Class: RepresentativeMicrohaplotypeSequence

the representative sequence for a microhaplotype, similar to a fast(a/q) format

URI: portable_microhaplotype_object:RepresentativeMicrohaplotypeSequence

classDiagram class RepresentativeMicrohaplotypeSequence click RepresentativeMicrohaplotypeSequence href "../RepresentativeMicrohaplotypeSequence" RepresentativeMicrohaplotypeSequence : alt_annotations RepresentativeMicrohaplotypeSequence : masking RepresentativeMicrohaplotypeSequence --> "*" MaskingInfo : masking click MaskingInfo href "../MaskingInfo" RepresentativeMicrohaplotypeSequence : microhaplotype_id RepresentativeMicrohaplotypeSequence : pseudocigar RepresentativeMicrohaplotypeSequence : quality RepresentativeMicrohaplotypeSequence : seq

Slots

Name	Cardinality and Range	Description	Inheritance
seq	1 String	the DNA sequence	direct
microhaplotype_id	1 String	name of the microhaplotype, should be unique to this microhaplotype	direct
quality	0..1 String	the ansi fastq per base quality score for this sequence, this is optional	direct
pseudocigar	0..1 String	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

Usages

used by	used in	type	used
RepresentativeMicrohaplotypesForTarget	seqs	range	RepresentativeMicrohaplotypeSequence

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: RepresentativeMicrohaplotypeSequence
description: the representative sequence for a microhaplotype, similar to a fast(a/q)
  format
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- seq
- microhaplotype_id
attributes:
  quality:
    name: quality
    description: the ansi fastq per base quality score for this sequence, this is
      optional
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    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:
    - RepresentativeMicrohaplotypeSequence
    range: string
    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:
    - RepresentativeMicrohaplotypeSequence
    range: MaskingInfo
    required: false
    multivalued: true
  alt_annotations:
    name: alt_annotations
    description: a list of additional annotations associated with this microhaplotype,
      e.g. wildtype, amino acid changes etc
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: RepresentativeMicrohaplotypeSequence
description: the representative sequence for a microhaplotype, similar to a fast(a/q)
  format
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  quality:
    name: quality
    description: the ansi fastq per base quality score for this sequence, this is
      optional
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: quality
    owner: RepresentativeMicrohaplotypeSequence
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    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: RepresentativeMicrohaplotypeSequence
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    range: string
    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: RepresentativeMicrohaplotypeSequence
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    range: MaskingInfo
    required: false
    multivalued: true
  alt_annotations:
    name: alt_annotations
    description: a list of additional annotations associated with this microhaplotype,
      e.g. wildtype, amino acid changes etc
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: alt_annotations
    owner: RepresentativeMicrohaplotypeSequence
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  seq:
    name: seq
    description: the DNA sequence
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: seq
    owner: RepresentativeMicrohaplotypeSequence
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    - PrimerInfo
    range: string
    required: true
    pattern: ^[A-z]$
  microhaplotype_id:
    name: microhaplotype_id
    description: name of the microhaplotype, should be unique to this microhaplotype
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: microhaplotype_id
    owner: RepresentativeMicrohaplotypeSequence
    domain_of:
    - RepresentativeMicrohaplotypeSequence
    - MicrohaplotypeForTarget
    range: string
    required: true
    pattern: ^[A-z-._0-9]$