def test_nisin_complete(self):
with TemporaryDirectory() as output_dir:
args = [
"--minimal", "--enable-tta", "--tta-threshold", "0",
"--output-dir", output_dir,
helpers.get_path_to_nisin_genbank()
]
options = build_config(args,
isolated=True,
modules=antismash.get_all_modules())
antismash.run_antismash(helpers.get_path_to_nisin_genbank(),
options)
# regen the results
update_config(
{"reuse_results": os.path.join(output_dir, "nisin.json")})
prior_results = read_data(None, options)
record = prior_results.records[0]
results = prior_results.results[0]
tta_results = tta.regenerate_previous_results(
results.get("antismash.modules.tta"), record, options)
assert isinstance(tta_results, tta.TTAResults)
assert len(tta_results.features) == 174
# raise the threshold above the gc_content and ensure regenned has no hits
update_config({"tta_threshold": 0.65})
tta_results = tta.regenerate_previous_results(
results.get("antismash.modules.tta"), record, options)
assert isinstance(tta_results, tta.TTAResults)
assert not tta_results.features
def test_nisin_complete(self):
with TemporaryDirectory() as output_dir:
args = [
"run_antismash.py", "--minimal", "--enable-lanthipeptides",
"--output-dir", output_dir
]
options = build_config(args,
isolated=True,
modules=antismash.get_all_modules())
antismash.run_antismash(helpers.get_path_to_nisin_genbank(),
options)
# make sure the html_output section was tested
with open(os.path.join(output_dir, "index.html")) as handle:
content = handle.read()
assert "nisA leader / core peptide" in content
def main(args: List[str]) -> int:
""" The entrypoint of antiSMASH as if it was on the command line
Arguments:
args: a list of args as would be given on the command line
e.g. ["inputfile", "--minimal", "--enable-nrps_pks"]
Returns:
zero if successful, non-zero otherwise
"""
all_modules = antismash.get_all_modules()
parser = antismash.config.args.build_parser(from_config_file=True,
modules=all_modules)
# if --help, show help texts and exit
if set(args).intersection({"-h", "--help", "--help-showall"}):
parser.print_help(None, "--help-showall" in args)
return 0
options = antismash.config.build_config(args, parser=parser)
if options.write_config_file:
parser.write_to_config_file(options.write_config_file,
options.__dict__)
return 0
# if -V, show version text and exit
if options.version:
print("antiSMASH %s" % get_version())
return 0
if len(options.sequences) > 1:
parser.error("Only one sequence file should be provided")
return 1
if len(options.sequences) < 1 and not options.reuse_results \
and not options.check_prereqs_only and not options.list_plugins:
parser.error(
"One of an input file or --reuse-results must be specified")
return 1
if options.sequences and options.reuse_results:
parser.error("Provide a sequence file or results to reuse, not both.")
return 1
if options.sequences:
sequence = options.sequences[0]
if not os.path.exists(sequence):
parser.error("Input file does not exist: %s" % sequence)
return 1
else:
sequence = ""
if options.reuse_results and not os.path.exists(options.reuse_results):
parser.error("Input file does not exist: %s" % options.reuse_results)
return 1
options.version = get_version()
return antismash.run_antismash(sequence, options)
def test_trees_complete(self):
with TemporaryDirectory() as output_dir:
args = [
"--minimal", "--enable-genefunctions", "--smcog-trees",
"--output-dir", output_dir,
helpers.get_path_to_nisin_genbank()
]
options = build_config(args,
isolated=True,
modules=antismash.get_all_modules())
antismash.run_antismash(helpers.get_path_to_nisin_genbank(),
options)
with open(os.path.join(output_dir, "nisin.json")) as res_file:
assert "antismash.modules.smcog_trees" in res_file.read()
tree_files = list(
glob.glob(os.path.join(output_dir, "smcogs", "*.png")))
assert len(tree_files) == 7
sample_tree = tree_files[0]
# regen the results
update_config(
{"reuse_results": os.path.join(output_dir, "nisin.json")})
prior_results = read_data(None, options)
record = prior_results.records[0]
results = prior_results.results[0]
tree_results = results["antismash.modules.smcog_trees"]
smcogs_results = smcog_trees.regenerate_previous_results(
tree_results, record, options)
assert len(smcogs_results.tree_images) == 7
assert os.path.exists(sample_tree)
os.unlink(sample_tree)
assert not os.path.exists(sample_tree)
# attempt to regen the results, the deleted tree image will prevent it
prior_results = read_data(None, options)
record = prior_results.records[0]
results = prior_results.results[0]
smcogs_results = smcog_trees.regenerate_previous_results(
tree_results, record, options)
assert smcogs_results is None
def test_nisin_complete(self):
with TemporaryDirectory() as output_dir:
args = [
"--minimal", "--tta", "--output-dir", output_dir,
helpers.get_path_to_nisin_genbank()
]
options = build_config(args,
isolated=True,
modules=antismash.get_all_modules())
antismash.run_antismash(helpers.get_path_to_nisin_genbank(),
options)
# regen the results
update_config(
{"reuse_results": os.path.join(output_dir, "nisin.json")})
prior_results = read_data(None, options)
record = prior_results.records[0]
results = prior_results.results[0]
regenned = regenerate_results_for_record(record, options, [tta],
results)
tta_results = regenned["antismash.modules.tta"]
assert isinstance(tta_results, tta.TTAResults)
assert len(tta_results.features) == 174
def main(args):
all_modules = antismash.get_detection_modules(
) + antismash.get_analysis_modules()
parser = antismash.config.args.build_parser(from_config_file=True,
modules=all_modules)
# if --help, show help texts and exit
if set(args).intersection({"-h", "--help", "--help-showall"}):
parser.print_help(None, "--help-showall" in args)
return 0
options = antismash.config.build_config(args, parser=parser)
if options.write_config_file:
parser.write_to_config_file(options.write_config_file,
options.__dict__)
return 0
# if -V, show version text and exit
if options.version:
print("antiSMASH %s" % get_version())
return 0
if len(options.sequences) > 1:
parser.error("Only one sequence file should be provided")
return 1
if len(options.sequences) < 1 and not options.reuse_results \
and not options.check_prereqs_only and not options.list_plugins:
parser.error(
"One of an input file or --reuse-results must be specified")
return 1
if options.sequences and options.reuse_results:
parser.error("Provide a sequence file or results to reuse, not both.")
return 1
if options.sequences:
sequence = options.sequences[0]
options.__dict__.pop("sequences")
else:
sequence = ""
options.version = get_version()
return antismash.run_antismash(sequence, options)
