def get_arguments() -> ModuleArgs:
""" Build and return arguments. """
args = ModuleArgs('Additional analysis', 'asf')
args.add_analysis_toggle('--asf',
dest='asf',
action='store_true',
default=False,
help="Run active site finder analysis.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'tta')
args.add_analysis_toggle('--tta',
dest='tta',
action='store_true',
default=False,
help="Run TTA codon detection module.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'pfam2go')
args.add_analysis_toggle('--pfam2go',
dest='pfam2go',
action='store_true',
default=False,
help="Run Pfam to Gene Ontology mapping module.")
return args
def get_arguments() -> ModuleArgs:
""" Builds the module args """
args = ModuleArgs('TIGRFam options', 'tigrfam')
args.add_analysis_toggle('tigrfam',
dest='tigrfam',
action='store_true',
default=False,
help="Annotate clusters using TIGRFam profiles.")
return args
def get_arguments() -> ModuleArgs:
""" Build and return arguments. No extra options beyond a switch to enable """
args = ModuleArgs('Additional analysis', 'cassis')
args.add_analysis_toggle(
'--cassis',
dest='cassis',
action='store_true',
default=False,
help="Motif based prediction of SM gene cluster regions.")
return args
def get_arguments() -> ModuleArgs:
""" Sets up arguments for this module.
"""
args = ModuleArgs('ClusterFinder rule-based options', 'cfrules')
args.add_analysis_toggle('cfrules',
dest='cfrules',
action='store_true',
default=False,
help="Find loose rule-based clusters defined by cluster-finder.")
return args
def get_arguments() -> ModuleArgs:
""" Construct the arguments.
Classification is enabled by default, but an extra option for generating
trees is also required.
"""
group = ModuleArgs("Basic analysis options", "smcog", basic_help=True)
group.add_analysis_toggle('--smcog-trees',
dest='smcog_trees',
action='store_true',
default=False,
help="Generate phylogenetic trees of sec. "
"met. cluster orthologous groups.")
return group
def get_arguments() -> ModuleArgs:
""" Builds the module args """
args = ModuleArgs('Full HMMer options', 'fullhmmer')
args.add_analysis_toggle('fullhmmer',
dest='fullhmmer',
action='store_true',
default=False,
help="Run a whole-genome HMMer analysis.")
args.add_option('pfamdb-version',
dest='pfamdb_version',
type=str,
default='latest',
help="PFAM database version number (e.g. 27.0) (default: %(default)s).")
return args
def get_arguments() -> ModuleArgs:
""" Sets up arguments for this module. Must return a ModuleArgs object.
override_safeties is only set here to allow for the destinations of the
arguments to not include the 'dummy' prefix for the placeholder
arguments.
"""
args = ModuleArgs('ClusterFinder options', 'cf')
args.add_analysis_toggle(
'borders-only',
dest='borders_only',
action='store_true',
default=False,
help="Only annotate borders of existing clusters.")
args.add_analysis_toggle('create-clusters',
dest='create_clusters',
action='store_true',
default=False,
help="Find extra clusters.")
args.add_option(
'min-cds',
dest='min_cds_features',
metavar="INT",
type=int,
default=5,
help="Minimum size of a ClusterFinder cluster, in number of"
" CDS features (default: %(default)s).")
args.add_option(
'mean-threshold',
dest='cf_threshold',
metavar="FLOAT",
type=float,
default=0.6,
help="Minimum mean probability threshold (default: %(default)s).")
args.add_option('min-pfams',
dest='min_pfams',
metavar="INT",
type=int,
default=5,
help="Minimum number of biosynthetic PFam domains in a"
" ClusterFinder cluster (default: %(default)s).")
return args
def get_arguments() -> ModuleArgs:
""" Builds any commandline argument constructs that may be required
Returns:
an empty or populated ModuleArgs instance
"""
args = ModuleArgs('Additional analysis', 'rre')
args.add_analysis_toggle('run',
dest='run',
default=False, # disabled by default
action='store_true',
help="Run RREFinder precision mode on all RiPP gene clusters.")
args.add_option('cutoff',
dest='cutoff',
type=float,
default=25.0,
help="Bitscore cutoff for RRE pHMM detection (default: 25.0).")
args.add_option('min_length',
dest='min_length',
type=int,
default=50,
help='Minimum amino acid length of RRE domains (default: 50).')
return args
def get_arguments() -> ModuleArgs:
""" Builds the args for the clusterblast module """
args = ModuleArgs('ClusterBlast options', 'cb')
args.add_analysis_toggle('general',
dest='general',
action='store_true',
default=False,
help="Compare identified clusters against a "
"database of antiSMASH-predicted clusters.")
args.add_analysis_toggle('subclusters',
dest='subclusters',
action='store_true',
default=False,
help="Compare identified clusters against known "
"subclusters responsible for synthesising "
"precursors.")
args.add_analysis_toggle('knownclusters',
dest='knownclusters',
action='store_true',
default=False,
help="Compare identified clusters against known "
"gene clusters from the MIBiG database.")
args.add_option(
'diamond-executable',
dest='diamond_executable',
metavar='filename',
type=str,
default='diamond',
help="The path to the diamond executable. (default: %(default)s)")
args.add_option('nclusters',
dest='nclusters',
metavar="count",
type=int,
default=10,
help="Number of clusters from ClusterBlast to display,"
" cannot be greater than %d. (default: %%(default)s)" %
get_result_limit())
args.add_option(
'min-homology-scale',
dest='min_homology_scale',
metavar="LIMIT",
type=float,
default=0.0,
help=
"A minimum scaling factor for the query BGC in ClusterBlast results."
" Valid range: 0.0 - 1.0. "
" Warning: some homologous genes may no longer be visible!"
" (default: %(default)s)")
return args