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Class: RepresentativeMicrohaplotype

the representative sequence for a microhaplotype

URI: portable_microhaplotype_object:RepresentativeMicrohaplotype

classDiagram class RepresentativeMicrohaplotype click RepresentativeMicrohaplotype href "../RepresentativeMicrohaplotype" RepresentativeMicrohaplotype : alt_annotations RepresentativeMicrohaplotype : associated_protein_variants RepresentativeMicrohaplotype --> "*" ProteinVariant : associated_protein_variants click ProteinVariant href "../ProteinVariant" RepresentativeMicrohaplotype : associated_seq_variants RepresentativeMicrohaplotype --> "*" GenomicLocation : associated_seq_variants click GenomicLocation href "../GenomicLocation" RepresentativeMicrohaplotype : masking RepresentativeMicrohaplotype --> "*" MaskingInfo : masking click MaskingInfo href "../MaskingInfo" RepresentativeMicrohaplotype : microhaplotype_name RepresentativeMicrohaplotype : pseudocigar RepresentativeMicrohaplotype --> "0..1" Pseudocigar : pseudocigar click Pseudocigar href "../Pseudocigar" RepresentativeMicrohaplotype : quality RepresentativeMicrohaplotype : seq

Slots

Name Cardinality and Range Description Inheritance
seq 1
String		 the sequence direct
microhaplotype_name 0..1
String		 an optional name for this microhaplotype direct
quality 0..1
String		 the ASCII fastq per base quality score for this sequence, this is optional, m... direct
pseudocigar 0..1
Pseudocigar		 the pseudocigar of the haplotype direct
masking *
MaskingInfo		 masking info for the sequence direct
alt_annotations *
String		 a list of additional annotations associated with this microhaplotype, e direct
associated_protein_variants *
ProteinVariant		 a list of protein variants for this haplotype, e direct
associated_seq_variants *
GenomicLocation		 a list of sequence variants for this haplotype, e direct

Usages

used by used in type used
RepresentativeMicrohaplotypesForTarget microhaplotypes range RepresentativeMicrohaplotype

Identifier and Mapping Information

Schema Source

  • from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type Mapped Value
self portable_microhaplotype_object:RepresentativeMicrohaplotype
native portable_microhaplotype_object:RepresentativeMicrohaplotype

LinkML Source

Direct

name: RepresentativeMicrohaplotype
description: the representative sequence for a microhaplotype
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- seq
attributes:
  microhaplotype_name:
    name: microhaplotype_name
    description: an optional name for this microhaplotype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  quality:
    name: quality
    description: the ASCII fastq per base quality score for this sequence, this is
      optional, must be same length as the sequence
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  pseudocigar:
    name: pseudocigar
    description: the pseudocigar of the haplotype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: Pseudocigar
    required: false
    pattern: ^[A-z-._0-9]+$
  masking:
    name: masking
    description: masking info for the sequence
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: MaskingInfo
    required: false
    multivalued: true
  alt_annotations:
    name: alt_annotations
    description: a list of additional annotations associated with this microhaplotype,
      e.g. wildtype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  associated_protein_variants:
    name: associated_protein_variants
    description: a list of protein variants for this haplotype, e.g. amino acid changes/INDELS
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: ProteinVariant
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  associated_seq_variants:
    name: associated_seq_variants
    description: a list of sequence variants for this haplotype, e.g. SNPS, indels
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotype
    range: GenomicLocation
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: RepresentativeMicrohaplotype
description: the representative sequence for a microhaplotype
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  microhaplotype_name:
    name: microhaplotype_name
    description: an optional name for this microhaplotype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: microhaplotype_name
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  quality:
    name: quality
    description: the ASCII fastq per base quality score for this sequence, this is
      optional, must be same length as the sequence
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: quality
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  pseudocigar:
    name: pseudocigar
    description: the pseudocigar of the haplotype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: pseudocigar
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: Pseudocigar
    required: false
    pattern: ^[A-z-._0-9]+$
  masking:
    name: masking
    description: masking info for the sequence
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: masking
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: MaskingInfo
    required: false
    multivalued: true
  alt_annotations:
    name: alt_annotations
    description: a list of additional annotations associated with this microhaplotype,
      e.g. wildtype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: alt_annotations
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  associated_protein_variants:
    name: associated_protein_variants
    description: a list of protein variants for this haplotype, e.g. amino acid changes/INDELS
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: associated_protein_variants
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: ProteinVariant
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  associated_seq_variants:
    name: associated_seq_variants
    description: a list of sequence variants for this haplotype, e.g. SNPS, indels
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: associated_seq_variants
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    range: GenomicLocation
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  seq:
    name: seq
    description: the sequence
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq
    owner: RepresentativeMicrohaplotype
    domain_of:
    - RepresentativeMicrohaplotype
    - PrimerInfo
    range: string
    required: true
    pattern: ^[A-z]+$