bkbit package

Subpackages

• bkbit.data_translators package
  • Submodules
    • bkbit.data_translators.anatomical_structure_translator module
      • AnS
    • bkbit.data_translators.file_manifest_translator module
      • process_csv()
      • process_row()
      • serialize_to_jsonld()
    • bkbit.data_translators.genome_annotation_translator module
      • Gff3
    • bkbit.data_translators.library_generation_translator module
      • SpecimenPortal
      • parse_multiple_nashids()
      • parse_single_nashid()
  • Module contents
• bkbit.model_converters package
  • Submodules
    • bkbit.model_converters.sheets_converter module
      • adding_template()
      • bican_fix()
      • download_google_sheet_as_tsv()
      • download_gsheets()
      • fix_tsv_files()
      • read_and_parse_gsheet_yaml()
    • bkbit.model_converters.yaml2sheet_converter module
      • create_classes_slots_cvs()
      • create_enums_cvs()
      • create_prefix_headers_csv()
  • Module contents
• bkbit.model_editors package
  • Submodules
    • bkbit.model_editors.add_dunderMethods_genomeAnnotation module
    • bkbit.model_editors.linkml_trimmer module
      • YamlTrimmer
  • Module contents
• bkbit.models package
  • Submodules
    • bkbit.models.anatomical_structure module
      • ANATOMICALDIRECTION
      • Activity
      • ActivityAndBehavior
      • AnatomicalAnnotationSet
      • AnatomicalSpace
      • Annotation
      • Attribute
      • BiologicalEntity
      • Checksum
      • ChemicalEntityOrGeneOrGeneProduct
      • ConfiguredBaseModel
      • DISTANCEUNIT
      • Dataset
      • DigestType
      • Entity
      • Gene
      • GeneOrGeneProduct
      • Genome
      • GenomicEntity
      • ImageDataset
      • InformationContentEntity
      • LinkMLMeta
      • MacromolecularMachineMixin
      • MaterialSample
      • NamedThing
      • Occurrent
      • OntologyClass
      • OrganismTaxon
      • ParcellationAnnotation
      • ParcellationAnnotationTermMap
      • ParcellationAtlas
      • ParcellationColorAssignment
      • ParcellationColorScheme
      • ParcellationTerm
      • ParcellationTermSet
      • ParcellationTerminology
      • PhysicalEntity
      • PhysicalEssence
      • PhysicalEssenceOrOccurrent
      • Procedure
      • QuantityValue
      • SubjectOfInvestigation
      • TaxonomicRank
      • ThingWithTaxon
      • VersionedNamedThing
    • bkbit.models.genome_annotation module
      • Activity
      • ActivityAndBehavior
      • Annotation
      • AnnotationCollection
      • Attribute
      • AuthorityType
      • BioType
      • BiologicalEntity
      • Checksum
      • ChemicalEntityOrGeneOrGeneProduct
      • ConfiguredBaseModel
      • Dataset
      • DigestType
      • Entity
      • Gene
      • GeneAnnotation
      • GeneOrGeneProduct
      • Genome
      • GenomeAnnotation
      • GenomeAssembly
      • GenomicEntity
      • InformationContentEntity
      • LinkMLMeta
      • MacromolecularMachineMixin
      • MaterialSample
      • NamedThing
      • Occurrent
      • OntologyClass
      • OrganismTaxon
      • PhysicalEntity
      • PhysicalEssence
      • PhysicalEssenceOrOccurrent
      • Procedure
      • QuantityValue
      • RelativeFrequencyAnalysisResult
      • StudyResult
      • SubjectOfInvestigation
      • TaxonomicRank
      • ThingWithTaxon
      • VersionedNamedThing
    • bkbit.models.library_generation module
      • Activity
      • ActivityAndBehavior
      • AgeAtDeathReferencePoint
      • AgeAtDeathUnit
      • AmplifiedCdna
      • AmplifiedCdnaRnaAmplificationPassFail
      • Annotation
      • Attribute
      • BarcodedCellSample
      • BarcodedCellSampleTechnique
      • BiologicalEntity
      • BrainSlab
      • CdnaAmplification
      • CellBarcoding
      • CellDissociation
      • CellEnrichment
      • CellLabelBarcode
      • Checksum
      • ChemicalEntityOrGeneOrGeneProduct
      • ConfiguredBaseModel
      • Dataset
      • DigestType
      • DigitalAsset
      • DissectionRoiDelineation
      • DissectionRoiPolygon
      • DissociatedCellSample
      • DissociatedCellSampleCellPrepType
      • Donor
      • EnrichedCellSample
      • EnrichedCellSampleSplitting
      • Entity
      • FastqFileAlignmentStatus
      • Gene
      • GeneOrGeneProduct
      • Genome
      • GenomicEntity
      • InformationContentEntity
      • Library
      • LibraryAliquot
      • LibraryConstruction
      • LibraryPool
      • LibraryPooling
      • LibraryPrepPassFail
      • LibraryR1R2Index
      • LibraryTechnique
      • LinkMLMeta
      • MacromolecularMachineMixin
      • MaterialSample
      • NamedThing
      • Occurrent
      • OntologyClass
      • OrganismTaxon
      • PhysicalEntity
      • PhysicalEssence
      • PhysicalEssenceOrOccurrent
      • Procedure
      • ProvActivity
      • ProvEntity
      • QuantityValue
      • RelativeFrequencyAnalysisResult
      • Sex
      • Species
      • StudyResult
      • SubjectOfInvestigation
      • TaxonomicRank
      • ThingWithTaxon
      • TissueDissection
      • TissueSample
      • VersionedNamedThing
  • Module contents
• bkbit.utils package
  • Submodules
    • bkbit.utils.get_ncbi_taxonomy module
      • build_full_cache()
      • download_and_extract_zip_in_memory()
      • parse_dmp_content()
      • process_and_save_taxdmp_in_memory()
    • bkbit.utils.load_json module
      • load_json()
    • bkbit.utils.ncbi_taxonomy_cache module
      • build_full_cache()
      • data_dir()
      • download_and_extract_zip_in_memory()
      • ensure_full_cache()
      • full_cache_paths()
      • lookup_common_name()
      • lookup_scientific_name()
      • lookup_taxid()
      • parse_dmp_content()
    • bkbit.utils.nimp_api_endpoints module
      • get_ancestors()
      • get_data()
      • get_descendants()
      • get_donor()
    • bkbit.utils.setup_logger module
      • LOG_LEVELS
      • setup_logger()
  • Module contents

Submodules

• bkbit.cli module

Module contents