Class: Google::Apis::GenomicsV1::ReferenceSet

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable, Core::JsonObjectSupport
Defined in:
generated/google/apis/genomics_v1/classes.rb,
generated/google/apis/genomics_v1/representations.rb,
generated/google/apis/genomics_v1/representations.rb

Overview

A reference set is a set of references which typically comprise a reference assembly for a species, such as GRCh38 which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references. For more genomics resource definitions, see Fundamentals of Google Genomics

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::JsonObjectSupport

#to_json

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ ReferenceSet

Returns a new instance of ReferenceSet



2285
2286
2287
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2285

def initialize(**args)
   update!(**args)
end

Instance Attribute Details

#assembly_id ⇒ String

Public id of this reference set, such as GRCh37. Corresponds to the JSON property assemblyId

Returns:

  • (String) 


2238
2239
2240
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2238

def assembly_id
  @assembly_id
end

#description ⇒ String

Free text description of this reference set. Corresponds to the JSON property description

Returns:

  • (String) 


2243
2244
2245
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2243

def description
  @description
end

#id ⇒ String

The server-generated reference set ID, unique across all reference sets. Corresponds to the JSON property id

Returns:

  • (String) 


2248
2249
2250
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2248

def id
  @id
end

#md5checksum ⇒ String

Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string reference.md5checksum (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format. Corresponds to the JSON property md5checksum

Returns:

  • (String) 


2257
2258
2259
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2257

def md5checksum
  @md5checksum
end

#ncbi_taxon_id ⇒ Fixnum

ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the species which this reference set is intended to model. Note that contained references may specify a different ncbiTaxonId, as assemblies may contain reference sequences which do not belong to the modeled species, for example EBV in a human reference genome. Corresponds to the JSON property ncbiTaxonId

Returns:

  • (Fixnum) 


2266
2267
2268
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2266

def ncbi_taxon_id
  @ncbi_taxon_id
end

#reference_ids ⇒ Array<String>

The IDs of the reference objects that are part of this set. Reference.md5checksum must be unique within this set. Corresponds to the JSON property referenceIds

Returns:

  • (Array<String>) 


2272
2273
2274
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2272

def reference_ids
  @reference_ids
end

#source_accessions ⇒ Array<String>

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example NC_000001.11. Corresponds to the JSON property sourceAccessions

Returns:

  • (Array<String>) 


2278
2279
2280
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2278

def source_accessions
  @source_accessions
end

#source_uri ⇒ String

The URI from which the references were obtained. Corresponds to the JSON property sourceUri

Returns:

  • (String) 


2283
2284
2285
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2283

def source_uri
  @source_uri
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



2290
2291
2292
2293
2294
2295
2296
2297
2298
2299
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2290

def update!(**args)
  @assembly_id = args[:assembly_id] if args.key?(:assembly_id)
  @description = args[:description] if args.key?(:description)
  @id = args[:id] if args.key?(:id)
  @md5checksum = args[:md5checksum] if args.key?(:md5checksum)
  @ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
  @reference_ids = args[:reference_ids] if args.key?(:reference_ids)
  @source_accessions = args[:source_accessions] if args.key?(:source_accessions)
  @source_uri = args[:source_uri] if args.key?(:source_uri)
end