def build_blast_database(
self,
database_name: str,
options: Dict[str, str] = {}) -> AbstractBlastDatabase:
"""
Builds a staramr.blast.AbstractBlastDatabase from the given parameters.
:param database_name: The name of the database to build.
:param options: Options for the particular database in the form of a map {'key': 'value'}
:return: A new staramr.blast.AbstractBlastDatabase.
"""
if database_name not in self._database_repositories:
raise Exception("database_name={} not registered", database_name)
if database_name == 'resfinder':
return ResfinderBlastDatabase(self.get_repo_dir(database_name))
elif database_name == 'pointfinder':
return PointfinderBlastDatabase(self.get_repo_dir(database_name),
options['organism'])
else:
raise Exception("Unknown database name [{}]", database_name)
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_repos = AMRDatabasesManager.create_default_manager(
).get_database_repos()
else:
database_repos = AMRDatabasesManager(
args.database).get_database_repos()
if not AMRDatabasesManager.is_database_repos_default_commits(
database_repos):
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 = database_repos.build_blast_database('resfinder')
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 = database_repos.build_blast_database(
'pointfinder', {'organism': args.pointfinder_organism})
else:
logger.info(
"No --pointfinder-organism specified. Will not search the PointFinder databases"
)
pointfinder_database = None
if (args.plasmidfinder_database_type):
if args.plasmidfinder_database_type not in PlasmidfinderBlastDatabase.get_available_databases(
):
raise CommandParseException(
"The only Plasmidfinder databases that are currently supported are "
+
str(PlasmidfinderBlastDatabase.get_available_databases()),
self._root_arg_parser)
plasmidfinder_database = database_repos.build_blast_database(
'plasmidfinder',
{'database_type': args.plasmidfinder_database_type})
else:
logger.info(
"No --plasmidfinder-database-type specified. Will search the entire PlasmidFinder database"
)
plasmidfinder_database = database_repos.build_blast_database(
'plasmidfinder')
hits_output_dir = None
output_summary = None
output_detailed_summary = None
output_resfinder = None
output_pointfinder = None
output_plasmidfinder = None
output_mlst = 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_detailed_summary or args.output_resfinder or args.output_pointfinder or args.output_plasmidfinder 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_plasmidfinder = path.join(args.output_dir,
"plasmidfinder.tsv")
output_summary = path.join(args.output_dir, "summary.tsv")
output_detailed_summary = path.join(args.output_dir,
"detailed_summary.tsv")
output_mlst = path.join(args.output_dir, "mlst.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 or args.output_detailed_summary:
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_plasmidfinder = args.output_plasmidfinder
output_summary = args.output_summary
output_detailed_summary = args.output_detailed_summary
output_mlst = args.output_mlst
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, --output-detailed-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_repos=database_repos,
resfinder_database=resfinder_database,
pointfinder_database=pointfinder_database,
plasmidfinder_database=plasmidfinder_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,
plength_threshold_plasmidfinder=args.
plength_threshold_plasmidfinder,
report_all_blast=args.report_all_blast,
genes_to_exclude=exclude_genes,
files=args.files,
ignore_invalid_files=args.ignore_valid_files,
mlst_scheme=args.mlst_scheme,
genome_size_lower_bound=args.genome_size_lower_bound,
genome_size_upper_bound=args.genome_size_upper_bound,
minimum_N50_value=args.minimum_N50_value,
minimum_contig_length=args.minimum_contig_length,
unacceptable_num_contigs=args.unacceptable_num_contigs)
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_plasmidfinder:
logger.info("Writing plasmidfinder to [%s]", output_plasmidfinder)
with open(output_plasmidfinder, 'w') as fh:
self._print_dataframe_to_text_file_handle(
amr_detection.get_plasmidfinder_results(), fh)
else:
logger.info(
"--output-dir or --output-plasmidfinder unset. No plasmidfinder 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_mlst:
logger.info("Writing MLST summary to [%s]", output_mlst)
with open(output_mlst, 'w') as fh:
self._print_dataframe_to_text_file_handle(
amr_detection.get_mlst_results(), fh)
else:
logger.info(
"--output-dir or --output-mlst unset. No mlst file will be written"
)
if output_detailed_summary:
logger.info("Writing detailed summary to [%s]",
output_detailed_summary)
with open(output_detailed_summary, 'w') as fh:
self._print_dataframe_to_text_file_handle(
amr_detection.get_detailed_summary_results(), fh)
else:
logger.info(
"--output-dir or --output-detailed-summary unset. No detailed 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(),
amr_detection.get_plasmidfinder_results(),
amr_detection.get_detailed_summary_results(),
amr_detection.get_mlst_results(), settings_dataframe,
args.minimum_contig_length)
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."
)
def _setup_args(self, arg_parser):
name = self._script_name
epilog = (
"Example:\n"
"\t" + name + " search -o out *.fasta\n"
"\t\tSearches the files *.fasta for AMR genes using only the ResFinder database, storing results in the out/ directory.\n\n"
+ "\t" + name +
" search --pointfinder-organism salmonella --output-excel results.xlsx *.fasta\n"
+
"\t\tSearches *.fasta for AMR genes using ResFinder and PointFinder database with the passed organism, storing results in results.xlsx."
)
arg_parser = self._subparser.add_parser(
'search',
epilog=epilog,
formatter_class=argparse.RawTextHelpFormatter,
help='Search for AMR genes')
self._default_database_dir = AMRDatabasesManager.get_default_database_directory(
)
cpu_count = multiprocessing.cpu_count()
arg_parser.add_argument(
'--pointfinder-organism',
action='store',
dest='pointfinder_organism',
type=str,
help='The organism to use for pointfinder {' +
', '.join(PointfinderBlastDatabase.get_available_organisms()) +
'}. Defaults to disabling search for point mutations. [None].',
default=None,
required=False)
arg_parser.add_argument(
'--plasmidfinder-database-type',
action='store',
dest='plasmidfinder_database_type',
type=str,
help='The database type to use for plasmidfinder {' +
', '.join(PlasmidfinderBlastDatabase.get_available_databases()) +
'}. Defaults to using all available database types to search for plasmids. [None].',
default=None,
required=False)
arg_parser.add_argument(
'-d',
'--database',
action='store',
dest='database',
type=str,
help=
'The directory containing the resfinder/pointfinder/plasmidfinder databases ['
+ self._default_database_dir + '].',
default=self._default_database_dir,
required=False)
arg_parser.add_argument(
'-n',
'--nprocs',
action='store',
dest='nprocs',
type=int,
help='The number of processing cores to use [' + str(cpu_count) +
'].',
default=cpu_count,
required=False)
arg_parser.add_argument('--ignore-invalid-files',
action='store_true',
dest='ignore_valid_files',
help='Skips over invalid input files',
required=False)
arg_parser.add_argument(
'--mlst-scheme',
action='store',
dest='mlst_scheme',
help=
'Specify scheme name, visit https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab for supported scheme genus available. [None] ',
required=False)
arg_parser.add_argument(
'--genome-size-lower-bound',
action='store',
dest='genome_size_lower_bound',
type=int,
help=
'The lower bound for our genome size for the quality metrics. Defaults to 4 Mbp. [4000000].',
default=4000000,
required=False)
arg_parser.add_argument(
'--genome-size-upper-bound',
action='store',
dest='genome_size_upper_bound',
type=int,
help=
'The upper bound for our genome size for the quality metrics. Defaults to 6 Mbp. [6000000].',
default=6000000,
required=False)
arg_parser.add_argument(
'--minimum-N50-value',
action='store',
dest='minimum_N50_value',
type=int,
help=
'The minimum N50 value for the quality metrics. Defaults to 10000. [10000].',
default=10000,
required=False)
arg_parser.add_argument(
'--minimum-contig-length',
action='store',
dest='minimum_contig_length',
type=int,
help=
'The minimum contig length for the quality metrics. Defaults to 300 bp. [300].',
default=300,
required=False)
arg_parser.add_argument(
'--unacceptable-number-contigs',
action='store',
dest='unacceptable_num_contigs',
type=int,
help=
'The minimum, unacceptable number of contigs which are equal to or above the minimum contig length for our quality metrics. Defaults to 1000. [1000].',
default=1000,
required=False)
threshold_group = arg_parser.add_argument_group('BLAST Thresholds')
threshold_group.add_argument(
'--pid-threshold',
action='store',
dest='pid_threshold',
type=float,
help='The percent identity threshold [98.0].',
default=98.0,
required=False)
threshold_group.add_argument(
'--percent-length-overlap-resfinder',
action='store',
dest='plength_threshold_resfinder',
type=float,
help='The percent length overlap for resfinder results [60.0].',
default=60.0,
required=False)
threshold_group.add_argument(
'--percent-length-overlap-pointfinder',
action='store',
dest='plength_threshold_pointfinder',
type=float,
help='The percent length overlap for pointfinder results [95.0].',
default=95.0,
required=False)
threshold_group.add_argument(
'--percent-length-overlap-plasmidfinder',
action='store',
dest='plength_threshold_plasmidfinder',
type=float,
help='The percent length overlap for resfinder results [60.0].',
default=60.0,
required=False)
report_group = arg_parser.add_argument_group('Reporting options')
report_group.add_argument(
'--no-exclude-genes',
action='store_true',
dest='no_exclude_genes',
help=
'Disable the default exclusion of some genes from ResFinder/PointFinder/PlasmidFinder [False].',
required=False)
report_group.add_argument(
'--exclude-genes-file',
action='store',
dest='exclude_genes_file',
help=
'A containing a list of ResFinder/PointFinder/PlasmidFinder gene names to exclude from results [{}].'
.format(ExcludeGenesList.get_default_exclude_file()),
default=ExcludeGenesList.get_default_exclude_file(),
required=False)
report_group.add_argument(
'--exclude-negatives',
action='store_true',
dest='exclude_negatives',
help=
'Exclude negative results (those sensitive to antimicrobials) [False].',
required=False)
report_group.add_argument(
'--exclude-resistance-phenotypes',
action='store_true',
dest='exclude_resistance_phenotypes',
help='Exclude predicted antimicrobial resistances [False].',
required=False)
report_group.add_argument(
'--report-all-blast',
action='store_true',
dest='report_all_blast',
help='Report all blast hits (vs. only top blast hits) [False].',
required=False)
output_group = arg_parser.add_argument_group(
title='Output',
description=
'Use either --output-dir or specify individual output files')
output_group.add_argument(
'-o',
'--output-dir',
action='store',
dest='output_dir',
type=str,
help="The output directory for results [None].",
default=None,
required=False)
output_group.add_argument(
'--output-summary',
action='store',
dest='output_summary',
type=str,
help=
"The name of the output file containing the summary results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-detailed-summary',
action='store',
dest='output_detailed_summary',
type=str,
help=
"The name of the output file containing the detailed summary results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-resfinder',
action='store',
dest='output_resfinder',
type=str,
help=
"The name of the output file containing the resfinder results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-pointfinder',
action='store',
dest='output_pointfinder',
type=str,
help=
"The name of the output file containing the pointfinder results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-plasmidfinder',
action='store',
dest='output_plasmidfinder',
type=str,
help=
"The name of the output file containing the plasmidfinder results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-settings',
action='store',
dest='output_settings',
type=str,
help=
"The name of the output file containing the settings. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-excel',
action='store',
dest='output_excel',
type=str,
help=
"The name of the output file containing the excel results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-hits-dir',
action='store',
dest='hits_output_dir',
type=str,
help=
"The name of the directory to contain the BLAST hit files. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-mlst',
action='store',
dest='output_mlst',
type=str,
help=
"The name of the output file containing the mlst results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
arg_parser.add_argument('files', nargs='+')
return arg_parser
def _setup_args(self, arg_parser):
name = self._script_name
epilog = (
"Example:\n"
"\t" + name + " search -o out *.fasta\n"
"\t\tSearches the files *.fasta for AMR genes using only the ResFinder database, storing results in the out/ directory.\n\n"
+ "\t" + name +
" search --pointfinder-organism salmonella --output-excel results.xlsx *.fasta\n"
+
"\t\tSearches *.fasta for AMR genes using ResFinder and PointFinder database with the passed organism, storing results in results.xlsx."
)
arg_parser = self._subparser.add_parser(
'search',
epilog=epilog,
formatter_class=argparse.RawTextHelpFormatter,
help='Search for AMR genes')
self._default_database_dir = AMRDatabasesManager.get_default_database_directory(
)
cpu_count = multiprocessing.cpu_count()
arg_parser.add_argument(
'--pointfinder-organism',
action='store',
dest='pointfinder_organism',
type=str,
help='The organism to use for pointfinder {' +
', '.join(PointfinderBlastDatabase.get_available_organisms()) +
'}. Defaults to disabling search for point mutations. [None].',
default=None,
required=False)
arg_parser.add_argument(
'-d',
'--database',
action='store',
dest='database',
type=str,
help=
'The directory containing the resfinder/pointfinder databases [' +
self._default_database_dir + '].',
default=self._default_database_dir,
required=False)
arg_parser.add_argument(
'-n',
'--nprocs',
action='store',
dest='nprocs',
type=int,
help='The number of processing cores to use [' + str(cpu_count) +
'].',
default=cpu_count,
required=False)
threshold_group = arg_parser.add_argument_group('BLAST Thresholds')
threshold_group.add_argument(
'--pid-threshold',
action='store',
dest='pid_threshold',
type=float,
help='The percent identity threshold [98.0].',
default=98.0,
required=False)
threshold_group.add_argument(
'--percent-length-overlap-resfinder',
action='store',
dest='plength_threshold_resfinder',
type=float,
help='The percent length overlap for resfinder results [60.0].',
default=60.0,
required=False)
threshold_group.add_argument(
'--percent-length-overlap-pointfinder',
action='store',
dest='plength_threshold_pointfinder',
type=float,
help='The percent length overlap for pointfinder results [95.0].',
default=95.0,
required=False)
report_group = arg_parser.add_argument_group('Reporting options')
report_group.add_argument(
'--no-exclude-genes',
action='store_true',
dest='no_exclude_genes',
help=
'Disable the default exclusion of some genes from ResFinder/PointFinder [False].',
required=False)
report_group.add_argument(
'--exclude-genes-file',
action='store',
dest='exclude_genes_file',
help=
'A containing a list of ResFinder/PointFinder gene names to exclude from results [{}].'
.format(ExcludeGenesList.get_default_exclude_file()),
default=ExcludeGenesList.get_default_exclude_file(),
required=False)
report_group.add_argument(
'--exclude-negatives',
action='store_true',
dest='exclude_negatives',
help=
'Exclude negative results (those sensitive to antimicrobials) [False].',
required=False)
report_group.add_argument(
'--exclude-resistance-phenotypes',
action='store_true',
dest='exclude_resistance_phenotypes',
help='Exclude predicted antimicrobial resistances [False].',
required=False)
report_group.add_argument(
'--report-all-blast',
action='store_true',
dest='report_all_blast',
help='Report all blast hits (vs. only top blast hits) [False].',
required=False)
output_group = arg_parser.add_argument_group(
title='Output',
description=
'Use either --output-dir or specify individual output files')
output_group.add_argument(
'-o',
'--output-dir',
action='store',
dest='output_dir',
type=str,
help="The output directory for results [None].",
default=None,
required=False)
output_group.add_argument(
'--output-summary',
action='store',
dest='output_summary',
type=str,
help=
"The name of the output file containing the summary results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-resfinder',
action='store',
dest='output_resfinder',
type=str,
help=
"The name of the output file containing the resfinder results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-pointfinder',
action='store',
dest='output_pointfinder',
type=str,
help=
"The name of the output file containing the pointfinder results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-settings',
action='store',
dest='output_settings',
type=str,
help=
"The name of the output file containing the settings. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-excel',
action='store',
dest='output_excel',
type=str,
help=
"The name of the output file containing the excel results. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
output_group.add_argument(
'--output-hits-dir',
action='store',
dest='hits_output_dir',
type=str,
help=
"The name of the directory to contain the BLAST hit files. Not be be used with '--output-dir'. [None]",
default=None,
required=False)
arg_parser.add_argument('files', nargs='+')
return arg_parser