Class: Google::Apis::GenomicsV1::Reference

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 is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets. 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) ⇒ Reference

Returns a new instance of Reference



2182
2183
2184
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2182

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

Instance Attribute Details

#id ⇒ String

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

Returns:

  • (String) 


2146
2147
2148
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2146

def id
  @id
end

#length ⇒ Fixnum

The length of this reference's sequence. Corresponds to the JSON property length

Returns:

  • (Fixnum) 


2151
2152
2153
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2151

def length
  @length
end

#md5checksum ⇒ String

MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is represented in lower case hexadecimal format. Corresponds to the JSON property md5checksum

Returns:

  • (String) 


2158
2159
2160
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2158

def md5checksum
  @md5checksum
end

#name ⇒ String

The name of this reference, for example 22. Corresponds to the JSON property name

Returns:

  • (String) 


2163
2164
2165
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2163

def name
  @name
end

#ncbi_taxon_id ⇒ Fixnum

ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human. Corresponds to the JSON property ncbiTaxonId

Returns:

  • (Fixnum) 


2168
2169
2170
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2168

def ncbi_taxon_id
  @ncbi_taxon_id
end

#source_accessions ⇒ Array<String>

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example GCF_000001405.26. Corresponds to the JSON property sourceAccessions

Returns:

  • (Array<String>) 


2174
2175
2176
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2174

def source_accessions
  @source_accessions
end

#source_uri ⇒ String

The URI from which the sequence was obtained. Typically specifies a FASTA format file. Corresponds to the JSON property sourceUri

Returns:

  • (String) 


2180
2181
2182
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2180

def source_uri
  @source_uri
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



2187
2188
2189
2190
2191
2192
2193
2194
2195
 
# File 'generated/google/apis/genomics_v1/classes.rb', line 2187

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