def test_run_prodigal_out_exists_ok():
"""
Test that when the output directory already exists, and files inside are OK,
run_prodigal returns True, with a warning message indicating that prodigal did not rerun.
"""
logger = my_logger("test_run_prodigal_out_exists_ok")
utils.init_logger(LOGFILE_BASE, 0, 'prodigal_out_exists_ok')
gpath = "path/to/nogenome/original_name.fna"
cores_prodigal = 1
name = "prodigal.outtest.ok"
force = False
nbcont = 7
trn_file = os.path.join(TEST_DIR, "A_H738-and-B2_A3_5.fna.trn")
arguments = (gpath, TEST_DIR, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert afunc.run_prodigal(arguments)
q = logger[0]
assert q.qsize() == 4
# start annotating :
assert q.get().message.startswith(
"Start annotating prodigal.outtest.ok (from "
"path/to/nogenome/original_name.fna sequence) with Prodigal")
# # warning prodigal results folder exists:
assert q.get().message.startswith(
"Prodigal results folder test/data/annotate/test_files/"
"original_name.fna-prodigalRes already exists.")
# Results in result folder are ok
assert q.get().message.startswith(
"Prodigal did not run again. Formatting step will use "
"already generated results of Prodigal in "
"test/data/annotate/test_files/"
"original_name.fna-prodigalRes.")
# End annotation:
assert q.get().message.startswith("End annotating")
def test_run_prodigal_out_exists_force():
"""
Test that when the output directory already exists with wrong files, but force is on,
prodigal is rerun and outputs the right files
"""
logger = my_logger("test_run_prodigal_out_exists_force")
utils.init_logger(LOGFILE_BASE, 0, 'force')
gpath = os.path.join(GEN_PATH, "H299_H561.fasta")
out_prokdir = os.path.join(GENEPATH, "H299_H561.fasta-prodigalRes")
name = "test_runprodigal_H299"
# Put empty tbl, faa, ffn files in prodigal output dir, to check that they are overridden
os.makedirs(out_prokdir)
open(os.path.join(out_prokdir, name + ".gff"), "w").close()
open(os.path.join(out_prokdir, name + ".faa"), "w").close()
open(os.path.join(out_prokdir, name + ".ffn"), "w").close()
cores_prodigal = 2
force = True
nbcont = 3
trn_file = os.path.join(TEST_DIR, "A_H738-and-B2_A3_5.fna.trn")
arguments = (gpath, GENEPATH, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert afunc.run_prodigal(arguments)
# As we used 'force', tbl, faa and ffn files, which were empty, must have been replaced
# by the prodigal output
exp_dir = os.path.join(EXP_DIR, "H299_H561.fasta-prodigalRes",
"ESCO.1015.00001")
out_gff = os.path.join(out_prokdir, name + ".gff")
out_faa = os.path.join(out_prokdir, name + ".faa")
out_ffn = os.path.join(out_prokdir, name + ".ffn")
# Check that faa and ffn files are as expected
assert os.path.isfile(out_faa)
assert tutil.compare_order_content(exp_dir + ".faa", out_faa)
assert os.path.isfile(out_ffn)
assert tutil.compare_order_content(exp_dir + ".ffn", out_ffn)
q = logger[0]
assert q.qsize() == 4
assert q.get().message.startswith(
"Prodigal results folder already exists, but is "
"removed because --force option was used")
assert q.get().message.startswith(
"Start annotating test_runprodigal_H299 (from test/data/"
"annotate/genomes/H299_H561.fasta sequence) "
"with Prodigal")
assert q.get().message.startswith(
"Prodigal command: prodigal -i test/data/annotate/genomes/"
"H299_H561.fasta -d test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_H299.ffn -a test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_H299.faa -f gff -o test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_H299.gff -t "
"test/data/annotate/test_files/A_H738-and-B2_A3_5.fna.trn "
"-q")
assert q.get().message.startswith(
"End annotating test_runprodigal_H299 "
"(from test/data/annotate/genomes/H299_H561.fasta)")
def test_run_prodigal_small():
"""
Test that when the output directory does not exist, it creates it, and runs prodigal
with all expected outfiles. Here, we run prodigal with --small option (on a small genome)
"""
logger = my_logger("test_run_prodigal_small")
utils.init_logger(LOGFILE_BASE, 0, 'test_run_prodigal_small')
gpath = os.path.join(GEN_PATH, "H299_H561.fasta")
out_dir = os.path.join(GENEPATH, "H299_H561.fasta-prodigalRes")
cores_prodigal = 2
name = "test_runprodigal_small_H299"
force = False
trn_file = "small option"
nbcont = 3
arguments = (gpath, GENEPATH, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert afunc.run_prodigal(arguments)
# Check content of tbl, ffn and faa files
exp_dir = os.path.join(EXP_DIR, "H299_H561.fasta_small-prodigalRes",
"test_runprodigal_small_H299")
out_faa = os.path.join(out_dir, name + ".faa")
out_ffn = os.path.join(out_dir, name + ".ffn")
out_gff = os.path.join(out_dir, name + ".gff")
# Check that faa and ffn files are as expected
assert os.path.isfile(out_faa)
assert tutil.compare_order_content(exp_dir + ".faa", out_faa)
assert os.path.isfile(out_ffn)
assert tutil.compare_order_content(exp_dir + ".ffn", out_ffn)
assert os.path.isfile(out_ffn)
assert tutil.compare_order_content(exp_dir + ".gff", out_gff)
# Check logs
q = logger[0]
assert q.qsize() == 3
assert q.get().message.startswith("Start annotating")
prodigal_cmd = q.get().message
assert ("Prodigal command: prodigal -i test/data/annotate/genomes/"
"H299_H561.fasta -d test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_small_H299.ffn -a test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_small_H299.faa -f gff -o test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_small_H299.gff -p meta -q") in prodigal_cmd
assert q.get().message.startswith("End annotating")
def test_run_prodigal_out_doesnt_exist():
"""
Test that when the output directory does not exist, it creates it, and runs prodigal
with all expected outfiles
"""
logger = my_logger("test_run_prodigal_out_doesnt_exist")
utils.init_logger(LOGFILE_BASE, 0, 'test_run_prodigal_out_doesnt_exist')
gpath = os.path.join(GEN_PATH, "H299_H561.fasta")
out_dir = os.path.join(GENEPATH, "H299_H561.fasta-prodigalRes")
cores_prodigal = 2
name = "test_runprodigal_H299"
force = False
trn_file = os.path.join(TEST_DIR, "A_H738-and-B2_A3_5.fna.trn")
nbcont = 3
arguments = (gpath, GENEPATH, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert afunc.run_prodigal(arguments)
# Check content of tbl, ffn and faa files
exp_dir = os.path.join(EXP_DIR, "H299_H561.fasta-prodigalRes",
"ESCO.1015.00001")
out_faa = os.path.join(out_dir, name + ".faa")
out_ffn = os.path.join(out_dir, name + ".ffn")
out_gff = os.path.join(out_dir, name + ".gff")
# Check that faa and ffn files are as expected
assert os.path.isfile(out_faa)
assert tutil.compare_order_content(exp_dir + ".faa", out_faa)
assert os.path.isfile(out_ffn)
assert tutil.compare_order_content(exp_dir + ".ffn", out_ffn)
assert os.path.isfile(out_ffn)
assert tutil.compare_order_content(exp_dir + ".gff", out_gff)
q = logger[0]
assert q.qsize() == 3
assert q.get().message.startswith("Start annotating")
assert q.get().message == (
"Prodigal command: prodigal -i test/data/annotate/genomes/"
"H299_H561.fasta -d test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_H299.ffn -a test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_H299.faa -f gff -o test/data/annotate/"
"generated_by_unit-tests/H299_H561.fasta-prodigalRes/"
"test_runprodigal_H299.gff -t "
"test/data/annotate/test_files/A_H738-and-B2_A3_5.fna.trn "
"-q")
assert q.get().message.startswith("End annotating")
def test_run_prodigal_out_exists_error():
"""
Test that when the output directory already exists, and 1 file is missing,
run_prodigal returns False, and writes the warning message saying that prodigal did not
rerun, + the warning message for the missing file(s).
"""
logger = my_logger("test_run_prodigal_out_exists_error")
utils.init_logger(LOGFILE_BASE, 0, 'prodigal_out_error')
ori_prok_dir = os.path.join(TEST_DIR, "original_name.fna-prodigalRes")
ori_name = "prodigal.outtest.ok"
new_prok_dir = os.path.join(GENEPATH, "original_name-error-prodigalRes")
name = "prodigal_out_for_test-wrongCDS"
os.makedirs(new_prok_dir)
shutil.copyfile(os.path.join(ori_prok_dir, ori_name + ".ffn"),
os.path.join(new_prok_dir, name + ".ffn"))
shutil.copyfile(os.path.join(ori_prok_dir, ori_name + ".faa"),
os.path.join(new_prok_dir, name + ".faa"))
open(os.path.join(new_prok_dir, name + ".gff"), "w").close()
gpath = "path/to/nogenome/original_name-error"
cores_prodigal = 1
force = False
trn_file = os.path.join(TEST_DIR, "A_H738-and-B2_A3_5.fna.trn")
nbcont = 7
arguments = (gpath, GENEPATH, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert not afunc.run_prodigal(arguments)
q = logger[0]
assert q.qsize() == 4
# start annotating :
assert q.get().message.startswith("Start annotating")
# warning prodigal results folder exists:
assert q.get().message == (
"Prodigal results folder test/data/annotate/"
"generated_by_unit-tests/"
"original_name-error-prodigalRes already exists.")
# error, empty gff
msg = ("Genome prodigal_out_for_test-wrongCDS (from original_name-error): "
"At least one of your Prodigal result file is empty.")
assert q.get().message == msg
# warning, files in outdir are not as expected
assert q.get().message.startswith(
"Problems in the files contained in your already existing "
"output dir (test/data/annotate/generated_by_unit-tests/"
"original_name-error-prodigalRes")
def test_run_prodigal_noout_notrain():
"""
Prodigal result directory does not exist (not already run)
training file does not exist (probably, problem while trying to train)
-> return False
"""
logger = my_logger("test_run_prodigal_out_exists_error")
utils.init_logger(LOGFILE_BASE, 0, 'prodigal_out_error')
gpath = "path/to/nogenome/original_name-error"
cores_prodigal = 1
name = "prodigal_out_for_test-wrongCDS"
force = False
nbcont = 7
trn_file = "ghost_trn_file"
arguments = (gpath, GENEPATH, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert not afunc.run_prodigal(arguments)
q = logger[0]
assert q.qsize() == 0
def test_run_prodigal_out_problem_running():
"""
Check that when a problem occurs while trying to run prodigal, run_prodigal returns False,
and the error message indicating to read in the log why it couldn't run
"""
logger = my_logger("test_run_prodigal_out_problem_running")
utils.init_logger(LOGFILE_BASE, 0, 'test_run_prodigal_out_problem_running')
gpath = os.path.join(GEN_PATH, "H299_H561bis.fasta")
cores_prodigal = 2
name = "test_runprodigal_H299-error"
force = False
nbcont = 3
trn_file = os.path.join(TEST_DIR, "A_H738-and-B2_A3_5.fna.trn")
logf = os.path.join(GENEPATH, "H299_H561bis.fasta-prodigal.log")
arguments = (gpath, GENEPATH, cores_prodigal, name, force, nbcont,
trn_file, logger[0])
assert not afunc.run_prodigal(arguments)
# Check that output directory is empty
outdir = os.path.join(GENEPATH, "H299_H561bis.fasta-prodigalRes")
assert os.listdir(outdir) == []
# Check logs
q = logger[0]
assert q.qsize() == 3
assert q.get().message.startswith("Start annotating")
assert q.get().message.startswith(
"Prodigal command: prodigal -i test/data/annotate/genomes/"
"H299_H561bis.fasta -d test/data/annotate/"
"generated_by_unit-tests/H299_H561bis.fasta-prodigalRes/"
"test_runprodigal_H299-error.ffn -a test/data/annotate/"
"generated_by_unit-tests/H299_H561bis.fasta-prodigalRes/"
"test_runprodigal_H299-error.faa -f gff -o test/data/annotate/"
"generated_by_unit-tests/H299_H561bis.fasta-prodigalRes/"
"test_runprodigal_H299-error.gff -t "
"test/data/annotate/test_files/A_H738-and-B2_A3_5.fna.trn "
"-q")
assert q.get().message.startswith(
"Error while trying to run prodigal. See test/data/"
"annotate/generated_by_unit-tests/"
"H299_H561bis.fasta-prodigal.log.err.")