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)
fna_prokres = os.path.join(gpath_prokres, "prokka_out_for_test.fna")
open(fna_prokres, "w").close()
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(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_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_fna = os.path.join(orig_gpath + "-prokkaRes", "prokka_out_for_test.fna")
fna_prokres = os.path.join(used_respath, "prokka_out_for_test.fna")
shutil.copyfile(orig_fna, fna_prokres)
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_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)
orig_fna = os.path.join(TEST_ANNOTE, "original_name.fna-prokkaRes", "prokka_out_for_test.fna")
fna_prokres = os.path.join(used_respath, "prokka_out_for_test.fna")
shutil.copyfile(orig_fna, fna_prokres)
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