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)