def run(self, args):
super(Build, self).run(args)
if path.exists(args.destination):
if args.destination == self._default_dir:
raise CommandParseException("Error, default destination [" +
args.destination +
"] already exists",
self._root_arg_parser,
print_help=True)
else:
raise CommandParseException(
"Error, destination [" + args.destination +
"] already exists", self._root_arg_parser)
else:
mkdir(args.destination)
if args.destination == AMRDatabasesManager.get_default_database_directory(
):
database_handler = AMRDatabasesManager.create_default_manager(
).get_database_handler()
else:
database_handler = AMRDatabasesManager(
args.destination).get_database_handler()
database_handler.build(resfinder_commit=args.resfinder_commit,
pointfinder_commit=args.pointfinder_commit)
if not AMRDatabasesManager.is_handler_default_commits(
database_handler):
logger.warning(
"Built non-default ResFinder/PointFinder database version. This may lead to "
+
"differences in the detected AMR genes depending on how the database files are structured."
)
def run(self, args):
super(Info, self).run(args)
arg_drug_table = ARGDrugTable()
if len(args.directories) == 0:
database_handler = AMRDatabasesManager.create_default_manager(
).get_database_handler()
if not AMRDatabasesManager.is_handler_default_commits(
database_handler):
logger.warning(
"Using non-default ResFinder/PointFinder database versions. This may lead to differences in the detected "
+
"AMR genes depending on how the database files are structured."
)
try:
database_info = database_handler.info()
database_info.update(
arg_drug_table.get_resistance_table_info())
sys.stdout.write(get_string_with_spacing(database_info))
except DatabaseNotFoundException as e:
logger.error(
"No database found. Perhaps try restoring the default with 'staramr db restore-default'"
)
else:
for directory in args.directories:
try:
database_handler = AMRDatabasesManager(
directory).get_database_handler()
if not AMRDatabasesManager.is_handler_default_commits(
database_handler):
logger.warning(
"Using non-default ResFinder/PointFinder database version [%s]. This may lead to "
+
"differences in the detected AMR genes depending on how the database files are structured.",
directory)
database_info = database_handler.info()
database_info.update(
arg_drug_table.get_resistance_table_info())
sys.stdout.write(get_string_with_spacing(database_info))
except DatabaseNotFoundException as e:
logger.error(
"Database not found in [%s]. Perhaps try building with 'staramr db build --dir %s'",
directory, directory)
def testIsHandlerDefaultCommitsTrue(self):
# Setup default database
self.databases_manager.setup_default()
database_handler = self.databases_manager.get_database_handler()
self.assertTrue(
AMRDatabasesManager.is_handler_default_commits(database_handler),
"Database is not default")
def run(self, args):
super(Update, self).run(args)
if len(args.directories) == 0:
if not args.update_default:
raise CommandParseException(
"Must pass at least one directory to update, or use '--update-default'",
self._root_arg_parser,
print_help=True)
else:
try:
database_handler = AMRDatabasesManager.create_default_manager(
).get_database_handler(force_use_git=True)
database_handler.update(
resfinder_commit=args.resfinder_commit,
pointfinder_commit=args.pointfinder_commit)
if not AMRDatabasesManager.is_handler_default_commits(
database_handler):
logger.warning(
"Updated to non-default ResFinder/PointFinder database version. This may lead to "
+
"differences in the detected AMR genes depending on how the database files are structured."
)
except DatabaseErrorException as e:
logger.error(
"Could not update default database. Please try restoring with 'staramr db restore-default'"
)
raise e
else:
for directory in args.directories:
database_handler = AMRDatabasesManager(
directory).get_database_handler()
database_handler.update(
resfinder_commit=args.resfinder_commit,
pointfinder_commit=args.pointfinder_commit)
if not AMRDatabasesManager.is_handler_default_commits(
database_handler):
logger.warning(
"Updated to non-default ResFinder/PointFinder database version [%s]. This may lead to "
+
"differences in the detected AMR genes depending on how the database files are structured.",
directory)
def testIsHandlerDefaultCommitsFalse(self):
# Setup database
database_handler = self.databases_manager.get_database_handler(
force_use_git=True)
database_handler.update(
resfinder_commit='dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2')
self.assertFalse(
AMRDatabasesManager.is_handler_default_commits(database_handler),
"Database is default")
def run(self, args):
super(Search, self).run(args)
if (len(args.files) == 0):
raise CommandParseException("Must pass a fasta file to process", self._root_arg_parser, print_help=True)
for file in args.files:
if not path.exists(file):
raise CommandParseException('File [' + file + '] does not exist', self._root_arg_parser)
if not path.isdir(args.database):
if args.database == self._default_database_dir:
raise CommandParseException(
"Default database does not exist. Perhaps try restoring with 'staramr db restore-default'",
self._root_arg_parser)
else:
raise CommandParseException(
"Database directory [" + args.database + "] does not exist. Perhaps try building with" +
"'staramr db build --dir " + args.database + "'",
self._root_arg_parser)
if args.database == AMRDatabasesManager.get_default_database_directory():
database_handler = AMRDatabasesManager.create_default_manager().get_database_handler()
else:
database_handler = AMRDatabasesManager(args.database).get_database_handler()
if not AMRDatabasesManager.is_handler_default_commits(database_handler):
logger.warning("Using non-default ResFinder/PointFinder. This may lead to differences in the detected " +
"AMR genes depending on how the database files are structured.")
resfinder_database_dir = database_handler.get_resfinder_dir()
pointfinder_database_dir = database_handler.get_pointfinder_dir()
resfinder_database = ResfinderBlastDatabase(resfinder_database_dir)
if (args.pointfinder_organism):
if args.pointfinder_organism not in PointfinderBlastDatabase.get_available_organisms():
raise CommandParseException("The only Pointfinder organism(s) currently supported are " + str(
PointfinderBlastDatabase.get_available_organisms()), self._root_arg_parser)
pointfinder_database = PointfinderBlastDatabase(pointfinder_database_dir,
args.pointfinder_organism)
else:
logger.info("No --pointfinder-organism specified. Will not search the PointFinder databases")
pointfinder_database = None
hits_output_dir = None
output_summary = None
output_resfinder = None
output_pointfinder = None
output_excel = None
output_settings = None
if args.output_dir:
if path.exists(args.output_dir):
raise CommandParseException("Output directory [" + args.output_dir + "] already exists",
self._root_arg_parser)
elif args.output_summary or args.output_resfinder or args.output_pointfinder or args.output_excel or \
args.hits_output_dir:
raise CommandParseException('You cannot use --output-[type] with --output-dir', self._root_arg_parser)
else:
mkdir(args.output_dir)
hits_output_dir = path.join(args.output_dir, 'hits')
output_resfinder = path.join(args.output_dir, "resfinder.tsv")
output_pointfinder = path.join(args.output_dir, "pointfinder.tsv")
output_summary = path.join(args.output_dir, "summary.tsv")
output_settings = path.join(args.output_dir, "settings.txt")
output_excel = path.join(args.output_dir, 'results.xlsx')
mkdir(hits_output_dir)
logger.info("--output-dir set. All files will be output to [%s]", args.output_dir)
elif args.output_summary or args.output_excel:
logger.info('--output-dir not set. Files will be output to the respective --output-[type] setting')
output_resfinder = args.output_resfinder
output_pointfinder = args.output_pointfinder
output_summary = args.output_summary
output_settings = args.output_settings
output_excel = args.output_excel
hits_output_dir = args.hits_output_dir
if hits_output_dir is not None:
if path.exists(hits_output_dir) and not path.isdir(hits_output_dir):
raise CommandParseException(
"--output-hits-dir [" + hits_output_dir + "] exists and is not a directory",
self._root_arg_parser)
elif path.exists(hits_output_dir):
logger.debug("Found --output-hits-dir [%s] and is a directory. Will write hits here",
hits_output_dir)
else:
logger.debug("Making directory [%s]", hits_output_dir)
mkdir(hits_output_dir)
else:
raise CommandParseException('You must set one of --output-dir, --output-summary, or --output-excel',
self._root_arg_parser)
if args.no_exclude_genes:
logger.info("--no-exclude-genes enabled. Will not exclude any ResFinder/PointFinder genes.")
exclude_genes = []
else:
if not path.exists(args.exclude_genes_file):
raise CommandParseException('--exclude-genes-file [{}] does not exist'.format(args.exclude_genes_file),
self._root_arg_parser)
else:
logger.info("Will exclude ResFinder/PointFinder genes listed in [%s]. Use --no-exclude-genes to disable",args.exclude_genes_file)
exclude_genes=ExcludeGenesList(args.exclude_genes_file).tolist()
results = self._generate_results(database_handler=database_handler,
resfinder_database=resfinder_database,
pointfinder_database=pointfinder_database,
nprocs=args.nprocs,
include_negatives=not args.exclude_negatives,
include_resistances=not args.exclude_resistance_phenotypes,
hits_output=hits_output_dir,
pid_threshold=args.pid_threshold,
plength_threshold_resfinder=args.plength_threshold_resfinder,
plength_threshold_pointfinder=args.plength_threshold_pointfinder,
report_all_blast=args.report_all_blast,
genes_to_exclude=exclude_genes,
files=args.files)
amr_detection = results['results']
settings = results['settings']
if output_resfinder:
logger.info("Writing resfinder to [%s]", output_resfinder)
with open(output_resfinder, 'w') as fh:
self._print_dataframe_to_text_file_handle(amr_detection.get_resfinder_results(), fh)
else:
logger.info("--output-dir or --output-resfinder unset. No resfinder file will be written")
if args.pointfinder_organism and output_pointfinder:
logger.info("Writing pointfinder to [%s]", output_pointfinder)
with open(output_pointfinder, 'w') as fh:
self._print_dataframe_to_text_file_handle(amr_detection.get_pointfinder_results(), fh)
else:
logger.info("--output-dir or --output-pointfinder unset. No pointfinder file will be written")
if output_summary:
logger.info("Writing summary to [%s]", output_summary)
with open(output_summary, 'w') as fh:
self._print_dataframe_to_text_file_handle(amr_detection.get_summary_results(), fh)
else:
logger.info("--output-dir or --output-summary unset. No summary file will be written")
if output_settings:
logger.info("Writing settings to [%s]", output_settings)
self._print_settings_to_file(settings, output_settings)
else:
logger.info("--output-dir or --output-settings unset. No settings file will be written")
if output_excel:
logger.info("Writing Excel to [%s]", output_excel)
settings_dataframe = pd.DataFrame.from_dict(settings, orient='index')
settings_dataframe.index.name = 'Key'
settings_dataframe.set_axis(['Value'], axis='columns', inplace=True)
self._print_dataframes_to_excel(output_excel,
amr_detection.get_summary_results(),
amr_detection.get_resfinder_results(),
amr_detection.get_pointfinder_results(),
settings_dataframe)
else:
logger.info("--output-dir or --output-excel unset. No excel file will be written")
if hits_output_dir:
logger.info("BLAST hits are stored in [%s]", hits_output_dir)
else:
logger.info("--output-dir or --output-hits-dir not set. No BLAST hits will be saved.")