def only_primary_isoforms():
return argument_parameters(
'-o',
'--only_primary_isoforms',
action='store_true',
help='Restrict export to primary isoforms',
)
def paths():
return argument_parameters(
'--paths',
nargs='*',
metavar='',
help='A path(s) for export file(s)',
)
def type():
return argument_parameters(
'-t',
'--type',
choices=['proteomic', 'genomic_ptm'],
help=
'What type of mutations should be exported: proteomic or genomic_ptm (genomic affecting PTM).'
'By default proteomic mutations will be exported',
)
def restrict_to():
return argument_parameters(
'--restrict_to',
'-r',
default=None,
choices=['genome_proteome', 'aminoacid_refseq'],
help=
'Should only genome_proteome or aminoacid_refseq mappings be imported?'
)
def exporters():
data_exporters = EXPORTERS
return argument_parameters(
'-e',
'--exporters',
nargs='*',
help=('What should be exported?'
' Available: ' + ', '.join(data_exporters) + '.'
' By default everything will be exported.'),
choices=data_exporters,
metavar='',
default=data_exporters,
)
def models(self):
models = get_all_models('bio')
return argument_parameters('--models',
'-m',
nargs='+',
metavar='',
help=('Names of models to be removed.'
' Available models: ' +
', '.join(models) + '.'),
default=[],
choices=models.keys())
def sources():
mutation_importers = muts_import_manager.names
return argument_parameters(
'-s',
'--sources',
nargs='*',
help=('Which mutations should be loaded or removed?'
' Available sources are: ' + ', '.join(mutation_importers) +
'.'
' By default all sources will be used.'),
choices=mutation_importers,
metavar='',
default=mutation_importers)
def models():
models = get_all_models('bio')
models_names = [model.__name__ for model in models]
return argument_parameters('--models',
'-m',
nargs='+',
metavar='',
help=('Names of models to be removed.'
' Available models: ' +
', '.join(models_names) + '.'),
choices=models_names)
def importers_choice(data_importers):
return argument_parameters(
'-i',
'--importers',
nargs='*',
help=('What should be imported?'
' Available choices are: ' + ', '.join(data_importers) + '.'
' By default all data will be imported.'
' The order of imports matters; preferable order'
' is the same as order of choices listed above.'),
choices=data_importers,
metavar='',
default=data_importers,
)
def path():
return argument_parameters(
'--path',
type=str,
default='',
help='A path to dir where mappings dbs should be created')
def all(self):
return argument_parameters('--all',
'-a',
action='store_true',
help='Remove all bio models.')