cut, pat, genomes, soft, logger):
# LAST CONTIG
if cur_contig_name != "":
- num = format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, gresf,
+ num = format_contig(cut, pat, cur_seq, cur_contig_name, genome, contig_sizes, gresf,
num, logger)
if num == -1:
return False
@@ -274,7 +274,7 @@ def get_output_dir(soft, dbpath, tmp_path, genome, cut, pat):
return gpath, grespath
-def format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, gresf, num, logger):
+def format_contig(cut, pat, cur_seq, cur_contig_name, genome, contig_sizes, gresf, num, logger):
"""
Format given contig, and save to output file if needed
@@ -291,6 +291,8 @@ def format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, gresf, num,
current sequence (aa)
cur_contig_name : str
name of current contig
+ genome : str
+ name of current genome
cont_sizes : dict
{contig_name : sequence length}
gresf : io.TextIOWrappe
@@ -313,9 +315,9 @@ def format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, gresf, num,
# No cut -> no new file created, but check contig unique names
else:
if cur_contig_name in contig_sizes.keys():
- logger.error("{} contig name is used for several contigs. Please put "
- "different names for each contig. This genome will be "
- "ignored.".format(cur_contig_name))
+ logger.error(f"In genome {genome}, '{cur_contig_name}' contig name is used for "
+ "several contigs. Please put different names for each contig. "
+ "This genome will be ignored.")
return -1
else:
contig_sizes[cur_contig_name] = len(cur_seq)
diff --git a/test/test_unit/test_annotate/test_genome_func.py b/test/test_unit/test_annotate/test_genome_func.py
index b17924218c33dc9c60616fc9ea55411ac11eec08..e362b732e76f9449d68baf14829e23084b2769b8 100755
--- a/test/test_unit/test_annotate/test_genome_func.py
+++ b/test/test_unit/test_annotate/test_genome_func.py
@@ -203,7 +203,7 @@ def test_format_contig_cut():
gresf = open(resfile, "w")
num = 2
- assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, gresf,
+ assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, "genome", contig_sizes, gresf,
num, logger=None) == 4
gresf.close()
@@ -228,7 +228,7 @@ def test_format_contig_nocut():
gresf = None
num = 2
- assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, gresf,
+ assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, "genome", contig_sizes, gresf,
num, logger=None) == 2
exp_file = os.path.join(EXP_DIR, "exp_split_contig_nocut.fna")
@@ -252,9 +252,9 @@ def test_format_contig_nocut_notDuplicateName():
contig_sizes = {">mycontig": 155}
num = 1
- assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, None,
+ assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, "genome", contig_sizes, None,
num, logger=None) == 1
- assert gfunc.format_contig(cut, pat, cur_seq2, cur_contig_name2, contig_sizes, None,
+ assert gfunc.format_contig(cut, pat, cur_seq2, cur_contig_name2, "genome", contig_sizes, None,
num, logger=None) == 1
assert contig_sizes == {">my_contig_name_for_my_sequence": 56,
@@ -278,18 +278,19 @@ def test_format_contig_nocut_DuplicateName(caplog):
num = 1
# Try to add a contig already existing -> error log
- assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, contig_sizes, None,
+ assert gfunc.format_contig(cut, pat, cur_seq, cur_contig_name, "genome", contig_sizes, None,
num, logger) == -1
assert contig_sizes == {">my_contig_name_for_my_sequence": 45,
">mycontig": 155}
# Check logs
caplog.set_level(logging.DEBUG)
- assert (">my_contig_name_for_my_sequence contig name is used for several contigs. "
+ assert ("In genome genome, '>my_contig_name_for_my_sequence' contig name is used for "
+ "several contigs. "
"Please put different names for each contig. This genome will be "
"ignored.") in caplog.text
# Add a contig with new name. contig_sizes is completed
- assert gfunc.format_contig(cut, pat, cur_seq2, cur_contig_name2, contig_sizes, None,
+ assert gfunc.format_contig(cut, pat, cur_seq2, cur_contig_name2, "genome", contig_sizes, None,
num, logger) == 1
assert contig_sizes == {">my_contig_name_for_my_sequence": 45,
">my_contig2": 17,
@@ -487,7 +488,8 @@ def test_analyse1genome_same_names_nocut(caplog):
pat = None
assert not gfunc.analyse_genome(genome, GEN_PATH, GENEPATH, cut, pat, genomes,
"prodigal", logger)
- assert ("myheader contig name is used for several contigs. Please put different names for "
+ assert ("In genome genome_2_identical_headers.fst, '>myheader' contig name is used for "
+ "several contigs. Please put different names for "
"each contig. This genome will be ignored") in caplog.text
@@ -503,7 +505,8 @@ def test_analyse1genome_same_last_name_nocut(caplog):
pat = None
assert not gfunc.analyse_genome(genome, GEN_PATH, GENEPATH, cut, pat, genomes,
"prodigal", logger)
- assert ("myheader contig name is used for several contigs. Please put different names for "
+ assert ("In genome genome_2_identical_headers-lastContig.fst, '>myheader' contig name "
+ "is used for several contigs. Please put different names for "
"each contig. This genome will be ignored") in caplog.text
diff --git a/test/test_unit/test_prepare/test_filter.py b/test/test_unit/test_prepare/test_filter.py
index 86d907fb252f355b1b9f3f172e2f220b87e194ed..d71669e0c54c45768f81193e2e0dbe8e9712d3dc 100755
--- a/test/test_unit/test_prepare/test_filter.py
+++ b/test/test_unit/test_prepare/test_filter.py
@@ -40,7 +40,7 @@ EXP_GENOMES = {
1587120, 1, 1]
}
-LOGFILE_BASE = "logfile_test.txt"
+LOGFILE_BASE = os.path.join(GENEPATH, "logfile_test.txt")
LEVEL = logging.DEBUG
LOGFILES = [LOGFILE_BASE + ext for ext in [".log", ".log.debug", ".log.details", ".log.err"]]
@@ -58,7 +58,7 @@ def setup_teardown_module():
- remove all log files
- remove directory with generated results
"""
- utils.init_logger(LOGFILE_BASE, LEVEL, 'test_filter', verbose=1)
+ # utils.init_logger(LOGFILE_BASE, LEVEL, 'test_filter', verbose=1)
os.mkdir(GENEPATH)
print("setup")
@@ -283,6 +283,7 @@ def test_sketch_all(caplog):
"""
Test that all genomes are sketch, in the provided order
"""
+ utils.init_logger(LOGFILE_BASE, LEVEL, 'test_filter', verbose=1)
caplog.set_level(logging.DEBUG)
# We give 5 genomes
genomes = {"genome1": ["g1_name", "g1_ori", os.path.join(GENOMES_DIR, "ACOR001.0519.fna"),
@@ -721,6 +722,65 @@ def test_check_quality_no_tmpdir(caplog):
assert "tmp_dir_check_quality does not exist" in caplog.text
+def test_check_quality_same_contname(caplog):
+ """
+ quality control of all genomes in the database when one genome contains 2 contigs
+ with the same name: this genome is discarded + warning message
+ """
+ caplog.set_level(logging.DEBUG)
+ species_linked = "my-test-genomes"
+ db_path = os.path.join(DATA_TEST_DIR, "genomes", "genomes_comparison")
+ tmp_dir = os.path.join(GENEPATH, "tmp_dir_check_quality")
+ os.makedirs(tmp_dir)
+ # Copy all genomes to new database
+ db_path_used = os.path.join(GENEPATH, "database")
+ shutil.copytree(db_path, db_path_used)
+ # Add another genome, with 2 identical contig names
+ new_genome = os.path.join(db_path_used, "genome_duplicate.fst")
+ with open(new_genome, "w") as ng:
+ ng.write(">my_contig\nAACTATATAGGAAGACACACAATTAAGGGACAGG\n")
+ ng.write(">my_contig2\nCCNNCCGATTCGAGCACACAATTAAGGGACAGG\n")
+ ng.write(">my_contig\nCCANNCCATCTCTCTTATCTCTCTAANNNNCTCTANCCNNNNNNCCATTCA\n")
+ max_l90 = 100
+ max_cont = 100
+ cutn = 0
+
+ # Get genomes information
+ genomes = filterg.check_quality(species_linked, db_path_used, tmp_dir, max_l90, max_cont, cutn)
+
+ # Even if there was 1 more genome in the database, output list of genomes is the same,
+ # as the supplementary genome contains identical contig names
+ exp_genomes = {
+ "ACOR001.0519.fna": ["ACOR001.0519",
+ os.path.join(db_path_used, "ACOR001.0519.fna"),
+ os.path.join(db_path_used, "ACOR001.0519.fna"),
+ 3013644, 269, 37],
+ "ACOR001.0519-bis.fna": ["ACOR001.0519-bis",
+ os.path.join(db_path_used, "ACOR001.0519-bis.fna"),
+ os.path.join(db_path_used, "ACOR001.0519-bis.fna"),
+ 3013644, 269, 37],
+ "ACOR001.0519-almost-same.fna": ["ACOR001.0519-almost-same",
+ os.path.join(db_path_used, "ACOR001.0519-almost-same.fna"),
+ os.path.join(db_path_used, "ACOR001.0519-almost-same.fna"),
+ 3012665, 261, 37],
+ "ACOR002.0519.fna": ["ACOR002.0519",
+ os.path.join(db_path_used, "ACOR002.0519.fna"),
+ os.path.join(db_path_used, "ACOR002.0519.fna"),
+ 2997537, 78, 23],
+ "ACOC.1019.fna": ["ACOC.1019", os.path.join(db_path_used, "ACOC.1019.fna"),
+ os.path.join(db_path_used, "ACOC.1019.fna"),
+ 1587120, 1, 1]
+ }
+
+ assert genomes == exp_genomes
+
+ # Check logs
+ assert ("Total number of genomes for my-test-genomes: 6") in caplog.text
+ assert ("In genome genome_duplicate.fst, '>my_contig' contig name is used for several "
+ "contigs. Please put different names for each contig. This genome will be "
+ "ignored.") in caplog.text
+
+
def test_check_quality_no_genome(caplog):
"""
quality control of all genomes in the database where there is no genome to annotate: