Source code for czbenchmarks.datasets.types

from enum import Enum

from omegaconf import OmegaConf


[docs] class Organism(Enum): 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", "") # Mixed prefixes: LOC and GeneID # Todo: add other organisms def __init__(self, name: str, prefix: str): self._value_ = (name, prefix) # This is handled automatically by Enum
[docs] def __str__(self): return self.value[0] # Access the name from the tuple
[docs] def __repr__(self): return self.value[0] # Access the name from the tuple
@property def name(self): return self.value[0] @property def prefix(self): return self.value[1]
# Register Organism resolver if not OmegaConf.has_resolver("organism"): # Required for dataset test cases OmegaConf.register_new_resolver("organism", lambda name: getattr(Organism, name))