gain.gene_sets package

Subpackages

• gain.gene_sets.implementations package
  • Submodules
  • gain.gene_sets.implementations.gene_sets_impl module
  • Module contents

Submodules

gain.gene_sets.gene_set module

Classes for handling of gene sets and gene set collections.

class BaseGeneSetCollection(collection_id: str)

Bases: ABC

Base class for gene set collections.

abstractmethod get_all_gene_sets() → list[GeneSet]

Return list of all gene sets in the collection.

abstractmethod get_gene_set(gene_set_id: str) → GeneSet | None

Return the gene set if found; returns None if not found.

abstractmethod load() → BaseGeneSetCollection

Load the gene sets from the resource.

class BaseResourceSchema(*, type: str | None = None, meta: MetaSchema | None = None)

Bases: BaseModel

meta: MetaSchema | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

type: str | None

class CategoricalHistogramSchema(*, type: Literal['categorical'], displayed_values_count: int | None = None, displayed_values_percent: float | None = None, value_order: list[str | int] | None = None, y_log_scale: bool | None = None, label_rotation: int | None = None, plot_function: str | None = None, enforce_type: bool | None = None, natural_order: bool | None = None)

Bases: BaseModel

displayed_values_count: int | None

displayed_values_percent: float | None

enforce_type: bool | None

label_rotation: int | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

natural_order: bool | None

plot_function: str | None

type: Literal['categorical']

value_order: list[str | int] | None

y_log_scale: bool | None

class GeneSet(name: str, desc: str, syms: list[str])

Bases: object

A named set of genes.

Variables:

• name (str) – The name of the gene set, unique in its collection.

• desc (str) – The description of the gene set. It can be empty.

• count (int) – The number of gene symbols in syms.

• syms (list[str]) – The gene symbols of the set.

count: int

desc: str

name: str

syms: list[str]

class GeneSetCollection(resource: GenomicResource)

Bases: BaseGeneSetCollection

The gene sets of a gene_set_collection resource.

Build a collection with build_gene_set_collection_from_resource_id or build_gene_set_collection_from_resource. The built collection may not be loaded: call load() before the first read.

Variables:

• resource (GenomicResource) – The resource that holds the gene sets.

• config (GeneSetResourceSchema) – The validated config of the resource.

• collection_id (str) – The id: key of the resource config.

• web_label (str) – The label that a web interface shows for the collection. Empty when the config sets no web_label.

• web_format_str (str) – The format string that a web interface uses to show a gene set. Empty when the config sets no web_format_str.

• gene_sets (dict[str, GeneSet]) – The loaded gene sets by name. The dictionary is empty until load() runs.

property files: set[str]

Return the names of the resource files that hold the gene sets.

gene_sets: dict[str, GeneSet]

get_all_gene_sets() → list[GeneSet]

Return all the gene sets of the collection.

Returns:

The gene sets in the order of the resource. The list is empty when the collection is not loaded.

Return type:

list[GeneSet]

get_gene_collection_count_statistics() → dict | None

Read the stored counts of the collection.

Returns:

A dictionary with the keys number_of_gene_sets and number_of_unique_genes. None when the resource has no stored counts because no statistics build ran.

Return type:

dict | None

get_gene_set(gene_set_id: str) → GeneSet | None

Return one gene set by its name.

Parameters:

gene_set_id (str) – The name of the gene set.

Returns:

The gene set, or None when the collection has no set with this name. The collection logs a warning in that case. An unloaded collection has no sets, so it always returns None.

Return type:

GeneSet | None

get_gene_sets_list_statistics() → list[dict] | None

Read the stored list of gene sets with their sizes.

Returns:

One dictionary for each gene set, with the keys name, count and desc, ordered by falling count. None when the resource has no stored list because no statistics build ran.

Return type:

list[dict] | None

get_gene_sets_per_gene_hist() → NullHistogram | CategoricalHistogram | NumberHistogram | None

Read the stored histogram of the gene sets that contain a gene.

Returns:

The histogram, or None when the resource has no stored histogram because no statistics build ran.

Return type:

Histogram | None

get_genes_per_gene_set_hist() → NullHistogram | CategoricalHistogram | NumberHistogram | None

Read the stored histogram of the number of genes in a gene set.

Returns:

The histogram, or None when the resource has no stored histogram because no statistics build ran.

Return type:

Histogram | None

is_loaded() → bool

Return whether the collection holds any loaded gene set.

Returns:

True after load() read at least one gene set. A resource with no gene sets always reports False.

Return type:

bool

load() → GeneSetCollection

Read the gene sets from the resource.

A call on a loaded collection does nothing.

Returns:

This collection, so the call chains.

Return type:

GeneSetCollection

Raises:

ValueError – If the format: key of the resource is not directory, gmt or map.

class GeneSetResourceSchema(*, id: str, filename: str | None = None, directory: str | None = None, format: str | None, web_label: str | None = None, web_format_str: str | None = None, histograms: dict[Literal['genes_per_gene_set', 'gene_sets_per_gene'], Annotated[NumericHistogramSchema | CategoricalHistogramSchema, FieldInfo(annotation=NoneType, required=True, discriminator='type')]] | None = None)

Bases: BaseModel

directory: str | None

filename: str | None

histograms: dict[Literal['genes_per_gene_set', 'gene_sets_per_gene'], HistogramConfig] | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

resource_format: str | None

resource_id: str

web_format_str: str | None

web_label: str | None

class MetaSchema(*, description: str | None = None, labels: dict[str, Any] | None = None)

Bases: BaseModel

description: str | None

labels: dict[str, Any] | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class NumericHistogramSchema(*, type: Literal['number'], plot_function: str | None = None, number_of_bins: int | None = None, view_range: ViewRangeSchema | None = None, x_log_scale: bool | None = None, y_log_scale: bool | None = None, x_min_log: float | None = None, value_order: list[str | int] | None = None, displayed_values_count: int | None = None)

Bases: BaseModel

displayed_values_count: int | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

number_of_bins: int | None

plot_function: str | None

type: Literal['number']

value_order: list[str | int] | None

view_range: ViewRangeSchema | None

x_log_scale: bool | None

x_min_log: float | None

y_log_scale: bool | None

class ViewRangeSchema(*, min: float | None = None, max: float | None = None)

Bases: BaseModel

max: float | None

min: float | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

build_gene_set_collection_from_file(filename: str, collection_id: str | None = None, collection_format: str | None = None, web_label: str | None = None, web_format_str: str | None = None) → GeneSetCollection

Return a Gene Set Collection by adapting a file to a local resource.

build_gene_set_collection_from_resource(resource: GenomicResource) → GeneSetCollection

Build the gene set collection of a genomic resource.

The returned collection may not be loaded. Calls with the same resource return the same object, so an earlier caller may have loaded it.

Parameters:

resource (GenomicResource) – A resource of type gene_set_collection.

Returns:

The collection of the resource. Check is_loaded() or call load() before any read.

Return type:

GeneSetCollection

Raises:

ValueError – If the resource is not of type gene_set_collection.

build_gene_set_collection_from_resource_id(resource_id: str, grr: GenomicResourceRepo | None = None) → GeneSetCollection

Build the gene set collection of the resource with a given id.

The returned collection may not be loaded. Calls that find the same resource return the same object, so an earlier caller may have loaded it.

Parameters:

• resource_id (str) – The id of a resource of type gene_set_collection in the repository.

• grr (GenomicResourceRepo | None) – The repository that resolves resource_id. When it is None, the function builds the default repository with build_genomic_resource_repository().

Returns:

The collection of the resource. Check is_loaded() or call load() before any read.

Return type:

GeneSetCollection

Raises:

• FileNotFoundError – If a protocol-backed repository has no resource with this id.

• ValueError – If a group repository has no resource with this id, or if the resource is not of type gene_set_collection.

gain.gene_sets.gene_term module

class GeneInfo(gene_id: str, gene_sym: str, synonyms: set[str], description: str)

Bases: object

description: str

gene_id: str

gene_sym: str

synonyms: set[str]

class GeneTerms

Bases: object

Class representing gene terms.

filter_genes(filter_fun: Callable[[list[str]], list[str]]) → None

Filter the genes.

g2t: dict[str, Any]

gene_ns: str | None

rename_genes(gene_ns: str | None, rename_fn: Callable[[str], str | None]) → None

Rename genese.

save(fname: str) → None

Save to fname.

t2g: dict[str, Any]

t_desc: dict[str, Any]

class NCBIGeneInfo(genes: dict[str, gain.gene_sets.gene_term.GeneInfo], ns_tokens: dict[str, dict[str, list[gain.gene_sets.gene_term.GeneInfo]]])

Bases: object

genes: dict[str, GeneInfo]

ns_tokens: dict[str, dict[str, list[GeneInfo]]]

dd() → dict[str, int]

get_clean_gene_id(ncbi_gene_info: NCBIGeneInfo, ns: str, term: str) → str | None

Gene gene ID from NCBI gene info data.

load_gene_terms(path: str) → GeneTerms | None

Load gene terms from a file.

load_ncbi_gene_info(gene_info_file: str) → NCBIGeneInfo

read_ewa_set_file(set_files: list[IO]) → GeneTerms

Read a set of ewa files.

read_gmt_file(input_file: IO) → GeneTerms

Read a gmt file.

read_mapping_file(input_file: IO, names_file: IO | None) → GeneTerms

Read a mapping file.

rename_gene_terms(gene_terms: GeneTerms, gene_ns: str, ncbi_gene_info: NCBIGeneInfo) → GeneTerms

Rename gene terms using NCBI gene info data.

Module contents