gain.genomic_resources.implementations package

Subpackages

• gain.genomic_resources.implementations.genomic_scores_impl package
  • Submodules
  • gain.genomic_resources.implementations.genomic_scores_impl.allele module
  • gain.genomic_resources.implementations.genomic_scores_impl.base module
  • gain.genomic_resources.implementations.genomic_scores_impl.builders module
  • gain.genomic_resources.implementations.genomic_scores_impl.fragment module
  • gain.genomic_resources.implementations.genomic_scores_impl.position module
  • gain.genomic_resources.implementations.genomic_scores_impl.scan module
  • Module contents

Submodules

gain.genomic_resources.implementations.ann_data_resource_impl module

Provides the ann_data resource implementation.

class gain.genomic_resources.implementations.ann_data_resource_impl.AnnDataResourceImplementation(genomic_resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

AnnData resource implementation.

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

property files: set[str]

Return a list of resource files the implementation utilises.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

gain.genomic_resources.implementations.annotation_pipeline_impl module

class gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation(resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Resource implementation for annotation pipeline.

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

property files: set[str]

Return a list of resource files the implementation utilises.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

gain.genomic_resources.implementations.basic_resource_impl module

Provides the catch-all basic resource implementation.

class gain.genomic_resources.implementations.basic_resource_impl.BasicResourceImplementation(genomic_resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Implementation for resources without a more specific type.

A resource whose config carries no type resolves to the basic type (see GenomicResource.get_type). It has no schema or statistics of its own; it only renders a minimal info page and – crucially – exposes every data file via files so caching covers the whole resource, the same way untyped resources were cached before they had an implementation (gain#78).

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

property files: set[str]

Return a list of resource files the implementation utilises.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

gain.genomic_resources.implementations.data_frame_resource_impl module

Provides the data_frame resource implementation.

class gain.genomic_resources.implementations.data_frame_resource_impl.DataFrameResourceImplementation(genomic_resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

DataFrame resource implementation.

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

property files: set[str]

Return a list of resource files the implementation utilises.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

gain.genomic_resources.implementations.gene_models_impl module

class gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl(resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Provides class for gene models.

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

property files: set[str]

Return a list of resource files the implementation utilises.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics() → GeneModelsStatistics | None

Try and load resource statistics.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

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

class gain.genomic_resources.implementations.gene_models_impl.GeneModelsStatistics(resource_id: str, chromosome_count: int, global_statistic: StatisticsData, chrom_statistics: dict[str, StatisticsData])

Bases: ResourceStatistics

Class for accessing reference genome statistics.

static deserialize(data: str) → GeneModelsStatistics

Deserialize gene models statistics.

serialize() → str

Serialize gene models statistics.

class gain.genomic_resources.implementations.gene_models_impl.StatisticsData(transcript_number: int, protein_coding_transcript_number: int, gene_number: int, protein_coding_gene_number: int)

Bases: object

Class for storing gene models statistics.

gene_number: int

protein_coding_gene_number: int

protein_coding_transcript_number: int

transcript_number: int

gain.genomic_resources.implementations.liftover_chain_impl module

Provides LiftOver chain resource.

class gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation(resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Defines Lift Over chain resource implementation.

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

gain.genomic_resources.implementations.reference_genome_impl module

class gain.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic(chromosome: str, length: int = 0, nucleotide_counts: dict[str, int] | None = None, nucleotide_pair_counts: dict[str, int] | None = None)

Bases: Statistic

Class for individual chromosome statistics.

add_value(value: tuple[str | None, str]) → None

Add a value to the statistic.

static deserialize(content: str) → ChromosomeStatistic

Create a statistic from serialized data.

finish() → None

Perform final calculations for the statistic.

This step is optional.

This is called when resource iteration is complete.

Can also be used when creating more complex resources via deserialization.

merge(other: Statistic) → None

Merge the values from another statistic in place.

serialize() → str

Return a serialized version of this statistic.

class gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic(chromosomes: list[str], length: int = 0, nucleotide_distribution: dict[str, float] | None = None, bi_nucleotide_distribution: dict[str, float] | None = None, chromosome_statistics: dict[str, ChromosomeStatistic] | None = None)

Bases: Statistic

Class for the global reference genome statistic.

add_value(value: Any) → None

Add a value to the statistic.

property chrom_count: int

static deserialize(content: str) → GenomeStatistic

Create a statistic from serialized data.

finish() → None

Perform final calculations for the statistic.

This step is optional.

This is called when resource iteration is complete.

Can also be used when creating more complex resources via deserialization.

merge(other: Statistic) → None

Merge the values from another statistic in place.

serialize() → str

Return a serialized version of this statistic.

class gain.genomic_resources.implementations.reference_genome_impl.GenomeStatisticsMixin

Bases: object

Mixin for reference genome statistics access.

static get_chrom_file(chrom: str) → str

static get_global_statistic_file() → str

class gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation(resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Resource implementation for reference genome.

calc_info_hash() → bytes

Compute and return the info hash.

calc_statistics_hash() → bytes

Compute the statistics hash.

This hash is used to decide whether the resource statistics should be recomputed.

create_statistics_build_tasks(**kwargs: Any) → list[TaskDesc]

Create tasks for calculating resource statistics for task graph.

property files: set[str]

Return a list of resource files the implementation utilises.

get_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML info page.

get_statistics() → ReferenceGenomeStatistics | None

Try and load resource statistics.

get_statistics_info(**kwargs: Any) → str

Construct the contents of the implementation’s HTML statistics info page.

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

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

class gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeStatistics(resource_id: str, global_statistic: GenomeStatistic, chrom_statistics: dict[str, ChromosomeStatistic])

Bases: ResourceStatistics, GenomeStatisticsMixin

Class for accessing reference genome statistics.

static build_statistics(genomic_resource: GenomicResource) → ReferenceGenomeStatistics | None

Load reference genome statistics.

Module contents