gain.gene_sets.implementations package

Submodules

gain.gene_sets.implementations.gene_sets_impl module

class GeneSetCollectionImpl(resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Gene sets collection resource implementations.

Not a ResourceConfigValidationMixin: a gene-set collection validates its config on construction through pydantic’s GeneSetResourceSchema, in the collection this builds, so there is no cerberus schema to declare (ADR 0031).

calc_info_hash() → bytes

Compute the digest of the inputs of the info page.

The page is rendered again only when the digest changes.

Returns:

The digest of everything that get_info depends on.

Return type:

bytes

calc_statistics_hash() → bytes

Compute the digest of the inputs of the statistics build.

grr_manage compares the digest with the stored one to decide whether it must compute the statistics again.

Returns:

The digest of everything that the statistics tasks read.

Return type:

bytes

create_statistics_build_tasks(*, region_size: int = 3000000000, grr: GenomicResourceRepo | None = None) → list[TaskDesc]

Create the task graph tasks that compute the statistics.

grr_manage calls every kind with the same two keyword-only arguments. An implementation declares both, even when it ignores them, and declares no other argument.

Parameters:

• region_size (int) – The longest region that one task covers. A kind that splits its build by genomic region reads it. 0 means do not split: a genomic score then scans the resource in one pass and a reference genome uses one region for each chromosome. A kind that does not split ignores it.

• grr (GenomicResourceRepo | None) – The repository that holds the resource. None means that the caller names no repository.

Returns:

The tasks of the build. An empty list means that the kind has no statistics to compute.

Return type:

list[TaskDesc]

Raises:

ValueError – If region_size is negative.

get_info(**kwargs: Any) → str

Render the HTML of the info page of the resource.

Parameters:

**kwargs (Any) – Options of the renderer. The caller defines them.

Returns:

The HTML of the page.

Return type:

str

get_statistics_info(**kwargs: Any) → str

Render the HTML of the statistics page of the resource.

Parameters:

**kwargs (Any) – Options of the renderer. The caller defines them.

Returns:

The HTML of the page.

Return type:

str

styles_template_name: ClassVar[str] = 'gene_set_collection_styles.jinja'

template_name: ClassVar[str] = 'gene_set_collection.jinja'

Module contents