Class: Google::Apis::GenomicsV1beta2::Reference

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable
Defined in:
generated/google/apis/genomics_v1beta2/classes.rb,
generated/google/apis/genomics_v1beta2/representations.rb,
generated/google/apis/genomics_v1beta2/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.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ Reference

Returns a new instance of Reference



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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2028

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

Instance Attribute Details

#id ⇒ String

The Google generated immutable ID of the reference. Corresponds to the JSON property id

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1991

def id
  @id
end

#length ⇒ String

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

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 1996

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) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2003

def md5checksum
  @md5checksum
end

#name ⇒ String

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

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2008

def name
  @name
end

#ncbi_taxon_id ⇒ Fixnum

ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set. Corresponds to the JSON property ncbiTaxonId

Returns:

  • (Fixnum) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2014

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>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2020

def source_accessions
  @source_accessions
end

#source_uri ⇒ String

The URI from which the sequence was obtained. Specifies a FASTA format file/ string with one name, sequence pair. Corresponds to the JSON property sourceURI

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2026

def source_uri
  @source_uri
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2033

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