torchcell.datamodels.schema.GenomicSpan

class GenomicSpan(*, chromosome: str, start: int, end: int, assembly: Literal['ecoli_K12_MG1655_ASM584v2', 'ecoli_K12_BW25113_ASM75055v1', 'pputida_KT2440_ASM756v2', 'ecoli_B_REL606_ASM1798v1', 'ecoli_K12_W3110_ASM1024v1', 'sgd_S288C_R64-4-1_20230830', 'scerevisiae_CENPK113-7D_ASM257140v2'])[source]

Bases: ModelStrict

A 1-based, end-inclusive interval on one replicon of a deposited assembly set.

assembly is the deposited set the coordinates are on (an AssemblySet id, never a release name): coordinates shift between assemblies, and the set is what torchcell.sequence.genome.registry.resolve dereferences. A span a release read on SGD R64-1-1 is on sgd_S288C_R64-4-1_20230830, whose 16 nuclear chromosomes are measured sequence-identical to GCA_000146045.2.

model_config: ClassVar[ConfigDict] = {'extra': 'forbid', 'frozen': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].