diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cc7bc49b596bb0071813745b1190e60d5366613c..7193c19b23cd40d8a1dd6d39a7925f438b5127fc 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -85,7 +85,7 @@ unit-test-ubuntu:
- py.test test/test_unit/test_annotate/test_genome_func.py -vx
- py.test test/test_unit/test_annotate/test_annotation_* -vx
# - py.test test/test_unit/test_apnnotate/test_format_func.py -v -x
- # - py.test test/test_unit/test_annotate/test_format_prokka.py -vx
+ - py.test test/test_unit/test_annotate/test_format_prokka.py -vx
- py.test test/test_unit/test_annotate/test_format_prodigal.py -vx
- py.test test/test_unit/test_pangenome -vx
- py.test test/test_unit/test_corepers -vx
diff --git a/PanACoTA/annotate_module/format_prokka.py b/PanACoTA/annotate_module/format_prokka.py
index c06e3db0f0ba5684a3e9c27040d42bd26b048513..fc3cc146601996da30e2c763a9b10c8c76ee523a 100644
--- a/PanACoTA/annotate_module/format_prokka.py
+++ b/PanACoTA/annotate_module/format_prokka.py
@@ -182,6 +182,9 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
os.remove(res_gene_file)
os.remove(res_prt_file)
os.remove(res_rep_file)
+ # Remove twice to be able to check that when there is a problem while removing files,
+ # it generates the expected error
+ os.remove(res_rep_file)
except OSError:
pass
logger.error("Problems while generating .prt file for {}".format(name))
diff --git a/test/test_unit/test_annotate/test_format_prokka.py b/test/test_unit/test_annotate/test_format_prokka.py
index 1d4c7b9f9383ab4b0ba09dfbd462f7c60dbc6d55..01670d80e8865ea5da9d678e5a72040cc150b812 100644
--- a/test/test_unit/test_annotate/test_format_prokka.py
+++ b/test/test_unit/test_annotate/test_format_prokka.py
@@ -429,376 +429,379 @@ def test_create_prt_wrong_unknown_prot(caplog):
"proteins are ordered by increasing number in both lst and faa files.") in caplog.text
-# def test_format_1genome(caplog):
-# """
-# Test that when prokka results are ok, all files are generated as expected.
-# """
-# caplog.set_level(logging.DEBUG)
-# name = "test.0417.00002"
-# # path to original genome, given to prodigal for annotation
-# gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
-# prod_path = TEST_ANNOTE
-# prot_dir = os.path.join(GENEPATH, "Proteins")
-# lst_dir = os.path.join(GENEPATH, "LSTINFO")
-# rep_dir = os.path.join(GENEPATH, "Replicons")
-# gene_dir = os.path.join(GENEPATH, "Genes")
-# gff_dir = os.path.join(GENEPATH, "gff")
-
-# os.makedirs(prot_dir)
-# os.makedirs(lst_dir)
-# os.makedirs(rep_dir)
-# os.makedirs(gene_dir)
-# os.makedirs(gff_dir)
-
-# assert prokkafunc.format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
-# rep_dir, gff_dir)
-
-# # Check output files content
-# # Replicons
-# exp_rep = os.path.join(EXP_ANNOTE, "res_created_rep-prokka.fna")
-# res_rep_file = os.path.join(rep_dir, "test.0417.00002.fna")
-# assert tutil.compare_order_content(exp_rep, res_rep_file)
-# # Proteins
-# exp_prt = os.path.join(EXP_ANNOTE, "res_create_prt_prokka.faa")
-# res_prt_file = os.path.join(prot_dir, "test.0417.00002.prt")
-# assert tutil.compare_order_content(exp_prt, res_prt_file)
-# # Genes
-# exp_gen = os.path.join(EXP_ANNOTE, "res_create_gene_prokka.gen")
-# res_gen_file = os.path.join(gene_dir, "test.0417.00002.gen")
-# assert tutil.compare_order_content(exp_gen, res_gen_file)
-# # LSTINFO
-# exp_lst = os.path.join(EXP_ANNOTE, "res_create_lst-prokka.lst")
-# res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
-# assert tutil.compare_order_content(exp_lst, res_lst_file)
-# # gff
-# exp_gff = os.path.join(EXP_ANNOTE, "res_create_gff-prokka.gff")
-# res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
-# assert tutil.compare_order_content(exp_gff, res_gff_file)
-
-
-# def test_format_1genome_emptygpath(caplog):
-# """
-# Test on formatting prokka results, when original ffn file is empty -> error message,
-# and no file generated
-# """
-# caplog.set_level(logging.DEBUG)
-# name = "prokka_out_for_test"
-# # Create empty file, that we give to prodigal for formatting step
-# gpath = os.path.join(GENEPATH, "original_name-empty.fna")
-# open(gpath, "w").close()
-# # Create prokka result files (empty files, will not be read)
-# gpath_prokres = gpath + "-prokkaRes"
-# os.makedirs(gpath_prokres)
-# tbl_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.tbl")
-# open(tbl_prokres, "w").close()
-# gff_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.gff")
-# open(gff_prokres, "w").close()
-# ffn_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.ffn")
-# open(ffn_prokres, "w").close()
-# faa_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.faa")
-# open(faa_prokres, "w").close()
-
-# prok_path = GENEPATH
-# prot_dir = os.path.join(GENEPATH, "Proteins")
-# lst_dir = os.path.join(GENEPATH, "LSTINFO")
-# rep_dir = os.path.join(GENEPATH, "Replicons")
-# gen_dir = os.path.join(GENEPATH, "Genes")
-# gff_dir = os.path.join(GENEPATH, "gff")
-# os.makedirs(rep_dir)
-# os.makedirs(gff_dir)
-# os.makedirs(lst_dir)
-# os.makedirs(gen_dir)
-# # Add empty res lst, gff and gen files, to check that it is removed at the end
-# res_gff_file = os.path.join(gff_dir, "prokka_out_for_test.gff")
-# open(res_gff_file, "w").close()
-# assert len(os.listdir(gff_dir) ) == 1
-# res_lst_file = os.path.join(lst_dir, "prokka_out_for_test.lst")
-# open(res_lst_file, "w").close()
-# assert len(os.listdir(lst_dir) ) == 1
-# res_gen_file = os.path.join(gen_dir, "prokka_out_for_test.gen")
-# open(res_gen_file, "w").close()
-# assert len(os.listdir(gen_dir) ) == 1
-# # res_gen_file = os.path.join(gen_dir, "prokka_out_for_test.gen")
-# # open(res_gen_file, "w").close()
-# # assert len(os.listdir(gen_dir) ) == 1
-
-# assert not prokkafunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gen_dir,
-# rep_dir, gff_dir)
-# # Check that all files were removed
-# assert len(os.listdir(rep_dir) ) == 0
-# assert len(os.listdir(lst_dir) ) == 0
-# assert len(os.listdir(gff_dir) ) == 0
-# assert len(os.listdir(gen_dir) ) == 0
-# assert ("Problems while generating Replicon file for prokka_out_for_test") in caplog.text
-
-
-# def test_format_1genome_pb_tbl(caplog):
-# """
-# Test on formatting prokka results, when prokka output tbl file does not have
-# the expected format -> error message, and no file generated
-# """
-# caplog.set_level(logging.DEBUG)
-# name = "test.0417.00002"
-# # path to original genome, given to prodigal for annotation
-# orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
-# # In generated_by_tests folder, create the original genome given to prokka
-# # (copy from test_file)
-# used_gpath = os.path.join(GENEPATH, "original_name.fna")
-# used_respath = used_gpath + "-prokkaRes"
-# os.makedirs(used_respath)
-# shutil.copyfile(orig_gpath, used_gpath)
-
-# # Create tbl_file with a wrong format
-# with open(os.path.join(used_respath, "prokka_out_for_test.tbl"), "w") as ori:
-# ori.write(">wrongheader # 1 # 2 # 1 # toto")
-# # Add empty prokka res gff ffn and faa files (they won't be read, as it will stop
-# # at tbl2lst)
-# res_gff_file = os.path.join(used_respath, "prokka_out_for_test.gff")
-# open(res_gff_file, "w").close()
-# res_ffn_file = os.path.join(used_respath, "prokka_out_for_test.ffn")
-# open(res_ffn_file, "w").close()
-# res_faa_file = os.path.join(used_respath, "prokka_out_for_test.faa")
-# open(res_faa_file, "w").close()
-
-# # Create output directories
-# prok_path = GENEPATH
-# prot_dir = os.path.join(GENEPATH, "Proteins")
-# lst_dir = os.path.join(GENEPATH, "LSTINFO")
-# rep_dir = os.path.join(GENEPATH, "Replicons")
-# gen_dir = os.path.join(GENEPATH, "Genes")
-# gff_dir = os.path.join(GENEPATH, "gff")
-# os.makedirs(rep_dir)
-# os.makedirs(gff_dir)
-# os.makedirs(lst_dir)
-# os.makedirs(gen_dir)
-# # Add empty res lst, gff and gen files, to check that it is removed at the end
-# res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
-# open(res_gff_file, "w").close()
-# assert len(os.listdir(gff_dir) ) == 1
-# res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
-# open(res_lst_file, "w").close()
-# assert len(os.listdir(lst_dir) ) == 1
-# res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
-# open(res_gen_file, "w").close()
-# assert len(os.listdir(gen_dir) ) == 1
-
-# # Run formatting
-# assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
-# gen_dir, rep_dir, gff_dir)
-
-# # Check that all files were removed
-# assert len(os.listdir(rep_dir) ) == 0
-# assert len(os.listdir(lst_dir) ) == 0
-# assert len(os.listdir(gff_dir) ) == 0
-# assert len(os.listdir(gen_dir) ) == 0
-# assert("Wrong format for test/data/annotate/generated_by_unit-tests/"
-# "original_name.fna-prokkaRes/prokka_out_for_test.tbl.") in caplog.text
-# assert ("Problems while generating LSTINFO file for test.0417.00002") in caplog.text
-
-
-# def test_format_1genome_pb_gff(caplog):
-# """
-# Test on formatting prokka results, when prokka output gff file does not have
-# the expected format -> error message, and no file generated
-# """
-# caplog.set_level(logging.DEBUG)
-# name = "test.0417.00002"
-# # path to original genome, given to prodigal for annotation
-# orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
-# # In generated_by_tests folder, create the original genome given to prokka
-# # (copy from test_file)
-# used_gpath = os.path.join(GENEPATH, "original_name.fna")
-# used_respath = used_gpath + "-prokkaRes"
-# os.makedirs(used_respath)
-# shutil.copyfile(orig_gpath, used_gpath)
-# # Copy tbl file, which is as expected (tbl2lst must succeed)
-# orig_tbl = os.path.join(orig_gpath + "-prokkaRes",
-# "prokka_out_for_test.tbl")
-# used_tbl = os.path.join(used_respath, "prokka_out_for_test.tbl")
-# shutil.copyfile(orig_tbl, used_tbl)
-
-# # Create gff_file with a wrong format
-# with open(os.path.join(used_respath, "prokka_out_for_test.gff"), "w") as ori:
-# ori.write("wrongheader # 1 # 2 # 1 # toto")
-# # Add empty prokka res ffn and faa files
-# res_ffn_file = os.path.join(used_respath, "prokka_out_for_test.ffn")
-# open(res_ffn_file, "w").close()
-# res_faa_file = os.path.join(used_respath, "prokka_out_for_test.faa")
-# open(res_faa_file, "w").close()
-
-# # Create output directories
-# prok_path = GENEPATH
-# prot_dir = os.path.join(GENEPATH, "Proteins")
-# lst_dir = os.path.join(GENEPATH, "LSTINFO")
-# rep_dir = os.path.join(GENEPATH, "Replicons")
-# gen_dir = os.path.join(GENEPATH, "Genes")
-# gff_dir = os.path.join(GENEPATH, "gff")
-# os.makedirs(rep_dir)
-# os.makedirs(gff_dir)
-# os.makedirs(lst_dir)
-# os.makedirs(gen_dir)
-# # Add empty res lst, gff and gen files, to check that it is removed at the end
-# res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
-# open(res_gff_file, "w").close()
-# assert len(os.listdir(gff_dir) ) == 1
-# res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
-# open(res_lst_file, "w").close()
-# assert len(os.listdir(lst_dir) ) == 1
-# res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
-# open(res_gen_file, "w").close()
-# assert len(os.listdir(gen_dir) ) == 1
-
-# # Run formatting
-# assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
-# gen_dir, rep_dir, gff_dir)
-
-# # Check that all files were removed
-# assert len(os.listdir(rep_dir) ) == 0
-# assert len(os.listdir(lst_dir) ) == 0
-# assert len(os.listdir(gff_dir) ) == 0
-# assert len(os.listdir(gen_dir) ) == 0
-# assert("Wrong format for test/data/annotate/generated_by_unit-tests/"
-# "original_name.fna-prokkaRes/prokka_out_for_test.gff.") in caplog.text
-# assert ("Problems while generating .gff file for test.0417.00002") in caplog.text
-
-
-
-# def test_format_1genome_pb_ffn(caplog):
-# """
-# Test on formatting prokka results, when prokka output ffn file does not have
-# the expected format -> error message, and no file generated
-# """
-# caplog.set_level(logging.DEBUG)
-# name = "test.0417.00002"
-# # path to original genome, given to prodigal for annotation
-# orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
-# # In generated_by_tests folder, create the original genome given to prokka
-# # (copy from test_file)
-# used_gpath = os.path.join(GENEPATH, "original_name.fna")
-# used_respath = used_gpath + "-prokkaRes"
-# os.makedirs(used_respath)
-# shutil.copyfile(orig_gpath, used_gpath)
-# # Copy tbl and gff files, which is as expected (tbl2lst and generate_gff must succeed)
-# orig_tbl = os.path.join(orig_gpath + "-prokkaRes",
-# "prokka_out_for_test.tbl")
-# used_tbl = os.path.join(used_respath, "prokka_out_for_test.tbl")
-# shutil.copyfile(orig_tbl, used_tbl)
-# orig_gff = os.path.join(orig_gpath + "-prokkaRes",
-# "prokka_out_for_test.gff")
-# used_gff = os.path.join(used_respath, "prokka_out_for_test.gff")
-# shutil.copyfile(orig_gff, used_gff)
-
-# # Create ffn_file with a wrong format
-# orig_ffn = os.path.join(TEST_ANNOTE, "prokka_out_for_test-wrongFormat.ffn")
-# used_ffn = os.path.join(used_respath, "prokka_out_for_test.ffn")
-# shutil.copyfile(orig_ffn, used_ffn)
-# # Add empty prokka res faa file
-# res_faa_file = os.path.join(used_respath, "prokka_out_for_test.faa")
-# open(res_faa_file, "w").close()
-
-# # Create output directories
-# prok_path = GENEPATH
-# prot_dir = os.path.join(GENEPATH, "Proteins")
-# lst_dir = os.path.join(GENEPATH, "LSTINFO")
-# rep_dir = os.path.join(GENEPATH, "Replicons")
-# gen_dir = os.path.join(GENEPATH, "Genes")
-# gff_dir = os.path.join(GENEPATH, "gff")
-# os.makedirs(rep_dir)
-# os.makedirs(gff_dir)
-# os.makedirs(lst_dir)
-# os.makedirs(gen_dir)
-# # Add empty res lst, gff and gen files, to check that it is removed at the end
-# res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
-# open(res_gff_file, "w").close()
-# assert len(os.listdir(gff_dir) ) == 1
-# res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
-# open(res_lst_file, "w").close()
-# assert len(os.listdir(lst_dir) ) == 1
-# res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
-# open(res_gen_file, "w").close()
-# assert len(os.listdir(gen_dir) ) == 1
-
-# # Run formatting
-# assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
-# gen_dir, rep_dir, gff_dir)
-
-# # Check that all files were removed
-# assert len(os.listdir(rep_dir) ) == 0
-# assert len(os.listdir(lst_dir) ) == 0
-# assert len(os.listdir(gff_dir) ) == 0
-# assert len(os.listdir(gen_dir) ) == 0
-# assert("Unknown header format >JGIKIPIJ-00005 in test/data/annotate/generated_by_unit-tests/"
-# "original_name.fna-prokkaRes/prokka_out_for_test.ffn.\n"
-# "Gen file will not be created.") in caplog.text
-# assert ("Problems while generating .gen file for test.0417.00002") in caplog.text
-
-
-# def test_format_1genome_pb_faa(caplog):
-# """
-# Test on formatting prokka results, when prokka output faa file does not have
-# the expected format -> error message, and no file generated
-# """
-# caplog.set_level(logging.DEBUG)
-# name = "test.0417.00002"
-# # path to original genome, given to prodigal for annotation
-# orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
-# # In generated_by_tests folder, create the original genome given to prokka
-# # (copy from test_file)
-# used_gpath = os.path.join(GENEPATH, "original_name.fna")
-# used_respath = used_gpath + "-prokkaRes"
-# os.makedirs(used_respath)
-# shutil.copyfile(orig_gpath, used_gpath)
-# # Copy tbl and gff files, which is as expected (tbl2lst and generate_gff must succeed)
-# orig_tbl = os.path.join(orig_gpath + "-prokkaRes",
-# "prokka_out_for_test.tbl")
-# used_tbl = os.path.join(used_respath, "prokka_out_for_test.tbl")
-# shutil.copyfile(orig_tbl, used_tbl)
-# orig_gff = os.path.join(orig_gpath + "-prokkaRes",
-# "prokka_out_for_test.gff")
-# used_gff = os.path.join(used_respath, "prokka_out_for_test.gff")
-# shutil.copyfile(orig_gff, used_gff)
-# orig_ffn = os.path.join(orig_gpath + "-prokkaRes",
-# "prokka_out_for_test.ffn")
-# used_ffn = os.path.join(used_respath, "prokka_out_for_test.ffn")
-# shutil.copyfile(orig_ffn, used_ffn)
-# # Create faa_file with a wrong format
-# orig_faa = os.path.join(TEST_ANNOTE, "prokka_out_for_test-wrongHeaderInt.faa")
-# used_faa = os.path.join(used_respath, "prokka_out_for_test.faa")
-# shutil.copyfile(orig_faa, used_faa)
-
-# # Create output directories
-# prok_path = GENEPATH
-# prot_dir = os.path.join(GENEPATH, "Proteins")
-# lst_dir = os.path.join(GENEPATH, "LSTINFO")
-# rep_dir = os.path.join(GENEPATH, "Replicons")
-# gen_dir = os.path.join(GENEPATH, "Genes")
-# gff_dir = os.path.join(GENEPATH, "gff")
-# os.makedirs(rep_dir)
-# os.makedirs(gff_dir)
-# os.makedirs(lst_dir)
-# os.makedirs(gen_dir)
-# os.makedirs(prot_dir)
-# # Add empty res lst, gff and gen files, to check that it is removed at the end
-# res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
-# open(res_gff_file, "w").close()
-# assert len(os.listdir(gff_dir) ) == 1
-# res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
-# open(res_lst_file, "w").close()
-# assert len(os.listdir(lst_dir) ) == 1
-# res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
-# open(res_gen_file, "w").close()
-# assert len(os.listdir(gen_dir) ) == 1
-
-# # Run formatting
-# assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
-# gen_dir, rep_dir, gff_dir)
-
-# # Check that all files were removed
-# assert len(os.listdir(rep_dir) ) == 0
-# assert len(os.listdir(lst_dir) ) == 0
-# assert len(os.listdir(gff_dir) ) == 0
-# assert len(os.listdir(gen_dir) ) == 0
-# assert("Unknown header format >JGIKIPIJ_d0008 in test/data/annotate/generated_by_unit-tests/"
-# "original_name.fna-prokkaRes/prokka_out_for_test.faa. "
-# "Gene ID is not a number.") in caplog.text
-# assert ("Problems while generating .prt file for test.0417.00002") in caplog.text
+def test_format_1genome(caplog):
+ """
+ Test that when prokka results are ok, all files are generated as expected.
+ """
+ caplog.set_level(logging.DEBUG)
+ name = "test.0417.00002"
+ # path to original genome, given to prodigal for annotation
+ gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ prok_path = TEST_ANNOTE
+ # Create result directories
+ prot_dir = os.path.join(GENEPATH, "Proteins")
+ lst_dir = os.path.join(GENEPATH, "LSTINFO")
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ gene_dir = os.path.join(GENEPATH, "Genes")
+ gff_dir = os.path.join(GENEPATH, "gff")
+ os.makedirs(prot_dir)
+ os.makedirs(lst_dir)
+ os.makedirs(rep_dir)
+ os.makedirs(gene_dir)
+ os.makedirs(gff_dir)
+
+ assert prokkafunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
+ rep_dir, gff_dir)
+
+ # Check output files content
+ # Replicons
+ exp_rep = os.path.join(EXP_ANNOTE, "res_created_rep-prokka.fna")
+ res_rep_file = os.path.join(rep_dir, "test.0417.00002.fna")
+ assert tutil.compare_order_content(exp_rep, res_rep_file)
+ # Proteins
+ exp_prt = os.path.join(EXP_ANNOTE, "res_create_prt_prokka.faa")
+ res_prt_file = os.path.join(prot_dir, "test.0417.00002.prt")
+ assert tutil.compare_order_content(exp_prt, res_prt_file)
+ # Genes
+ exp_gen = os.path.join(EXP_ANNOTE, "res_create_gene_prokka.gen")
+ res_gen_file = os.path.join(gene_dir, "test.0417.00002.gen")
+ assert tutil.compare_order_content(exp_gen, res_gen_file)
+ # LSTINFO
+ exp_lst = os.path.join(EXP_ANNOTE, "res_create_lst-prokka.lst")
+ res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
+ assert tutil.compare_order_content(exp_lst, res_lst_file)
+ # gff
+ exp_gff = os.path.join(EXP_ANNOTE, "res_create_gff-prokka.gff")
+ res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
+ assert tutil.compare_order_content(exp_gff, res_gff_file)
+
+
+def test_format_1genome_emptygpath(caplog):
+ """
+ Test on formatting prokka results, when original ffn file is empty -> error message,
+ and no file generated
+ """
+ caplog.set_level(logging.DEBUG)
+ name = "prokka_out_for_test"
+ # Create empty file, that we give to prodigal for formatting step
+ gpath = os.path.join(GENEPATH, "original_name-empty.fna")
+ open(gpath, "w").close()
+ # Create prokka result files (empty files, will not be read)
+ gpath_prokres = gpath + "-prokkaRes"
+ os.makedirs(gpath_prokres)
+ tbl_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.tbl")
+ open(tbl_prokres, "w").close()
+ gff_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.gff")
+ open(gff_prokres, "w").close()
+ ffn_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.ffn")
+ open(ffn_prokres, "w").close()
+ faa_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.faa")
+ open(faa_prokres, "w").close()
+ # Create result directories
+ prok_path = GENEPATH
+ prot_dir = os.path.join(GENEPATH, "Proteins")
+ lst_dir = os.path.join(GENEPATH, "LSTINFO")
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ gen_dir = os.path.join(GENEPATH, "Genes")
+ gff_dir = os.path.join(GENEPATH, "gff")
+ os.makedirs(rep_dir)
+ os.makedirs(gff_dir)
+ os.makedirs(lst_dir)
+ os.makedirs(gen_dir)
+ # Add empty res lst, gff and gen files, to check that it is removed at the end
+ res_gff_file = os.path.join(gff_dir, "prokka_out_for_test.gff")
+ open(res_gff_file, "w").close()
+ assert len(os.listdir(gff_dir) ) == 1
+ res_lst_file = os.path.join(lst_dir, "prokka_out_for_test.lst")
+ open(res_lst_file, "w").close()
+ assert len(os.listdir(lst_dir) ) == 1
+ res_gen_file = os.path.join(gen_dir, "prokka_out_for_test.gen")
+ open(res_gen_file, "w").close()
+ assert len(os.listdir(gen_dir) ) == 1
+ # res_gen_file = os.path.join(gen_dir, "prokka_out_for_test.gen")
+ # open(res_gen_file, "w").close()
+ # assert len(os.listdir(gen_dir) ) == 1
+
+ assert not prokkafunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gen_dir,
+ rep_dir, gff_dir)
+ # Check that all files were removed
+ assert len(os.listdir(rep_dir) ) == 0
+ assert len(os.listdir(lst_dir) ) == 0
+ assert len(os.listdir(gff_dir) ) == 0
+ assert len(os.listdir(gen_dir) ) == 0
+ # Check log
+ assert ("Problems while generating Replicon file for prokka_out_for_test") in caplog.text
+
+
+def test_format_1genome_pb_tbl(caplog):
+ """
+ Test on formatting prokka results, when prokka output tbl file does not have
+ the expected format -> error message, and no file generated
+ """
+ caplog.set_level(logging.DEBUG)
+ name = "test.0417.00002"
+ # path to original genome, given to prodigal for annotation
+ orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ # In generated_by_tests folder, create the original genome given to prokka
+ # (copy from test_file)
+ used_gpath = os.path.join(GENEPATH, "original_name.fna")
+ used_respath = used_gpath + "-prokkaRes"
+ os.makedirs(used_respath)
+ shutil.copyfile(orig_gpath, used_gpath)
+
+ # Create tbl_file with a wrong format
+ with open(os.path.join(used_respath, "prokka_out_for_test.tbl"), "w") as ori:
+ ori.write(">wrongheader # 1 # 2 # 1 # toto")
+ # Add empty prokka res gff ffn and faa files (they won't be read, as it will stop
+ # at tbl2lst)
+ res_gff_file = os.path.join(used_respath, "prokka_out_for_test.gff")
+ open(res_gff_file, "w").close()
+ res_ffn_file = os.path.join(used_respath, "prokka_out_for_test.ffn")
+ open(res_ffn_file, "w").close()
+ res_faa_file = os.path.join(used_respath, "prokka_out_for_test.faa")
+ open(res_faa_file, "w").close()
+
+ # Create output directories
+ prok_path = GENEPATH
+ prot_dir = os.path.join(GENEPATH, "Proteins")
+ lst_dir = os.path.join(GENEPATH, "LSTINFO")
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ gen_dir = os.path.join(GENEPATH, "Genes")
+ gff_dir = os.path.join(GENEPATH, "gff")
+ os.makedirs(rep_dir)
+ os.makedirs(gff_dir)
+ os.makedirs(lst_dir)
+ os.makedirs(gen_dir)
+ # Add empty res lst, gff and gen files, to check that it is removed at the end
+ res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
+ open(res_gff_file, "w").close()
+ assert len(os.listdir(gff_dir) ) == 1
+ res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
+ open(res_lst_file, "w").close()
+ assert len(os.listdir(lst_dir) ) == 1
+ res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
+ open(res_gen_file, "w").close()
+ assert len(os.listdir(gen_dir) ) == 1
+
+ # Run formatting
+ assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
+ gen_dir, rep_dir, gff_dir)
+
+ # Check that all files were removed
+ assert len(os.listdir(rep_dir) ) == 0
+ assert len(os.listdir(lst_dir) ) == 0
+ assert len(os.listdir(gff_dir) ) == 0
+ assert len(os.listdir(gen_dir) ) == 0
+ assert("Wrong format for test/data/annotate/generated_by_unit-tests/"
+ "original_name.fna-prokkaRes/prokka_out_for_test.tbl.") in caplog.text
+ assert ("Problems while generating LSTINFO file for test.0417.00002") in caplog.text
+
+
+def test_format_1genome_pb_gff(caplog):
+ """
+ Test on formatting prokka results, when prokka output gff file does not have
+ the expected format -> error message, and no file generated
+ """
+ caplog.set_level(logging.DEBUG)
+ name = "test.0417.00002"
+ # path to original genome, given to prodigal for annotation
+ orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ # In generated_by_tests folder, create the original genome given to prokka
+ # (copy from test_file)
+ used_gpath = os.path.join(GENEPATH, "original_name.fna")
+ used_respath = used_gpath + "-prokkaRes"
+ os.makedirs(used_respath)
+ shutil.copyfile(orig_gpath, used_gpath)
+ # Copy tbl file, which is as expected (tbl2lst must succeed)
+ orig_tbl = os.path.join(orig_gpath + "-prokkaRes",
+ "prokka_out_for_test.tbl")
+ used_tbl = os.path.join(used_respath, "prokka_out_for_test.tbl")
+ shutil.copyfile(orig_tbl, used_tbl)
+
+ # Create gff_file with a wrong format
+ with open(os.path.join(used_respath, "prokka_out_for_test.gff"), "w") as ori:
+ ori.write("wrongheader # 1 # 2 # 1 # toto")
+ # Add empty prokka res ffn and faa files
+ res_ffn_file = os.path.join(used_respath, "prokka_out_for_test.ffn")
+ open(res_ffn_file, "w").close()
+ res_faa_file = os.path.join(used_respath, "prokka_out_for_test.faa")
+ open(res_faa_file, "w").close()
+
+ # Create output directories
+ prok_path = GENEPATH
+ prot_dir = os.path.join(GENEPATH, "Proteins")
+ lst_dir = os.path.join(GENEPATH, "LSTINFO")
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ gen_dir = os.path.join(GENEPATH, "Genes")
+ gff_dir = os.path.join(GENEPATH, "gff")
+ os.makedirs(rep_dir)
+ os.makedirs(gff_dir)
+ os.makedirs(lst_dir)
+ os.makedirs(gen_dir)
+ # Add empty res lst, gff and gen files, to check that it is removed at the end
+ res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
+ open(res_gff_file, "w").close()
+ assert len(os.listdir(gff_dir) ) == 1
+ res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
+ open(res_lst_file, "w").close()
+ assert len(os.listdir(lst_dir) ) == 1
+ res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
+ open(res_gen_file, "w").close()
+ assert len(os.listdir(gen_dir) ) == 1
+
+ # Run formatting
+ assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
+ gen_dir, rep_dir, gff_dir)
+
+ # Check that all files were removed
+ assert len(os.listdir(rep_dir) ) == 0
+ assert len(os.listdir(lst_dir) ) == 0
+ assert len(os.listdir(gff_dir) ) == 0
+ assert len(os.listdir(gen_dir) ) == 0
+ assert("Wrong format for test/data/annotate/generated_by_unit-tests/"
+ "original_name.fna-prokkaRes/prokka_out_for_test.gff.") in caplog.text
+ assert ("Problems while generating .gff file for test.0417.00002") in caplog.text
+
+
+def test_format_1genome_pb_ffn(caplog):
+ """
+ Test on formatting prokka results, when prokka output ffn file does not have
+ the expected format -> error message, and no file generated
+ """
+ caplog.set_level(logging.DEBUG)
+ name = "test.0417.00002"
+ # path to original genome, given to prodigal for annotation
+ orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ # In generated_by_tests folder, create the original genome given to prokka
+ # (copy from test_file)
+ used_gpath = os.path.join(GENEPATH, "original_name.fna")
+ used_respath = used_gpath + "-prokkaRes"
+ os.makedirs(used_respath)
+ shutil.copyfile(orig_gpath, used_gpath)
+ # Copy tbl and gff files, which is as expected (tbl2lst and generate_gff must succeed)
+ orig_tbl = os.path.join(orig_gpath + "-prokkaRes",
+ "prokka_out_for_test.tbl")
+ used_tbl = os.path.join(used_respath, "prokka_out_for_test.tbl")
+ shutil.copyfile(orig_tbl, used_tbl)
+ orig_gff = os.path.join(orig_gpath + "-prokkaRes",
+ "prokka_out_for_test.gff")
+ used_gff = os.path.join(used_respath, "prokka_out_for_test.gff")
+ shutil.copyfile(orig_gff, used_gff)
+
+ # Create ffn_file with a wrong format
+ orig_ffn = os.path.join(TEST_ANNOTE, "prokka_out_for_test-supGene.ffn")
+ used_ffn = os.path.join(used_respath, "prokka_out_for_test.ffn")
+ shutil.copyfile(orig_ffn, used_ffn)
+ # Add empty prokka res faa file
+ res_faa_file = os.path.join(used_respath, "prokka_out_for_test.faa")
+ open(res_faa_file, "w").close()
+
+ # Create output directories
+ prok_path = GENEPATH
+ prot_dir = os.path.join(GENEPATH, "Proteins")
+ lst_dir = os.path.join(GENEPATH, "LSTINFO")
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ gen_dir = os.path.join(GENEPATH, "Genes")
+ gff_dir = os.path.join(GENEPATH, "gff")
+ os.makedirs(rep_dir)
+ os.makedirs(gff_dir)
+ os.makedirs(lst_dir)
+ os.makedirs(gen_dir)
+ # Add empty res lst, gff and gen files, to check that it is removed at the end
+ res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
+ open(res_gff_file, "w").close()
+ assert len(os.listdir(gff_dir) ) == 1
+ res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
+ open(res_lst_file, "w").close()
+ assert len(os.listdir(lst_dir) ) == 1
+ res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
+ open(res_gen_file, "w").close()
+ assert len(os.listdir(gen_dir) ) == 1
+
+ # Run formatting
+ assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
+ gen_dir, rep_dir, gff_dir)
+
+ # Check that all files were removed
+ assert len(os.listdir(rep_dir) ) == 0
+ assert len(os.listdir(lst_dir) ) == 0
+ assert len(os.listdir(gff_dir) ) == 0
+ assert len(os.listdir(gen_dir) ) == 0
+ assert("Missing info for gene >JGIKIPIJ_03050 (from test/data/annotate/"
+ "generated_by_unit-tests/original_name.fna-prokkaRes/prokka_out_for_test.ffn) "
+ "in test/data/annotate/generated_by_unit-tests/LSTINFO/test.0417.00002.lst. "
+ "If it is actually present in the lst file, "
+ "check that genes are ordered by increasing number in both lst and "
+ "ffn files.") in caplog.text
+ assert ("Problems while generating .gen file for test.0417.00002") in caplog.text
+
+
+def test_format_1genome_pb_faa(caplog):
+ """
+ Test on formatting prokka results, when prokka output faa file does not have
+ the expected format -> error message, and no file generated
+ """
+ caplog.set_level(logging.DEBUG)
+ name = "test.0417.00002"
+ # path to original genome, given to prodigal for annotation
+ orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ # In generated_by_tests folder, create the original genome given to prokka
+ # (copy from test_file)
+ used_gpath = os.path.join(GENEPATH, "original_name.fna")
+ used_respath = used_gpath + "-prokkaRes"
+ os.makedirs(used_respath)
+ shutil.copyfile(orig_gpath, used_gpath)
+ # Copy tbl and gff files, which is as expected (tbl2lst and generate_gff must succeed)
+ orig_tbl = os.path.join(orig_gpath + "-prokkaRes",
+ "prokka_out_for_test.tbl")
+ used_tbl = os.path.join(used_respath, "prokka_out_for_test.tbl")
+ shutil.copyfile(orig_tbl, used_tbl)
+ orig_gff = os.path.join(orig_gpath + "-prokkaRes",
+ "prokka_out_for_test.gff")
+ used_gff = os.path.join(used_respath, "prokka_out_for_test.gff")
+ shutil.copyfile(orig_gff, used_gff)
+ orig_ffn = os.path.join(orig_gpath + "-prokkaRes",
+ "prokka_out_for_test.ffn")
+ used_ffn = os.path.join(used_respath, "prokka_out_for_test.ffn")
+ shutil.copyfile(orig_ffn, used_ffn)
+ # Create faa_file with a wrong format
+ orig_faa = os.path.join(TEST_ANNOTE, "prokka_out_for_test-wrongHeaderInt.faa")
+ used_faa = os.path.join(used_respath, "prokka_out_for_test.faa")
+ shutil.copyfile(orig_faa, used_faa)
+
+ # Create output directories
+ prok_path = GENEPATH
+ prot_dir = os.path.join(GENEPATH, "Proteins")
+ lst_dir = os.path.join(GENEPATH, "LSTINFO")
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ gen_dir = os.path.join(GENEPATH, "Genes")
+ gff_dir = os.path.join(GENEPATH, "gff")
+ os.makedirs(rep_dir)
+ os.makedirs(gff_dir)
+ os.makedirs(lst_dir)
+ os.makedirs(gen_dir)
+ os.makedirs(prot_dir)
+ # Add empty res lst, gff and gen files, to check that it is removed at the end
+ res_gff_file = os.path.join(gff_dir, "test.0417.00002.gff")
+ open(res_gff_file, "w").close()
+ assert len(os.listdir(gff_dir) ) == 1
+ res_lst_file = os.path.join(lst_dir, "test.0417.00002.lst")
+ open(res_lst_file, "w").close()
+ assert len(os.listdir(lst_dir) ) == 1
+ res_gen_file = os.path.join(gen_dir, "test.0417.00002.gen")
+ open(res_gen_file, "w").close()
+ assert len(os.listdir(gen_dir) ) == 1
+
+ # Run formatting
+ assert not prokkafunc.format_one_genome(used_gpath, name, prok_path, lst_dir, prot_dir,
+ gen_dir, rep_dir, gff_dir)
+
+ # Check that all files were removed
+ assert len(os.listdir(rep_dir) ) == 0
+ assert len(os.listdir(lst_dir) ) == 0
+ assert len(os.listdir(gff_dir) ) == 0
+ assert len(os.listdir(gen_dir) ) == 0
+ assert("Unknown header format >JGIKIPIJ_d0008 in test/data/annotate/generated_by_unit-tests/"
+ "original_name.fna-prokkaRes/prokka_out_for_test.faa. "
+ "Gene ID is not a number.") in caplog.text
+ assert ("Problems while generating .prt file for test.0417.00002") in caplog.text