diff --git a/PanACoTA/annotate_module/general_format_functions.py b/PanACoTA/annotate_module/general_format_functions.py
index 68dd0c4cee9dab4202677b0b995493005b9720ff..1a1e30ce50e9c203fb3f6bcf9ef80e74f8f38966 100644
--- a/PanACoTA/annotate_module/general_format_functions.py
+++ b/PanACoTA/annotate_module/general_format_functions.py
@@ -84,7 +84,7 @@ def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, q
res_path : str
path to folder where the 4 directories must be created
annot_path : str
- path to folder named "<genome_name>-[prokka, prodigal]Res" where all prokka/prodigal
+ path to folder containing "<genome_name>-[prokka, prodigal]Res" where all prokka/prodigal
results are saved.
prodigal_only: True if it was annotated by prodigal, False if annotated by prokka
threads : int
@@ -94,10 +94,9 @@ def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, q
Returns
-------
- (skipped, skipped_format) : tuple
+ skipped_format : list
- * skipped : list of genomes skipped because they had a problem in annotation step
- * skipped_format : list of genomes skipped because they had a problem in format step
+ list of genomes skipped because they had a problem in format step
"""
main_logger.info("Formatting all genomes")
lst_dir = os.path.join(res_path, "LSTINFO")
diff --git a/test/test_unit/test_annotate/test_format_func.py b/test/test_unit/test_annotate/test_format_func.py
index 0a79462f5f2a00fe73e3e8637645e8d1d9cbcac6..99cc33ebd6aa5c4b3c2f5fc2bc23090b5265f5db 100755
--- a/test/test_unit/test_annotate/test_format_func.py
+++ b/test/test_unit/test_annotate/test_format_func.py
@@ -39,7 +39,7 @@ def setup_teardown_module():
print("setup")
yield
- shutil.rmtree(GENEPATH)
+ # shutil.rmtree(GENEPATH)
print("teardown")
# Define variables and functions used by several tests
@@ -287,138 +287,124 @@ def test_handle_genome_formatok_prodigal(caplog):
assert tutil.compare_order_content(exp_gff, res_gff_file)
-# def test_format_all_prokka():
-# """
-# Test that when giving a list of genomes, for which prokka ran without problem,
-# they are formatted, with all expected files created.
-# """
-# # genomes = {genome: [name, gpath, to_annot, size, nbcont, l90]}
-# initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-# initpaths = [os.path.join(ANNOTEDIR, "genomes", name) for name in initnames]
-# gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-# onames = ["test_runprokka_H299", "test.0417.00002"]
-# gpaths = [os.path.join(ANNOTEDIR, "genomes", name) for name in gnames]
-# for f1, f2 in zip(initpaths, gpaths):
-# shutil.copyfile(f1, f2)
-# genomes = {gnames[0]: [onames[0], gpaths[0], gpaths[0], 12656, 3, 1],
-# gnames[1]: [onames[1], gpaths[1], gpaths[1], 456464645, 5, 1]
-# }
-# prok_path = os.path.join(ANNOTEDIR, "exp_files")
-# res_path = GENEPATH
-# skipped_format = ffunc.format_genomes(genomes, res_path,
-# prok_path, False, threads=4)
-# assert skipped_format == []
-# lstfiles = [os.path.join(res_path, "LSTINFO", name + ".lst") for name in onames]
-# prtfiles = [os.path.join(res_path, "Proteins", name + ".prt") for name in onames]
-# genfiles = [os.path.join(res_path, "Genes", name + ".gen") for name in onames]
-# repfiles = [os.path.join(res_path, "Replicons", name + ".fna") for name in onames]
-# gfffiles = [os.path.join(res_path, "gff3", name + ".gff") for name in onames]
-# for f in lstfiles + prtfiles + genfiles + repfiles + gfffiles:
-# assert os.path.isfile(f)
-# shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-# shutil.rmtree(os.path.join(res_path, "Proteins"))
-# shutil.rmtree(os.path.join(res_path, "Genes"))
-# shutil.rmtree(os.path.join(res_path, "Replicons"))
-# shutil.rmtree(os.path.join(res_path, "gff3"))
-
-
-# def test_format_all_result_false():
-# """
-# Test that when giving a list of 2 genomes, 1 for which prokka ran without problem,
-# 1 for which prokka had problems (given with False in results),
-# the correct genome is formatted, with all
-# expected files created, and the genome with problems is not formatted.
-# """
-# # genomes = {genome: [name, gpath, size, nbcont, l90]}
-# initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-# initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
-# gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-# onames = ["test_runprokka_H299", "test.0417.00002"]
-# gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
-# for f1, f2 in zip(initpaths, gpaths):
-# shutil.copyfile(f1, f2)
-# genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
-# gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
-# }
-# prok_path = os.path.join("test", "data", "annotate", "exp_files")
-# res_path = os.path.join("test", "data", "annotate")
-# results = {gnames[0]: True, gnames[1]: False}
-# skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
-# assert skipped == ["B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-# assert skipped_format == []
-# lstfiles = os.path.join(res_path, "LSTINFO")
-# prtfiles = os.path.join(res_path, "Proteins")
-# genfiles = os.path.join(res_path, "Genes")
-# repfiles = os.path.join(res_path, "Replicons")
-# gfffiles = os.path.join(res_path, "gff3")
-# assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
-# assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
-# assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
-# assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
-# assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
-# assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
-# assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
-# assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
-# assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
-# assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
-# shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-# shutil.rmtree(os.path.join(res_path, "Proteins"))
-# shutil.rmtree(os.path.join(res_path, "Genes"))
-# shutil.rmtree(os.path.join(res_path, "Replicons"))
-# shutil.rmtree(os.path.join(res_path, "gff3"))
-# for f in gpaths:
-# os.remove(f)
-
-
-# def test_format_all_not_result():
-# """
-# Test that when giving a list of 2 genomes, but only 1 is in the results list (and prokka ran
-# without problems for it), the correct genome is formatted, with all
-# expected files created, and the other genome is not formatted, and does not appear in
-# skipped list (as it was removed from the study before annotation step, probably by QC).
-# """
-# # genomes = {genome: [name, gpath, size, nbcont, l90]}
-# initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-# initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
-# gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-# onames = ["test_runprokka_H299", "test.0417.00002"]
-# gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
-# for f1, f2 in zip(initpaths, gpaths):
-# shutil.copyfile(f1, f2)
-# genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
-# gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
-# }
-# prok_path = os.path.join("test", "data", "annotate", "exp_files")
-# res_path = os.path.join("test", "data", "annotate")
-# results = {gnames[0]: True}
-# skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
-# assert skipped == []
-# assert skipped_format == []
-# lstfiles = os.path.join(res_path, "LSTINFO")
-# prtfiles = os.path.join(res_path, "Proteins")
-# genfiles = os.path.join(res_path, "Genes")
-# repfiles = os.path.join(res_path, "Replicons")
-# gfffiles = os.path.join(res_path, "gff3")
-# assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
-# assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
-# assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
-# assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
-# assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
-# assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
-# assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
-# assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
-# assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
-# assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
-# shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-# shutil.rmtree(os.path.join(res_path, "Proteins"))
-# shutil.rmtree(os.path.join(res_path, "Genes"))
-# shutil.rmtree(os.path.join(res_path, "Replicons"))
-# shutil.rmtree(os.path.join(res_path, "gff3"))
-# for f in gpaths:
-# os.remove(f)
-
-# # probleme avec .fna de onames[0] qui n'est pas créé...
-
+def test_format_all_prokka(caplog):
+ """
+ Test that when giving a list of genomes, for which prokka ran without problem,
+ they are formatted, with all expected files created.
+ """
+ caplog.set_level(logging.DEBUG)
+ # genomes = {genome: [name, gpath, to_annot, size, nbcont, l90]}
+ # Get genome names we want to format (with their path)
+ gnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
+ gpaths = [os.path.join(ANNOTEDIR, "genomes", name) for name in gnames]
+ onames = ["test_runprokka_H299", "test.0417.00002"]
+ genomes = {gnames[0]: [onames[0], gpaths[0], gpaths[0], 12656, 3, 1],
+ gnames[1]: [onames[1], gpaths[1], gpaths[1], 456464645, 5, 1]
+ }
+ res_path = GENEPATH
+ annotated_path = os.path.join(ANNOTEDIR, "exp_files")
+ # Format both genomes
+ skipped_format = ffunc.format_genomes(genomes, res_path, annotated_path, False, threads=2)
+ assert skipped_format == []
+ # Get all names of expected output files
+ exp_dir = os.path.join(EXP_ANNOTE, "res_formatAll", "prokka")
+ exp_folders = ["LSTINFO", "Proteins", "Genes", "Replicons", "gff3"]
+ exp_extensions = [".lst", ".prt", ".gen", ".fna", ".gff"]
+ # Check that output files are created, and contain what is expected
+ for fol, ext in zip(exp_folders, exp_extensions):
+ exp_files = [os.path.join(exp_dir, fol, name + ext) for name in onames]
+ res_files = [os.path.join(res_path, fol, name + ext) for name in onames]
+ for res, exp in zip(res_files, exp_files):
+ assert os.path.isfile(res)
+ assert tutil.compare_order_content(res, exp)
+ # Check log
+ assert "Formatting all genomes" in caplog.text
+
+
+def test_format_all_prodigal(caplog):
+ """
+ Test that when giving a list of genomes, for which prokka ran without problem,
+ they are formatted, with all expected files created.
+ """
+ caplog.set_level(logging.DEBUG)
+ # genomes = {genome: [name, gpath, to_annot, size, nbcont, l90]}
+ # Get genome names we want to format (with their path)
+ gnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
+ gpaths = [os.path.join(ANNOTEDIR, "genomes", name) for name in gnames]
+ onames = ["test_runprokka_H299", "test.0417.00002"]
+ genomes = {gnames[0]: [onames[0], gpaths[0], gpaths[0], 12656, 3, 1],
+ gnames[1]: [onames[1], gpaths[1], gpaths[1], 456464645, 5, 1]
+ }
+ res_path = GENEPATH
+ annotated_path = os.path.join(ANNOTEDIR, "exp_files")
+ # Format both genomes
+ skipped_format = ffunc.format_genomes(genomes, res_path, annotated_path, True, threads=2)
+ assert skipped_format == []
+ # Get all names of expected output files
+ exp_dir = os.path.join(EXP_ANNOTE, "res_formatAll", "prodigal")
+ exp_folders = ["LSTINFO", "Proteins", "Genes", "Replicons", "gff3"]
+ exp_extensions = [".lst", ".prt", ".gen", ".fna", ".gff"]
+ # Check that output files are created, and contain what is expected
+ for fol, ext in zip(exp_folders, exp_extensions):
+ exp_files = [os.path.join(exp_dir, fol, name + ext) for name in onames]
+ res_files = [os.path.join(res_path, fol, name + ext) for name in onames]
+ for res, exp in zip(res_files, exp_files):
+ assert os.path.isfile(res)
+ assert tutil.compare_order_content(res, exp)
+ # Check log
+ assert "Formatting all genomes" in caplog.text
+
+
+def test_format_1pb_prodigal(caplog):
+ """
+ Test that when giving a list of genomes, 1 that is correctly formatted, and 1 has a pb,
+ it returns the last one in skipped_format
+ """
+ caplog.set_level(logging.DEBUG)
+ # GENOME 2: Create empty original genome file
+ genome1 = "wrong.fasta"
+ gpath1 = os.path.join(GENEPATH, "wrong.fasta")
+ open(gpath1, "w").close()
+ # Add prodigal (empty) result files to prodigalRes directory
+ prodi_path = gpath1 + "-prodigalRes"
+ os.makedirs(prodi_path)
+ gff_res = os.path.join(prodi_path, "toto.gff")
+ ffn_res = os.path.join(prodi_path, "toto.ffn")
+ faa_res = os.path.join(prodi_path, "toto.faa")
+ for file in [gff_res, ffn_res, faa_res]:
+ open(file, "w").close()
+ # Create output directory for .fna file
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ os.makedirs(rep_dir)
+ # GENOME 2
+ genome2 = "H299_H561.fasta"
+ gpath2 = os.path.join(ANNOTEDIR, "genomes", genome2)
+ # Copy results of prodigal for this genome to output dir (GENEPATH)
+ orig_res_files = os.path.join(EXP_ANNOTE, genome2 + '-prodigalRes')
+ used_res_path = os.path.join(GENEPATH, genome2 + "-prodigalRes")
+ shutil.copytree(orig_res_files, used_res_path)
+ # genomes = {genome: [name, gpath, to_annot, size, nbcont, l90]}
+ genomes = {genome1: ["test_genome1", gpath1, gpath1, 12656, 3, 1],
+ genome2: ["test_H299_H561", gpath2, gpath2, 456464645, 5, 1]
+ }
+ res_path = GENEPATH
+ annotated_path = GENEPATH
+ # Format both genomes
+ skipped_format = ffunc.format_genomes(genomes, res_path, annotated_path, True, threads=2)
+ assert skipped_format == ["wrong.fasta"]
+ # Get all names of expected output files
+ exp_dir = os.path.join(EXP_ANNOTE, "res_formatAll", "prodigal")
+ exp_folders = ["LSTINFO", "Proteins", "Genes", "Replicons", "gff3"]
+ exp_extensions = [".lst", ".prt", ".gen", ".fna", ".gff"]
+ # Check that output files are created, and contain what is expected
+ for fol, ext in zip(exp_folders, exp_extensions):
+ exp_files = [os.path.join(exp_dir, fol, name + ext) for name in onames]
+ res_files = [os.path.join(res_path, fol, name + ext) for name in onames]
+ for res, exp in zip(res_files, exp_files):
+ assert os.path.isfile(res)
+ assert tutil.compare_order_content(res, exp)
+ # Check log
+ assert "Formatting all genomes" in caplog.text
# def test_format_all_error():
# """