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.')