dae.annotation package
Submodules
dae.annotation.annotatable module
- class dae.annotation.annotatable.Annotatable(chrom: str, pos: int, pos_end: int, annotatable_type: Type)[source]
Bases:
object
Base class for annotatables used in annotation pipeline.
- class Type(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)[source]
Bases:
Enum
Defines annotatable types.
- COMPLEX = 5
- LARGE_DELETION = 7
- LARGE_DUPLICATION = 6
- POSITION = 0
- REGION = 1
- SMALL_DELETION = 4
- SMALL_INSERTION = 3
- SUBSTITUTION = 2
- property chrom: str
- property chromosome: str
- property end_position: int
- static from_string(value: str) Annotatable [source]
Deserialize an Annotatable instance from a string value.
- property pos: int
- property pos_end: int
- property position: int
- class dae.annotation.annotatable.CNVAllele(chrom: str, pos_begin: int, pos_end: int, cnv_type: Type)[source]
Bases:
Annotatable
Defines copy number variants annotatable.
- class dae.annotation.annotatable.Position(chrom: str, pos: int)[source]
Bases:
Annotatable
Annotatable class representing a single position in a chromosome.
- class dae.annotation.annotatable.Region(chrom: str, pos_begin: int, pos_end: int)[source]
Bases:
Annotatable
Annotatable class representing a region in a chromosome.
- class dae.annotation.annotatable.VCFAllele(chrom: str, pos: int, ref: str, alt: str)[source]
Bases:
Annotatable
Defines small variants annotatable.
- property alt: str
- property alternative: str
- static from_string(value: str) VCFAllele [source]
Deserialize an Annotatable instance from a string value.
- property ref: str
- property reference: str
dae.annotation.annotate_columns module
dae.annotation.annotate_doc module
dae.annotation.annotate_utils module
- dae.annotation.annotate_utils.add_input_files_to_task_graph(args: dict, task_graph: TaskGraph) None [source]
- dae.annotation.annotate_utils.build_output_path(raw_input_path: str, output_path: str | None) str [source]
Build an output filepath for an annotation tool’s output.
- dae.annotation.annotate_utils.cache_pipeline_resources(grr: GenomicResourceRepo, pipeline: AnnotationPipeline) None [source]
Cache resources that the given pipeline will use.
- dae.annotation.annotate_utils.get_stuff_from_context(cli_args: dict[str, Any]) tuple[AnnotationPipeline, GenomicContext, GenomicResourceRepo] [source]
Helper method to collect necessary objects from the genomic context.
- dae.annotation.annotate_utils.produce_partfile_paths(input_file_path: str, regions: list[Region], work_dir: str) list[str] [source]
Produce a list of file paths for output region part files.
- dae.annotation.annotate_utils.produce_regions(pysam_file: TabixFile, region_size: int) list[Region] [source]
Given a region size, produce contig regions to annotate by.
dae.annotation.annotate_vcf module
dae.annotation.annotation_config module
- class dae.annotation.annotation_config.AnnotationConfigParser[source]
Bases:
object
Parser for annotation configuration.
- static has_wildcard(string: str) bool [source]
Ascertain whether a string contains a valid wildcard.
- static match_labels_query(query: dict[str, str], resource_labels: dict[str, str]) bool [source]
Check if the labels query for a wildcard matches.
- static parse_complete(raw: dict[str, Any], idx: int, grr: GenomicResourceRepo | None = None) list[AnnotatorInfo] [source]
Parse a full-form annotation config.
- static parse_minimal(raw: str, idx: int) AnnotatorInfo [source]
Parse a minimal-form annotation config.
- static parse_raw(pipeline_raw_config: list[dict[str, Any]] | RawFullConfig | None, grr: GenomicResourceRepo | None = None) tuple[AnnotationPreamble | None, list[AnnotatorInfo]] [source]
Parse raw dictionary annotation pipeline configuration.
- static parse_raw_attribute_config(raw_attribute_config: dict[str, Any]) AttributeInfo [source]
Parse annotation attribute raw configuration.
- static parse_raw_attributes(raw_attributes_config: Any) list[AttributeInfo] [source]
Parse annotator pipeline attribute configuration.
- static parse_short(raw: dict[str, Any], idx: int, grr: GenomicResourceRepo | None = None) list[AnnotatorInfo] [source]
Parse a short-form annotation config.
- static parse_str(content: str, source_file_name: str | None = None, grr: GenomicResourceRepo | None = None) tuple[AnnotationPreamble | None, list[AnnotatorInfo]] [source]
Parse annotation pipeline configuration string.
- static query_resources(annotator_type: str, wildcard: str, grr: GenomicResourceRepo) list[str] [source]
Collect resources matching a given query.
- class dae.annotation.annotation_config.AnnotationPreamble(summary: 'str', description: 'str', input_reference_genome: 'str', input_reference_genome_res: 'GenomicResource | None', metadata: 'dict[str, Any]')[source]
Bases:
object
- description: str
- input_reference_genome: str
- input_reference_genome_res: GenomicResource | None
- metadata: dict[str, Any]
- summary: str
- class dae.annotation.annotation_config.AnnotatorInfo(_type: str, attributes: list[AttributeInfo], parameters: ParamsUsageMonitor | dict[str, Any], documentation: str = '', resources: list[GenomicResource] | None = None, annotator_id: str = 'N/A')[source]
Bases:
object
Defines annotator configuration.
- annotator_id: str
- attributes: list[AttributeInfo]
- documentation: str = ''
- parameters: ParamsUsageMonitor
- resources: list[GenomicResource]
- type: str
- class dae.annotation.annotation_config.AttributeInfo(name: str, source: str, *, internal: bool, parameters: ParamsUsageMonitor | dict[str, Any], _type: str = 'str', description: str = '', documentation: str | None = None)[source]
Bases:
object
Defines annotation attribute configuration.
- static create(source: str, name: str | None = None, *, internal: bool = False) AttributeInfo [source]
Create an AttributeInfo instance.
- description: str = ''
- property documentation: str
- internal: bool
- name: str
- parameters: ParamsUsageMonitor
- source: str
- type: str = 'str'
- class dae.annotation.annotation_config.ParamsUsageMonitor(data: dict[str, Any])[source]
Bases:
Mapping
Class to monitor usage of annotator parameters.
- class dae.annotation.annotation_config.RawFullConfig[source]
Bases:
TypedDict
- annotators: list[dict[str, Any]]
- preamble: RawPreamble
dae.annotation.annotation_factory module
Factory for creation of annotation pipeline.
- dae.annotation.annotation_factory.build_annotation_pipeline(config: list[dict[str, Any]] | RawFullConfig, grr: GenomicResourceRepo, *, allow_repeated_attributes: bool = False, work_dir: Path | None = None, config_old_raw: str | None = None, full_reannotation: bool = False) AnnotationPipeline [source]
Build an annotation pipeline.
- dae.annotation.annotation_factory.check_for_repeated_attributes_in_annotator(annotator_config: AnnotatorInfo) None [source]
Check for repeated attributes in annotator configuration.
- dae.annotation.annotation_factory.check_for_repeated_attributes_in_pipeline(pipeline: AnnotationPipeline, *, allow_repeated_attributes: bool = False) None [source]
Check for repeated attributes in pipeline configuration.
- dae.annotation.annotation_factory.check_for_unused_parameters(info: AnnotatorInfo) None [source]
Check annotator configuration for unused parameters.
- dae.annotation.annotation_factory.copy_annotation_pipeline(pipeline: AnnotationPipeline) AnnotationPipeline [source]
Copy an annotation pipeline instance.
- dae.annotation.annotation_factory.copy_reannotation_pipeline(pipeline: ReannotationPipeline) ReannotationPipeline [source]
Copy a reannotation pipeline instance.
- dae.annotation.annotation_factory.get_annotator_factory(annotator_type: str) Callable[[AnnotationPipeline, AnnotatorInfo], Annotator] [source]
Find and return a factory function for creation of an annotator type.
If the specified annotator type is not found, this function raises ValueError exception.
- Returns:
the annotator factory for the specified annotator type.
- Raises:
ValueError – when can’t find an annotator factory for the specified annotator type.
- dae.annotation.annotation_factory.get_available_annotator_types() list[str] [source]
Return the list of all registered annotator factory types.
- dae.annotation.annotation_factory.load_pipeline_from_file(raw_path: str, grr: GenomicResourceRepo, *, allow_repeated_attributes: bool = False, work_dir: Path | None = None) AnnotationPipeline [source]
Load an annotation pipeline from a configuration file.
- dae.annotation.annotation_factory.load_pipeline_from_yaml(raw: str, grr: GenomicResourceRepo, *, allow_repeated_attributes: bool = False, work_dir: Path | None = None) AnnotationPipeline [source]
Load an annotation pipeline from a YAML-formatted string.
- dae.annotation.annotation_factory.register_annotator_factory(annotator_type: str, factory: Callable[[AnnotationPipeline, AnnotatorInfo], Annotator]) None [source]
Register additional annotator factory.
By default all genotype storage factories should be registered at [dae.genotype_storage.factories] extenstion point. All registered factories are loaded automatically. This function should be used if you want to bypass extension point mechanism and register addition genotype storage factory programatically.
- dae.annotation.annotation_factory.resolve_repeated_attributes(pipeline: AnnotationPipeline, repeated_attributes: set[str]) None [source]
Resolve repeated attributes in pipeline configuration via renaming.
dae.annotation.annotation_pipeline module
Provides annotation pipeline class.
- class dae.annotation.annotation_pipeline.AnnotationPipeline(repository: GenomicResourceRepo)[source]
Bases:
object
Provides annotation pipeline abstraction.
- annotate(annotatable: Annotatable | None, context: dict | None = None) dict [source]
Apply all annotators to an annotatable.
- batch_annotate(annotatables: Sequence[Annotatable | None], contexts: list[dict] | None = None, batch_work_dir: str | None = None) list[dict] [source]
Apply all annotators to a list of annotatables.
- build_pipeline_genomic_context() GenomicContext [source]
Create a genomic context from the pipeline parameters.
- get_annotator_by_attribute_info(attribute_info: AttributeInfo) Annotator | None [source]
- get_attribute_info(attribute_name: str) AttributeInfo | None [source]
- get_attributes() list[AttributeInfo] [source]
- get_info() list[AnnotatorInfo] [source]
- open() AnnotationPipeline [source]
Open all annotators in the pipeline and mark it as open.
- class dae.annotation.annotation_pipeline.Annotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo)[source]
Bases:
ABC
Annotator provides a set of attrubutes for a given Annotatable.
- abstract annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- property attributes: list[AttributeInfo]
- batch_annotate(annotatables: Sequence[Annotatable | None], contexts: list[dict[str, Any]], batch_work_dir: str | None = None) Iterable[dict[str, Any]] [source]
- get_info() AnnotatorInfo [source]
- property resource_ids: set[str]
- property resources: list[GenomicResource]
- property used_context_attributes: tuple[str, ...]
- class dae.annotation.annotation_pipeline.AnnotatorDecorator(child: Annotator)[source]
Bases:
Annotator
Defines annotator decorator base class.
- class dae.annotation.annotation_pipeline.FullReannotationPipeline(pipeline_new: AnnotationPipeline, pipeline_old: AnnotationPipeline)[source]
Bases:
ReannotationPipeline
Special-case ReannotationPipeline.
Completely removes all old attributes and runs every new annotator, without reusing anything.
- class dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator(child: Annotator)[source]
Bases:
AnnotatorDecorator
Defines annotator decorator to use input annotatable if defined.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- property used_context_attributes: tuple[str, ...]
- class dae.annotation.annotation_pipeline.ReannotationPipeline(pipeline_new: AnnotationPipeline, pipeline_old: AnnotationPipeline)[source]
Bases:
AnnotationPipeline
Special pipeline that handles reannotation of a previous pipeline.
- AnnotationDependencyGraph
alias of
dict
[AnnotatorInfo
,list
[tuple
[AnnotatorInfo
,AttributeInfo
]]]
- annotate(annotatable: Annotatable | None, context: dict | None = None) dict [source]
Apply all annotators to an annotatable.
- static build_dependency_graph(pipeline: AnnotationPipeline) AnnotationDependencyGraph [source]
Make dependency graph for an annotation pipeline.
- get_attributes() list[AttributeInfo] [source]
- get_dependencies_for(info: AnnotatorInfo) set[AnnotatorInfo] [source]
Get all dependencies for a given annotator.
- get_dependents_for(info: AnnotatorInfo) set[AnnotatorInfo] [source]
Get all dependents for a given annotator.
- class dae.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator(child: Annotator, value_transformers: dict[str, Callable[[Any], Any]])[source]
Bases:
AnnotatorDecorator
Define value transformer annotator decorator.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
dae.annotation.annotator_base module
Provides base class for annotators.
- class dae.annotation.annotator_base.AnnotatorBase(pipeline: AnnotationPipeline | None, info: AnnotatorInfo, source_type_desc: dict[str, tuple[str, str]])[source]
Bases:
Annotator
Base implementation of the Annotator class.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- batch_annotate(annotatables: Sequence[Annotatable | None], contexts: list[dict[str, Any]], batch_work_dir: str | None = None) list[dict[str, Any]] [source]
dae.annotation.cnv_collection_annotator module
- class dae.annotation.cnv_collection_annotator.CnvCollectionAnnotator(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
Annotator
Simple effect annotator class.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- dae.annotation.cnv_collection_annotator.build_cnv_collection_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
dae.annotation.debug_annotator module
- class dae.annotation.debug_annotator.HelloWorldAnnotator(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
Annotator
Defines example annotator.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- dae.annotation.debug_annotator.build_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
Create an example hello world annotator.
dae.annotation.docker_annotator module
- class dae.annotation.docker_annotator.DockerAnnotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo)[source]
Bases:
AnnotatorBase
Base class for annotators that use docker containers.
dae.annotation.effect_annotator module
- class dae.annotation.effect_annotator.EffectAnnotatorAdapter(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
AnnotatorBase
Adapts effect annotator to be used in annotation infrastructure.
- dae.annotation.effect_annotator.build_effect_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
dae.annotation.gene_score_annotator module
Module containing the gene score annotator.
- class dae.annotation.gene_score_annotator.GeneScoreAnnotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo, gene_score_resource: GenomicResource, input_gene_list: str)[source]
Bases:
Annotator
Gene score annotator class.
- DEFAULT_AGGREGATOR_TYPE = 'dict'
- aggregate_gene_values(score_id: str, gene_symbols: list[str], aggregator_type: str) Any [source]
Aggregate gene score values.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- property used_context_attributes: tuple[str, ...]
- dae.annotation.gene_score_annotator.build_gene_score_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
Create a gene score annotator.
dae.annotation.gene_set_annotator module
- class dae.annotation.gene_set_annotator.GeneSetAnnotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo, gene_set_resource: GenomicResource, input_gene_list: str)[source]
Bases:
AnnotatorBase
Gene set annotator class.
- property used_context_attributes: tuple[str, ...]
- dae.annotation.gene_set_annotator.build_gene_set_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
Create a gene set annotator.
dae.annotation.genomic_context module
- class dae.annotation.genomic_context.CLIAnnotationContextProvider[source]
Bases:
CLIGenomicContextProvider
Defines annotation pipeline genomics context provider.
- static add_argparser_arguments(parser: ArgumentParser) None [source]
Add command line arguments to the argument parser.
- static init(**kwargs: Any) GenomicContext | None [source]
Build a CLI genomic context.
- dae.annotation.genomic_context.get_context_pipeline(context: GenomicContext) AnnotationPipeline | None [source]
Construct an annotation pipeline.
dae.annotation.liftover_annotator module
Provides a lift over annotator and helpers.
- class dae.annotation.liftover_annotator.AbstractLiftoverAnnotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo, chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome)[source]
Bases:
AnnotatorBase
Liftovver annotator class.
- liftover_cnv(cnv_allele: Annotatable) Annotatable | None [source]
Liftover CNV allele annotatable.
- liftover_position(position: Annotatable) Annotatable | None [source]
Liftover position annotatable.
- liftover_region(region: Annotatable) Annotatable | None [source]
Liftover region annotatable.
- class dae.annotation.liftover_annotator.BasicLiftoverAnnotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo, chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome)[source]
Bases:
AbstractLiftoverAnnotator
Basic liftover annotator class.
- class dae.annotation.liftover_annotator.BcfLiftoverAnnotator(pipeline: AnnotationPipeline | None, info: AnnotatorInfo, chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome)[source]
Bases:
AbstractLiftoverAnnotator
BCF tools liftover re-implementation annotator class.
- dae.annotation.liftover_annotator.basic_liftover_allele(chrom: str, pos: int, ref: str, alt: str, liftover_chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome) tuple[str, int, str, str] | None [source]
Basic liftover an allele.
- dae.annotation.liftover_annotator.basic_liftover_variant(chrom: str, pos: int, ref: str, alts: list[str], liftover_chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome) tuple[str, int, str, list[str]] | None [source]
Basic liftover variant utility function.
- dae.annotation.liftover_annotator.bcf_liftover_allele(chrom: str, pos: int, ref: str, alt: str, liftover_chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome) tuple[str, int, str, str] | None [source]
Liftover a variant.
- dae.annotation.liftover_annotator.bcf_liftover_variant(chrom: str, pos: int, ref: str, alts: list[str], liftover_chain: LiftoverChain, source_genome: ReferenceGenome, target_genome: ReferenceGenome) tuple[str, int, str, list[str]] | None [source]
BCF liftover variant utility function.
- dae.annotation.liftover_annotator.build_liftover_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
Create a liftover annotator.
dae.annotation.normalize_allele_annotator module
Provides normalize allele annotator and helpers.
- class dae.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
AnnotatorBase
Annotator to normalize VCF alleles.
- dae.annotation.normalize_allele_annotator.build_normalize_allele_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
- dae.annotation.normalize_allele_annotator.normalize_allele(allele: VCFAllele, genome: ReferenceGenome) VCFAllele [source]
Normalize an allele.
Using algorithm defined in following https://genome.sph.umich.edu/wiki/Variant_Normalization
dae.annotation.processing_pipeline module
- class dae.annotation.processing_pipeline.Annotation(annotatable: ~dae.annotation.annotatable.Annotatable | None, context: dict[str, ~typing.Any] = <factory>)[source]
Bases:
object
A pair of an annotatable and its relevant context.
The context can hold any key/value pair relevant to the annotatable and is typically used to store the results of annotators.
- annotatable: Annotatable | None
- context: dict[str, Any]
- class dae.annotation.processing_pipeline.AnnotationPipelineAnnotatablesBatchFilter(annotation_pipeline: AnnotationPipeline)[source]
Bases:
AnnotationsWithSourceBatchFilter
,AnnotationPipelineContextManager
Filter that annotates an AnnotationWithSource batch using a pipeline.
- class dae.annotation.processing_pipeline.AnnotationPipelineAnnotatablesFilter(annotation_pipeline: AnnotationPipeline)[source]
Bases:
AnnotationsWithSourceFilter
,AnnotationPipelineContextManager
Filter that annotates an AnnotationWithSource object using a pipeline.
- class dae.annotation.processing_pipeline.AnnotationPipelineContextManager(annotation_pipeline: AnnotationPipeline)[source]
Bases:
AbstractContextManager
A context manager for annotation pipelines.
- class dae.annotation.processing_pipeline.AnnotationsWithSource(source: Any, annotations: list[Annotation])[source]
Bases:
object
A pair of a list of Annotation instances and their source.
The source is typically a variant read from some format, with the ‘annotations’ attribute corresponding to its alleles.
- annotations: list[Annotation]
- source: Any
- class dae.annotation.processing_pipeline.AnnotationsWithSourceBatchFilter[source]
Bases:
Filter
Base class for filters that work on AnnotationsWithSource batches.
- filter(data: Sequence[AnnotationsWithSource]) Sequence[AnnotationsWithSource] [source]
Filter a batch of AnnotationsWithSource objects.
- class dae.annotation.processing_pipeline.AnnotationsWithSourceFilter[source]
Bases:
Filter
Base class for filters that work on AnnotationsWithSource objects.
- filter(data: AnnotationsWithSource) AnnotationsWithSource [source]
Filter a single AnnotationsWithSource object.
- class dae.annotation.processing_pipeline.DeleteAttributesFromAWSBatchFilter(attributes_to_remove: Sequence[str])[source]
Bases:
Filter
Filter to remove items from AWS batches. Works in-place.
- filter(data: Sequence[AnnotationsWithSource]) Sequence[AnnotationsWithSource] [source]
- class dae.annotation.processing_pipeline.DeleteAttributesFromAWSFilter(attributes_to_remove: Sequence[str])[source]
Bases:
Filter
Filter to remove items from AWSs. Works in-place.
- filter(data: AnnotationsWithSource) AnnotationsWithSource [source]
dae.annotation.reannotate_instance module
- class dae.annotation.reannotate_instance.ReannotateInstanceTool(raw_args: list[str] | None = None, gpf_instance: GPFInstance | None = None)[source]
Bases:
object
Annotation tool to reannotate the configured GPF instance
- dae.annotation.reannotate_instance.cli(raw_args: list[str] | None = None, gpf_instance: GPFInstance | None = None) None [source]
Entry point method for instance reannotation tool.
dae.annotation.record_to_annotatable module
- class dae.annotation.record_to_annotatable.CSHLAlleleRecordToAnnotatable(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
Transform a CSHL variant record into a VCF allele annotatable.
- build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.DaeAlleleRecordToAnnotatable(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
Transform a CSHL variant record into a VCF allele annotatable.
- build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.RecordToAnnotable(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
ABC
Base class for record to annotable transformation.
- abstract build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.RecordToCNVAllele(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
Transform a columns record into a CNV allele annotatable.
- build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.RecordToPosition(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
- build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.RecordToRegion(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
- build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.RecordToVcfAllele(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
- build(record: dict[str, str]) Annotatable [source]
- class dae.annotation.record_to_annotatable.VcfLikeRecordToVcfAllele(columns: tuple, ref_genome: ReferenceGenome | None)[source]
Bases:
RecordToAnnotable
Transform a columns record into VCF allele annotatable.
- build(record: dict[str, str]) Annotatable [source]
- dae.annotation.record_to_annotatable.add_record_to_annotable_arguments(parser: ArgumentParser) None [source]
- dae.annotation.record_to_annotatable.build_record_to_annotatable(parameters: dict[str, str], available_columns: set[str], ref_genome: ReferenceGenome | None = None) RecordToAnnotable [source]
Transform a variant record into an annotatable.
dae.annotation.score_annotator module
This contains the implementation of the three score annotators.
Genomic score annotators defined are positions_score, np_score, and allele_score.
- class dae.annotation.score_annotator.AlleleScoreAnnotator(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
GenomicScoreAnnotatorBase
This class implements allele_score annotator.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- build_score_aggregator_documentation(attr_info: AttributeInfo) list[str] [source]
Collect score aggregator documentation.
- class dae.annotation.score_annotator.GenomicScoreAnnotatorBase(pipeline: AnnotationPipeline, info: AnnotatorInfo, score: GenomicScore)[source]
Bases:
Annotator
Genomic score base annotator.
- add_score_aggregator_documentation(attribute_info: AttributeInfo, aggregator: str, attribute_conf_agg: str | None) None [source]
Collect score aggregator documentation.
- abstract build_score_aggregator_documentation(attr_info: AttributeInfo) list[str] [source]
Construct score aggregator documentation.
- class dae.annotation.score_annotator.PositionScoreAnnotator(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
GenomicScoreAnnotatorBase
This class implements the position_score annotator.
The position_score annotator requires the resrouce_id parameter, whose value must be an id of a genomic resource of type position_score.
The position_score resource provides a set of scores (see …) that the position_score annotator uses as attributes to assign to the annotatable.
The position_score annotator recognized one attribute level parameter called position_aggregator that controls how the position scores are aggregator for annotates that ref to a region of the reference genome.
- annotate(annotatable: Annotatable | None, context: dict[str, Any]) dict[str, Any] [source]
Produce annotation attributes for an annotatable.
- build_score_aggregator_documentation(attr_info: AttributeInfo) list[str] [source]
Collect score aggregator documentation.
- dae.annotation.score_annotator.build_allele_score_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
- dae.annotation.score_annotator.build_np_score_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
- dae.annotation.score_annotator.build_position_score_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]
- dae.annotation.score_annotator.get_genomic_resource(pipeline: AnnotationPipeline, info: AnnotatorInfo, resource_types: set[str]) GenomicResource [source]
Return genomic score resource used for given genomic score annotator.
dae.annotation.simple_effect_annotator module
- class dae.annotation.simple_effect_annotator.SimpleEffectAnnotator(pipeline: AnnotationPipeline, info: AnnotatorInfo)[source]
Bases:
AnnotatorBase
Simple effect annotator class.
- call_region(chrom: str, beg: int, end: int, transcripts: list[TranscriptModel], func_name: str, classification: str) tuple[str, set[str]] | None [source]
Call a region with a specific classification.
- cds_intron_regions(transcript: TranscriptModel) list[Region] [source]
Return whether region is CDS intron.
- noncoding_regions(transcript: TranscriptModel) list[Region] [source]
Return whether the region is noncoding.
- peripheral_regions(transcript: TranscriptModel) list[Region] [source]
Return whether the region is peripheral.
- run_annotate(chrom: str, beg: int, end: int) tuple[str, set[str]] [source]
Return classification with a set of affected genes.
- utr_regions(transcript: TranscriptModel) Sequence[Region] [source]
Return whether the region is classified as UTR.
- dae.annotation.simple_effect_annotator.build_simple_effect_annotator(pipeline: AnnotationPipeline, info: AnnotatorInfo) Annotator [source]