dae.genomic_resources.implementations package

Submodules

dae.genomic_resources.implementations.annotation_pipeline_impl module

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

Bases: GenomicResourceImplementation, InfoImplementationMixin

Resource implementation for annotation pipeline.

add_statistics_build_tasks(task_graph: TaskGraph, **kwargs: Any) → list[Task]

Add tasks for calculating resource statistics to a task graph.

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.

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.

get_template() → Template

dae.genomic_resources.implementations.gene_models_impl module

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

Bases: GenomicResourceImplementation, InfoImplementationMixin

Provides class for gene models.

add_statistics_build_tasks(task_graph: TaskGraph, **kwargs: Any) → list[Task]

Add tasks for calculating resource statistics to a task graph.

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.

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.

get_template() → Template

class dae.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 dae.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

dae.genomic_resources.implementations.genomic_scores_impl module

class dae.genomic_resources.implementations.genomic_scores_impl.CnvCollectionImplementation(resource: GenomicResource)

Bases: GenomicScoreImplementation

Assists in the management of resource of type cnv_collection.

add_statistics_build_tasks(task_graph: TaskGraph, **kwargs: Any) → list[Task]

Add tasks for calculating resource statistics to a task graph.

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.

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.

class dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation(resource: GenomicResource)

Bases: GenomicResourceImplementation, InfoImplementationMixin

Genomic scores base class.

add_statistics_build_tasks(task_graph: TaskGraph, **kwargs: Any) → list[Task]

Add tasks for calculating resource statistics to a task graph.

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.

property files: set[str]

Return a list of resource files the implementation utilises.

get_config_histograms() → dict[str, Any]

Collect all configurations of histograms for the genomic score.

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.

get_template() → Template

property resource_id: str

dae.genomic_resources.implementations.genomic_scores_impl.build_score_implementation_from_resource(resource: GenomicResource) → GenomicScoreImplementation | CnvCollectionImplementation

Builds score implementation based on resource type

dae.genomic_resources.implementations.liftover_chain_impl module

Provides LiftOver chain resource.

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

Bases: GenomicResourceImplementation, InfoImplementationMixin

Defines Lift Over chain resource implementation.

add_statistics_build_tasks(task_graph: TaskGraph, **kwargs: Any) → list[Task]

Add tasks for calculating resource statistics to a task graph.

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.

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.

get_template() → Template

dae.genomic_resources.implementations.reference_genome_impl module

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

Bases: GenomicResourceImplementation, InfoImplementationMixin

Resource implementation for reference genome.

add_statistics_build_tasks(task_graph: TaskGraph, **kwargs: Any) → list[Task]

Add tasks for calculating resource statistics to a task graph.

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.

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.

get_template() → Template

class dae.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