dae Interface

• Genomic Resources
  • Classes and Functions
    • dae.genomic_resources package
      • Submodules
      • dae.genomic_resources.aggregators module
      • dae.genomic_resources.cached_repository module
      • dae.genomic_resources.cli module
      • dae.genomic_resources.clinvar module
      • dae.genomic_resources.fsspec_protocol module
      • dae.genomic_resources.gene_models module
      • dae.genomic_resources.genomic_position_table module
      • dae.genomic_resources.genomic_context module
      • dae.genomic_resources.genomic_scores module
      • dae.genomic_resources.group_repository module
      • dae.genomic_resources.histogram module
      • dae.genomic_resources.liftover_resource module
      • dae.genomic_resources.reference_genome module
      • dae.genomic_resources.repository module
      • dae.genomic_resources.repository_factory module
      • dae.genomic_resources.testing module
      • Module contents
• Annotation
  • Classes and Functions
    • dae.annotation package
      • Submodules
      • dae.annotation.annotatable module
      • dae.annotation.annotate_columns module
      • dae.annotation.annotate_vcf module
      • dae.annotation.annotation_factory module
      • dae.annotation.annotation_pipeline module
      • dae.annotation.annotator_base module
      • dae.annotation.clinvar_annotator module
      • dae.annotation.context module
      • dae.annotation.effect_annotator module
      • dae.annotation.gene_score_annotator module
      • dae.annotation.liftover_annotator module
      • dae.annotation.normalize_allele_annotator module
      • dae.annotation.record_to_annotatable module
      • dae.annotation.schema module
      • dae.annotation.score_annotator module
      • dae.annotation.utils module
      • Module contents
• Effect Annotation
  • Classes and Functions
    • dae.effect_annotation package
      • Subpackages
      • Submodules
      • dae.effect_annotation.annotation_effects module
      • dae.effect_annotation.annotation_request module
      • dae.effect_annotation.annotator module
      • dae.effect_annotation.cli module
      • dae.effect_annotation.effect module
      • dae.effect_annotation.gene_codes module
      • dae.effect_annotation.variant module
      • Module contents
• Genomic Variants
  • Apache Parquet variants schema
    • Summary Variants/Alleles flat schema
    • Family Variants schema
    • Family Alleles schema
    • Variant Scores schema
    • Pedigree file schema
  • Family variants query interface
    • Query by regions
    • Query by genes and effect types
    • Query by inheritance
    • Query by family IDs
    • Query by person IDs
    • Query by sexes
    • Query by roles
    • Query by variant types
    • Query with real value variant attributes (scores)
    • Query with filter function
  • Genomic Variants Classes and Functions
    • dae.variants package
      • Submodules
      • dae.variants.attributes module
      • dae.variants.core module
      • dae.variants.family_variant module
      • dae.variants.variant module
      • Module contents
• Pedigrees Tools
  • Classes and Functions
    • dae.pedigrees package
      • Submodules
      • dae.pedigrees.drawing module
      • dae.pedigrees.family module
      • dae.pedigrees.family_role_builder module
      • dae.pedigrees.family_tag_builder module
      • dae.pedigrees.interval_sandwich module
      • dae.pedigrees.layout module
      • dae.pedigrees.loader module
      • dae.pedigrees.pedigrees module
      • dae.pedigrees.testing module
      • Module contents
• Variants Loaders
  • dae.variants_loaders package
    • Subpackages
      • dae.variants_loaders.cnv package
      • dae.variants_loaders.dae package
      • dae.variants_loaders.raw package
      • dae.variants_loaders.vcf package
    • Module contents
  • dae.variants_loaders.raw package
    • Submodules
    • dae.variants_loaders.raw.flexible_variant_loader module
      • adjust_chrom_prefix()
      • flexible_variant_loader()
      • location_variant_to_vcf_transformer()
      • variant_to_variant_type()
    • dae.variants_loaders.raw.loader module
      • AnnotationDecorator
      • AnnotationPipelineDecorator
      • ArgumentType
      • CLIArgument
      • CLILoader
      • EffectAnnotationDecorator
      • FamiliesGenotypes
      • StoredAnnotationDecorator
      • VariantsGenotypesLoader
      • VariantsLoader
      • VariantsLoaderDecorator
    • Module contents
  • dae.variants_loaders.dae package
    • Submodules
    • dae.variants_loaders.dae.loader module
      • DaeTransmittedFamiliesGenotypes
      • DaeTransmittedLoader
      • DenovoFamiliesGenotypes
      • DenovoLoader
    • Module contents
  • dae.variants_loaders.vcf package
    • Submodules
    • dae.variants_loaders.vcf.loader module
      • SingleVcfLoader
      • VcfFamiliesGenotypes
      • VcfLoader
    • Module contents
  • dae.variants_loaders.cnv package
    • Submodules
    • dae.variants_loaders.cnv.flexible_cnv_loader module
      • flexible_cnv_loader()
    • dae.variants_loaders.cnv.loader module
      • Copy Number Variants (CNV) loader CNVLoader
      • CNVLoader
    • Module contents
• Import Tools
  • What is Import Tools
  • Import Tools config files
  • Import Tools configuration format
  • Working with the Import Tools CLI
  • Running on a SGE cluster
  • Running on a Kubernetes cluster
  • Classes and Functions
    • dae.import_tools package
      • Submodules
      • dae.import_tools.import_tools module
      • dae.import_tools.parquet_writer module
      • dae.import_tools.task_graph module
      • Module contents
• Genotype Data Parquet Writers
  • dae.parquet package
    • Subpackages
      • dae.parquet.schema1 package
      • dae.parquet.schema2 package
    • Module contents
  • dae.parquet.schema1 package
    • Submodules
    • dae.parquet.schema1.parquet_io module
    • dae.parquet.schema1.serializers module
    • Module contents
  • dae.parquet.schema2 package
    • Submodules
    • dae.parquet.schema2.parquet_io module
      • ContinuousParquetFileWriter
      • VariantsParquetWriter
    • dae.parquet.schema2.serializers module
      • AlleleParquetSerializer
    • Module contents
• Query Genomic Variants
  • dae.query_variants package
    • Subpackages
      • dae.query_variants.sql package
    • Submodules
    • dae.query_variants.attributes_query module
      • AndNode
      • BaseQueryTransformerMatcher
      • BaseTreeTransformer
      • BitwiseTreeTransformer
      • ContainsNode
      • ElementOfNode
      • EqualsNode
      • GreaterThanEqNode
      • GreaterThanNode
      • LeafNode
      • LessThanEqNode
      • LessThanNode
      • Matcher
      • NotNode
      • OrNode
      • QueryTransformerMatcher
      • QueryTreeToBitwiseLambdaTransformer
      • QueryTreeToLambdaTransformer
      • QueryTreeToSQLBitwiseTransformer
      • QueryTreeToSQLTransformer
      • StringQueryToTreeTransformer
      • TreeNode
      • get_bit_and_str()
      • inheritance_converter()
      • roles_converter()
      • sex_converter()
      • variant_type_converter()
    • dae.query_variants.attributes_query_inheritance module
      • Expression
      • InheritanceTransformer
      • NegPrimitive
      • Primitive
    • dae.query_variants.query_runners module
      • QueryResult
      • QueryRunner
    • Module contents
  • dae.query_variants.sql package
    • Subpackages
      • dae.query_variants.sql.schema1 package
      • dae.query_variants.sql.schema2 package
    • Module contents
  • dae.query_variants.sql.schema1 package
    • Submodules
    • dae.query_variants.sql.schema1.base_query_builder module
    • dae.query_variants.sql.schema1.family_variants_query_builder module
    • dae.query_variants.sql.schema1.schema1_query_director module
    • dae.query_variants.sql.schema1.summary_variants_query_builder module
    • Module contents
  • dae.query_variants.sql.schema2 package
    • Subpackages
      • dae.query_variants.sql.schema2.tests package
    • Submodules
    • dae.query_variants.sql.schema2.base_query_builder module
      • BaseQueryBuilder
      • Dialect
    • dae.query_variants.sql.schema2.family_builder module
      • FamilyQueryBuilder
    • dae.query_variants.sql.schema2.summary_builder module
      • SummaryQueryBuilder
    • Module contents
• Genotype Storage
  • dae.genotype_storage package
    • Submodules
    • dae.genotype_storage.genotype_storage module
      • GenotypeStorage
    • dae.genotype_storage.genotype_storage_registry module
      • GenotypeStorageRegistry
    • Module contents
      • get_genotype_storage_factory()
      • get_genotype_storage_types()
      • register_genotype_storage_factory()
• In-Memory Genotype Storage
  • dae.inmemory_storage package
    • Submodules
    • dae.inmemory_storage.inmemory_genotype_storage module
      • InmemoryGenotypeStorage
    • dae.inmemory_storage.inmemory_import_storage module
      • InmemoryImportStorage
    • dae.inmemory_storage.raw_variants module
      • RawFamilyVariants
      • RawMemoryVariants
      • RawVariantsQueryRunner
    • Module contents
• Impala Genotype Storages
  • dae.impala_storage package
    • Subpackages
      • dae.impala_storage.helpers package
      • dae.impala_storage.schema1 package
      • dae.impala_storage.schema2 package
    • Module contents
  • dae.impala_storage.helpers package
    • Submodules
    • dae.impala_storage.helpers.hdfs_helpers module
    • dae.impala_storage.helpers.impala_helpers module
    • dae.impala_storage.helpers.rsync_helpers module
    • Module contents
  • dae.impala_storage.schema1 package
    • Submodules
    • dae.impala_storage.schema1.impala_genotype_storage module
    • dae.impala_storage.schema1.impala_schema1 module
    • dae.impala_storage.schema1.impala_variants module
    • dae.impala_storage.schema1.import_commons module
    • Module contents
  • dae.impala_storage.schema2 package
    • Submodules
    • dae.impala_storage.schema2.bigquery_variants module
    • dae.impala_storage.schema2.impala_variants module
    • dae.impala_storage.schema2.schema2_genotype_storage module
    • dae.impala_storage.schema2.schema2_import_storage module
    • dae.impala_storage.schema2.sql_query_runner module
    • Module contents
• Configuration
  • Classes and Functions
    • dae.configuration package
      • Subpackages
      • Submodules
      • dae.configuration.gpf_config_parser module
      • dae.configuration.study_config_builder module
      • dae.configuration.utils module
      • Module contents
• Genotype Data
  • Classes and Functions
    • dae.studies package
      • Submodules
      • dae.studies.study module
      • dae.studies.variants_db module
      • Module contents
• Phenotype Data
  • Pheno DB access
  • Example usage of PhenoDB
  • Classes and Functions
    • dae.pheno package
      • Subpackages
      • Submodules
      • dae.pheno.common module
      • dae.pheno.db module
      • dae.pheno.graphs module
      • dae.pheno.husl module
      • dae.pheno.palletes module
      • dae.pheno.pheno_db module
      • dae.pheno.plots module
      • dae.pheno.prepare_data module
      • Module contents
• Phenotype tool
  • Example usage of PhenoTool class
  • Example usage of PhenoTool class with pheno filters
  • Example with vineland_ii
  • Classes and Functions
    • dae.pheno_tool package
      • Submodules
      • dae.pheno_tool.tool module
      • Module contents
• Enrichment Tool
  • Example usage of EnrichmentTool class
  • Classes and Functions
    • dae.pheno_tool package
      • Submodules
      • dae.pheno_tool.tool module
      • Module contents
• Gene Properties
  • Example usage of Weights class
  • Classes and Functions
    • dae.gene package
      • Submodules
      • dae.gene.denovo_gene_set_collection module
      • dae.gene.denovo_gene_set_collection_factory module
      • dae.gene.denovo_gene_sets_db module
      • dae.gene.gene_scores module
      • dae.gene.gene_sets_db module
      • dae.gene.gene_term module
      • dae.gene.scores module
      • dae.gene.utils module
      • Module contents
• Tools
  • Classes and Functions
    • dae.annotation package
      • Submodules
      • dae.annotation.annotatable module
      • dae.annotation.annotate_columns module
      • dae.annotation.annotate_vcf module
      • dae.annotation.annotation_factory module
      • dae.annotation.annotation_pipeline module
      • dae.annotation.annotator_base module
      • dae.annotation.clinvar_annotator module
      • dae.annotation.context module
      • dae.annotation.effect_annotator module
      • dae.annotation.gene_score_annotator module
      • dae.annotation.liftover_annotator module
      • dae.annotation.normalize_allele_annotator module
      • dae.annotation.record_to_annotatable module
      • dae.annotation.schema module
      • dae.annotation.score_annotator module
      • dae.annotation.utils module
      • Module contents