czbenchmarks.datasets.types

Attributes

DataValue

Classes

Organism	Create a collection of name/value pairs.
DataTypeSpec	Specification for a data type in the system
DataType	Create a collection of name/value pairs.

Module Contents

class czbenchmarks.datasets.types.Organism(name: str, prefix: str)

Bases: enum.Enum

Create a collection of name/value pairs.

Example enumeration:

>>> class Color(Enum):
...     RED = 1
...     BLUE = 2
...     GREEN = 3

Access them by:

• attribute access:

>>> Color.RED
<Color.RED: 1>

• value lookup:

>>> Color(1)
<Color.RED: 1>

• name lookup:

>>> Color['RED']
<Color.RED: 1>

Enumerations can be iterated over, and know how many members they have:

>>> len(Color)
3

>>> list(Color)
[<Color.RED: 1>, <Color.BLUE: 2>, <Color.GREEN: 3>]

Methods can be added to enumerations, and members can have their own attributes – see the documentation for details.

HUMAN = ('homo_sapiens', 'ENSG')

MOUSE = ('mus_musculus', 'ENSMUSG')

TROPICAL_CLAWED_FROG = ('xenopus_tropicalis', 'ENSXETG')

AFRICAN_CLAWED_FROG = ('xenopus_laevis', 'ENSXLAG')

ZEBRAFISH = ('danio_rerio', 'ENSDARG')

MOUSE_LEMUR = ('microcebus_murinus', 'ENSMICG')

WILD_BOAR = ('sus_scrofa', 'ENSSSCG')

CRAB_EATING_MACAQUE = ('macaca_fascicularis', 'ENSMFAG')

RHESUS_MACAQUE = ('macaca_mulatta', 'ENSMMUG')

PLATYPUS = ('ornithorhynchus_anatinus', 'ENSOANG')

OPOSSUM = ('monodelphis_domestica', 'ENSMODG')

GORILLA = ('gorilla_gorilla', 'ENSGGOG')

CHIMPANZEE = ('pan_troglodytes', 'ENSPTRG')

MARMOSET = ('callithrix_jacchus', 'ENSCJAG')

CHICKEN = ('gallus_gallus', 'ENSGALG')

RABBIT = ('oryctolagus_cuniculus', 'ENSOCUG')

FRUIT_FLY = ('drosophila_melanogaster', 'FBgn')

RAT = ('rattus_norvegicus', 'ENSRNOG')

NAKED_MOLE_RAT = ('heterocephalus_glaber', 'ENSHGLG')

CAENORHABDITIS_ELEGANS = ('caenorhabditis_elegans', 'WBGene')

YEAST = ('saccharomyces_cerevisiae', '')

MALARIA_PARASITE = ('plasmodium_falciparum', 'PF3D7')

SEA_LAMPREY = ('petromyzon_marinus', 'ENSPMAG')

FRESHWATER_SPONGE = ('spongilla_lacustris', 'ENSLPGG')

CORAL = ('stylophora_pistillata', 'LOC')

SEA_URCHIN = ('lytechinus_variegatus', '')

__str__()

__repr__()

property name

The name of the Enum member.

property prefix

class czbenchmarks.datasets.types.DataTypeSpec

Specification for a data type in the system

name: str

dtype: Type

description: str

is_input: bool = True

class czbenchmarks.datasets.types.DataType(*args, **kwds)

Bases: enum.Enum

Create a collection of name/value pairs.

Example enumeration:

>>> class Color(Enum):
...     RED = 1
...     BLUE = 2
...     GREEN = 3

Access them by:

• attribute access:

>>> Color.RED
<Color.RED: 1>

• value lookup:

>>> Color(1)
<Color.RED: 1>

• name lookup:

>>> Color['RED']
<Color.RED: 1>

Enumerations can be iterated over, and know how many members they have:

>>> len(Color)
3

>>> list(Color)
[<Color.RED: 1>, <Color.BLUE: 2>, <Color.GREEN: 3>]

Methods can be added to enumerations, and members can have their own attributes – see the documentation for details.

METADATA

ANNDATA

ORGANISM

EMBEDDING

CONDITION_KEY

SPLIT_KEY

PERTURBATION_PRED

PERTURBATION_TRUTH

property spec: DataTypeSpec

property dtype: Type

property description: str

property is_input: bool

property is_output: bool

__hash__()

__eq__(other)

__str__()

__repr__()

czbenchmarks.datasets.types.DataValue