def list_available_genomes(provider=None): """ List all available genomes. Parameters ---------- provider : str, optional List genomes from specific provider. Genomes from all providers will be returned if not specified. Returns ------- list with genome names """ if provider: providers = [ProviderBase.create(provider)] else: # if provider is not specified search all providers providers = [ ProviderBase.create(p) for p in ProviderBase.list_providers() ] for p in providers: for row in p.list_available_genomes(): yield [p.name] + list(row)
def search(term, provider=None): """ Search for a genome. If provider is specified, search only that specific provider, else search all providers. Both the name and description are used for the search. Search term is case-insensitive. Parameters ---------- term : str Search term, case-insensitive. provider : str , optional Provider name Yields ------ tuple genome information (name/identfier and description) """ if provider: providers = [ProviderBase.create(provider)] else: # if provider is not specified search all providers (except direct url) providers = [ ProviderBase.create(p) for p in ProviderBase.list_providers() if p != "url" ] for p in providers: for row in p.search(term): yield [x.encode("latin-1") for x in [p.name] + list(row)]
def search(term, provider=None): """ Search for a genome. If provider is specified, search only that specific provider, else search all providers. Both the name and description are used for the search. Seacrch term is case-insensitive. Parameters ---------- term : str Search term, case-insensitive. provider : str , optional Provider name Yields ------ tuple genome information (name/identfier and description) """ if provider: providers = [ProviderBase.create(provider)] else: # if provider is not specified search all providers providers = [ProviderBase.create(p) for p in ProviderBase.list_providers()] for p in providers: for row in p.search(term): yield [x.encode('latin-1') for x in [p.name] + list(row)]
def list_available_providers(): """ List all available providers. Returns ------- list with provider names """ return ProviderBase.list_providers()
def _online_providers(): """Return a list of online providers as objects""" providers = [] for p in ProviderBase.list_providers(): try: providers.append(ProviderBase.create(p)) except ConnectionError as e: sys.stderr.write(str(e)) return providers
def list_available_providers(): """ List all available providers. Returns ------- list with provider names """ return ProviderBase.list_providers()
def list_available_genomes(provider=None): """ List all available genomes. Parameters ---------- provider : str, optional List genomes from specific provider. Genomes from all providers will be returned if not specified. Returns ------- list with genome names """ if provider: providers = [ProviderBase.create(provider)] else: # if provider is not specified search all providers providers = [ProviderBase.create(p) for p in ProviderBase.list_providers()] for p in providers: for row in p.list_available_genomes(): yield [p.name] + list(row)