diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7193c19b23cd40d8a1dd6d39a7925f438b5127fc..a45d544827e115e66afd2bb8f96157ede1bf5e6e 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -83,10 +83,8 @@ unit-test-ubuntu:
- py.test test/test_unit/test_utils-argparse.py -vx
- py.test test/test_unit/test_prepare -v -x
- 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_prodigal.py -vx
+ - py.test test/test_unit/test_annotate/test_annotation* -vx
+ - py.test test/test_unit/test_annotate/test_format* -v -x
- py.test test/test_unit/test_pangenome -vx
- py.test test/test_unit/test_corepers -vx
- py.test test/test_unit/test_align -vx
diff --git a/test/test_unit/test_annotate/test_format_func.py b/test/test_unit/test_annotate/test_format_func.py
index 99cc33ebd6aa5c4b3c2f5fc2bc23090b5265f5db..727db37dd7872e297e87bed4fe9d8ecc7997a2b3 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
@@ -355,6 +355,53 @@ def test_format_all_prodigal(caplog):
assert "Formatting all genomes" in caplog.text
+def test_format_allpb_prokka(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)
+ # Create empty original sequence files
+ genomes = ["wrong.fasta", "error.fasta"]
+ gpaths = [os.path.join(GENEPATH, name) for name in genomes]
+ for file in gpaths:
+ open(file, "w").close()
+ # Add prokka (empty) result files to prokkaRes directory
+ prok_paths = [gpath + "-prokkaRes" for gpath in gpaths]
+ for prok_path in prok_paths:
+ os.makedirs(prok_path)
+ tbl_res = os.path.join(prok_path, "toto.tbl")
+ gff_res = os.path.join(prok_path, "toto.gff")
+ ffn_res = os.path.join(prok_path, "toto.ffn")
+ faa_res = os.path.join(prok_path, "toto.faa")
+ for file in [tbl_res, gff_res, ffn_res, faa_res]:
+ open(file, "w").close()
+ # Create output directory for .fna files
+ rep_dir = os.path.join(GENEPATH, "Replicons")
+ os.makedirs(rep_dir)
+ # genomes = {genome: [name, gpath, to_annot, size, nbcont, l90]}
+ genomes = {genomes[0]: ["test_wrong-fasta", gpaths[0], gpaths[0], 12656, 3, 1],
+ genomes[1]: ["test_error-fasta", gpaths[1], gpaths[1], 456464645, 5, 1]
+ }
+ res_path = GENEPATH
+ annotated_path = GENEPATH
+ # Try to format both genomes
+ skipped_format = ffunc.format_genomes(genomes, res_path, annotated_path, False, threads=1)
+ assert skipped_format == ["wrong.fasta", "error.fasta"]
+ # Get all names of expected output files
+ exp_folders = ["LSTINFO", "Proteins", "Genes", "Replicons", "gff3"]
+ for res_folder in [os.path.join(res_path, folder) for folder in exp_folders]:
+ assert len(os.listdir(res_folder)) == 0
+ # Check log
+ assert "Formatting all genomes" in caplog.text
+ assert ("Your genome test/data/annotate/generated_by_unit-tests/wrong.fasta does not "
+ "contain any sequence, or is not in fasta format.") in caplog.text
+ assert ("Your genome test/data/annotate/generated_by_unit-tests/error.fasta does not "
+ "contain any sequence, or is not in fasta format.") in caplog.text
+ assert "Problems while generating Replicon file for test_wrong-fasta" in caplog.text
+ assert "Problems while generating Replicon file for test_error-fasta" 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,
@@ -385,7 +432,7 @@ def test_format_1pb_prodigal(caplog):
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]
+ genome2: ["test_runprokka_H299", gpath2, gpath2, 456464645, 5, 1]
}
res_path = GENEPATH
annotated_path = GENEPATH
@@ -398,70 +445,12 @@ def test_format_1pb_prodigal(caplog):
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)
+ exp_file = os.path.join(exp_dir, fol, "test_runprokka_H299" + ext)
+ res_file = os.path.join(res_path, fol, "test_runprokka_H299" + ext)
+ assert os.path.isfile(res_file)
+ assert tutil.compare_order_content(res_file, exp_file)
# Check log
assert "Formatting all genomes" in caplog.text
-
-# def test_format_all_error():
-# """
-# Test that when giving a list of 2 genomes, prokka ran without problem for both.
-# But a problem appears while formatting the 2nd one. So, the 2nd one is not formatted,
-# and appears in skipped_format. The first one is formated, and check that all
-# output files are created.
-# """
-# # genomes = {genome: [name, gpath, size, nbcont, l90]}
-# name = "test.0417.00002"
-# 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-problems.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")
-# tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-# name + ".tbl")
-# tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-# name + ".tbl")
-# shutil.copyfile(tbl_init, tblout)
-# gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-# name + ".gff")
-# gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-# name + ".gff")
-# shutil.copyfile(gff_init, gffout)
-# results = {gnames[0]: True, gnames[1]: True}
-# skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
-# assert skipped == []
-# assert skipped_format == ["B2_A3_5.fasta-problems.fna-short-contig.fna"]
-# 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"))
-# os.remove(tblout)
-# os.remove(gffout)
-# for f in gpaths:
-# os.remove(f)
+ assert ("Your genome test/data/annotate/generated_by_unit-tests/wrong.fasta does not "
+ "contain any sequence, or is not in fasta format.") in caplog.text
+ assert "Problems while generating Replicon file for test_genome1" in caplog.text