def test_wrong_conffile_name(capsys):
"""
test that when the given config file does not exist, it raises an error
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(parser, "-c conf.ini -o out-all -T 1234 -n TEST".split())
out, err = capsys.readouterr()
assert ("Error: config file conf.ini not found.") in out
def test_duplicate_value(capsys):
"""
test that when a parameter is given twice in the configfile, it raises an error
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(
parser,
"-c test/data/all/init_files/conffile-duplicate.ini -o out-all "
"-n TEST --threads 2 --soft quicktree".split())
out, err = capsys.readouterr()
assert ("option 'verbose' in section 'prepare' already exists") in out
def test_parser_cutn_l90_nbcont():
"""
When user gives custom value for cutn, l90 and/or nbcont, it keeps it. No replacement with annotate module.
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
# custom cutn from command line
options = allm.parse(parser,
"-o out-all -n TEST --cutn 10 -T 1234".split())
assert options.outdir == "out-all"
assert options.cutn == 10
assert options.l90 == 100
assert options.nbcont == 999
# custom l90 from command line
options = allm.parse(parser, "-o out-all -n TEST --l90 10 -T 1234".split())
assert options.outdir == "out-all"
assert options.cutn == 5
assert options.l90 == 10
assert options.nbcont == 999
# custom nbcont from command line
options = allm.parse(
parser, "-o out-all -n TEST --l90 11 --nbcont 998 -T 1234".split())
assert options.outdir == "out-all"
assert options.cutn == 5
assert options.l90 == 11
assert options.nbcont == 998
# all 3 custom from configfile
options = allm.parse(
parser,
"-c test/data/all/init_files/cutn-l90-nbcont.ini -o out-all-bis -n TEST -T 1234"
.split())
assert options.outdir == "out-all-bis"
assert options.cutn == 15
assert options.l90 == 70
assert options.nbcont == 998
# l90 and cutn custom from configfile, cutn from command line
options = allm.parse(
parser,
"-c test/data/all/init_files/cutn-l90-nbcont.ini -o out-all-bis -n TEST -T 1234 --cutn 55"
.split())
assert options.outdir == "out-all-bis"
assert options.cutn == 55
assert options.l90 == 70
assert options.nbcont == 998
def test_parser_thread_quicktree(capsys):
"""
Testing default that quicktree + threads != 1 gives an error
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(
parser,
"-c test/data/all/init_files/default-conffigfile.ini -o out-all "
"-n TEST --threads 2 --soft quicktree".split())
_, err = capsys.readouterr()
assert ("You cannot run quicktree with multiple threads. "
"Choose another software, or remove the --threads option") in err
def test_parser_conffile_protalichanged():
"""
Test running with arguments with config file.
arguments given in cmd line are kept, others are those in configfile,
where prot_ali has been changed to True
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
options = allm.parse(
parser,
"-c test/data/all/init_files/default-conffigfile2.ini -o out-all -n TEST"
.split())
assert options.outdir == "out-all"
assert options.threads == 10
assert not options.ncbi_species_taxid
assert options.prodigal_only == False
assert options.norefseq
assert options.l90 == 100
assert options.clust_mode == 1
assert options.min_id == 0.85
assert options.tol == 1
assert not options.multi
assert not options.boot
assert options.prot_ali
def test_parser_conffile_and_cmd():
"""
Test that when some arguments given in config file are also given in cmd,
the value kept is the one in cmd.
"""
import multiprocessing
nb = multiprocessing.cpu_count()
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
options = allm.parse(
parser,
"-c test/data/all/init_files/default-conffigfile.ini -o out-all "
"-n TEST --threads 0 -i 0.99 -Mu".split())
assert options.outdir == "out-all"
assert options.threads == nb
assert not options.ncbi_species_taxid
assert options.prodigal_only == False
assert options.norefseq
assert options.l90 == 99
assert options.clust_mode == 1
assert options.min_id == 0.99
assert options.tol == 1
assert not options.floor
assert options.multi
assert not options.boot
assert not options.prot_ali
def test_parser_noarg(capsys):
"""
Test that when the script is called without any argument, an error message appears,
indicating the required arguments.
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(parser, "".split())
_, err = capsys.readouterr()
assert "usage: " in err
assert "-o OUTDIR [--threads THREADS]" in err
assert "[-T NCBI_SPECIES_TAXID]" in err
assert "-o OUTDIR" in err
assert "[-s NCBI_SPECIES]" in err
assert "[-l LEVELS]" in err
assert "[--cutn CUTN] [--l90 L90]" in err
assert "[--tol TOL]" in err
assert "[-Mu] [-X]" in err
assert "[--soft {fasttree,fastme,quicktree,iqtree,iqtree2}]" in err
assert "the following arguments are required: -o, -n" in err
def test_parser_noconffile():
"""
Test running with arguments ok for prepare, no configfile given.
Only args given in line change, all others are by default
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
options = allm.parse(parser, "-o out-all -n TEST -T 1234".split())
assert options.outdir == "out-all"
assert options.threads == 1
assert options.ncbi_species_taxid == '1234'
assert options.prodigal_only == False
assert not options.norefseq
assert options.l90 == 100
assert options.clust_mode == 1
assert options.min_id == 0.8
assert options.tol == 1
assert options.boot == 0
def test_corepers_tol(capsys):
"""
Test when a float value is given for tol parameter of corepers
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
options = allm.parse(
parser,
"-c test/data/all/init_files/conffile-corepers.ini -o out-all -n TEST".
split())
assert options.outdir == "out-all"
assert options.threads == 10
assert not options.ncbi_species_taxid
assert options.prodigal_only == False
assert options.min_dist == 0.01
assert options.norefseq
assert options.l90 == 100
assert options.clust_mode == 1
assert options.min_id == 0.85
assert options.tol == 0.85
assert not options.multi
assert not options.boot
def test_annot_defvalue(capsys):
"""
Test when a value is given in 'default' section of config file, but redefined in
another section, it keeps the redefined value
"""
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
options = allm.parse(
parser,
"-c test/data/all/init_files/default-conffigfile.ini -o out-all -n TEST"
.split())
assert options.outdir == "out-all"
assert options.threads == 10
assert not options.ncbi_species_taxid
assert options.prodigal_only == False
assert options.min_dist == '5'
assert options.norefseq
assert options.l90 == 99
assert options.clust_mode == 1
assert options.min_id == 0.85
assert options.tol == 1
assert not options.multi
assert not options.boot
def test_parser_error_contig_annotate(capsys):
"""
Test that when L90, nbcont or cutn parameter is given in annotate section of config file, it returns an error.
Those parameters can only be defined in prepare step.
"""
# Error with nbcont in annotate section of configfile
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(
parser,
"-o out-all -n TEST -T 5678 -c test/data/all/init_files/error_nbcont.ini"
.split())
out, err = capsys.readouterr()
assert ("nbcont not allowed in annotate section.") in out
# Error with l90 in annotate section of configfile
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(
parser,
"-o out-all -n TEST -T 5678 -c test/data/all/init_files/error_l90.ini --nbcont 10"
.split())
out, err = capsys.readouterr()
assert ("l90 not allowed in annotate section.") in out
# Error with cutn in annotate section of configfile
parser = argparse.ArgumentParser(description="Run all modules",
add_help=False)
allm.build_parser(parser)
with pytest.raises(SystemExit):
allm.parse(
parser,
"-o out-all -n TEST -T 5678 -c test/data/all/init_files/error_cutn.ini"
.split())
out, err = capsys.readouterr()
assert ("cutn not allowed in annotate section.") in out