Class: Rafflesia::Genomes

Inherits:
Object
  • Object
show all
Defined in:
lib/rafflesia/genomes.rb

Instance Method Summary collapse

Constructor Details

#initialize(client) ⇒ Genomes

Returns a new instance of Genomes.



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# File 'lib/rafflesia/genomes.rb', line 9

def initialize(client)
  @client = client
end

Instance Method Details

#assembliesShow(assembly_id:, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeAssemblyData

POST /v1/genomes/assemblies/show

Parameters:

  • assembly_id (String) —

    Assembly identifier, e.g. GRCh38 or hg38 (case-insensitive, alias-aware).

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 17

def assembliesShow(
  assembly_id:,
  request_options: {}
)
  body = {
    'assembly_id' => assembly_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/genomes/assemblies/show',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeAssemblyData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#intervalsComplement(assembly_id:, bed:, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeIntervalsComplementData

POST /v1/genomes/intervals/complement

Parameters:

  • assembly_id (String) —

    Assembly identifier (case-insensitive, alias-aware) supplying contig bounds.

  • bed (String) —

    BED text for the input interval set (chrom start end [name ...]).

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 41

def intervalsComplement(
  assembly_id:,
  bed:,
  request_options: {}
)
  body = {
    'assembly_id' => assembly_id,
    'bed' => bed
  }
  response = @client.request(
    method: :post,
    path: '/v1/genomes/intervals/complement',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeIntervalsComplementData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#intervalsFlank(bed:, left:, right:, assembly_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeIntervalsFlankData

POST /v1/genomes/intervals/flank

Parameters:

  • assembly_id (String, nil) (defaults to: nil) —

    Optional assembly id used to clamp flanks to contig bounds.

  • bed (String) —

    BED text for the input interval set (chrom start end [name ...]).

  • left (Integer) —

    Left flank length in base pairs (0 to omit).

  • right (Integer) —

    Right flank length in base pairs (0 to omit).

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 69

def intervalsFlank(
  bed:,
  left:,
  right:,
  assembly_id: nil,
  request_options: {}
)
  body = {
    'assembly_id' => assembly_id,
    'bed' => bed,
    'left' => left,
    'right' => right
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/intervals/flank',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeIntervalsFlankData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#intervalsIntersect(a_bed:, b_bed:, a_name: nil, b_name: nil, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeIntervalsIntersectData

POST /v1/genomes/intervals/intersect

Parameters:

  • a_bed (String) —

    BED text for the A interval set (chrom start end [name ...]).

  • a_name (String, nil) (defaults to: nil) —

    Label for the A interval set.

  • b_bed (String) —

    BED text for the B interval set (chrom start end [name ...]).

  • b_name (String, nil) (defaults to: nil) —

    Label for the B interval set.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 101

def intervalsIntersect(
  a_bed:,
  b_bed:,
  a_name: nil,
  b_name: nil,
  request_options: {}
)
  body = {
    'a_bed' => a_bed,
    'a_name' => a_name,
    'b_bed' => b_bed,
    'b_name' => b_name
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/intervals/intersect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeIntervalsIntersectData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#intervalsMerge(bed:, min_gap: nil, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeIntervalsMergeData

POST /v1/genomes/intervals/merge

Parameters:

  • bed (String) —

    BED text for the input interval set (chrom start end [name ...]).

  • min_gap (Integer, nil) (defaults to: nil) —

    Maximum gap in base pairs between intervals to still merge them (0 merges overlapping or book-ended intervals).

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 131

def intervalsMerge(
  bed:,
  min_gap: nil,
  request_options: {}
)
  body = {
    'bed' => bed,
    'min_gap' => min_gap
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/intervals/merge',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeIntervalsMergeData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#intervalsSubtract(a_bed:, b_bed:, a_name: nil, b_name: nil, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeIntervalsSubtractData

POST /v1/genomes/intervals/subtract

Parameters:

  • a_bed (String) —

    BED text for the A interval set (chrom start end [name ...]).

  • a_name (String, nil) (defaults to: nil) —

    Label for the A interval set.

  • b_bed (String) —

    BED text for the B interval set (chrom start end [name ...]).

  • b_name (String, nil) (defaults to: nil) —

    Label for the B interval set.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 159

def intervalsSubtract(
  a_bed:,
  b_bed:,
  a_name: nil,
  b_name: nil,
  request_options: {}
)
  body = {
    'a_bed' => a_bed,
    'a_name' => a_name,
    'b_bed' => b_bed,
    'b_name' => b_name
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/intervals/subtract',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeIntervalsSubtractData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#regionsGet(assembly_id:, region:, request_options: {}) ⇒ Rafflesia::EnvelopeGenomeRegionData

POST /v1/genomes/regions/get

Parameters:

  • assembly_id (String) —

    Assembly identifier (case-insensitive, alias-aware).

  • region (String) —

    Region string, e.g. chr17:43,044,295-43125483 (1-based inclusive).

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 189

def regionsGet(
  assembly_id:,
  region:,
  request_options: {}
)
  body = {
    'assembly_id' => assembly_id,
    'region' => region
  }
  response = @client.request(
    method: :post,
    path: '/v1/genomes/regions/get',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGenomeRegionData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#variantsAnnotate(path:, sources:, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeVariantAnnotateData

POST /v1/genomes/variants/annotate

Parameters:

  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • output_format (Rafflesia::Types::VariantAnnotateRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • path (String) —

    Path to a VCF file readable by the server.

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • sources (Array<String>, nil) —

    Annotation source names to query, e.g. clinvar, gnomad.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 223

def variantsAnnotate(
  path:,
  sources:,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'path' => path,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'sources' => sources
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/variants/annotate',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantAnnotateData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#variantsMap(path:, to:, assembly: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeVariantMapGenomicData

POST /v1/genomes/variants/map

Parameters:

  • assembly (Rafflesia::Types::VariantMapGenomicRequestAssembly, nil) (defaults to: nil) —

    Reference assembly id.

  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • output_format (Rafflesia::Types::VariantMapGenomicRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • path (String) —

    Path to a VCF file readable by the server.

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • to (Rafflesia::Types::VariantMapGenomicRequestTo) —

    Mapping target: transcripts or proteins.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 274

def variantsMap(
  path:,
  to:,
  assembly: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'assembly' => assembly,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'path' => path,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'to' => to
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/variants/map',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantMapGenomicData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#variantsNearby(features:, path:, request_options: {}) ⇒ Rafflesia::EnvelopeVariantNearbyData

POST /v1/genomes/variants/nearby

Parameters:

  • features (Array<String>, nil) —

    Genome/structure feature classes: exons, pockets, interfaces.

  • path (String) —

    Path to a VCF file readable by the server.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 318

def variantsNearby(
  features:,
  path:,
  request_options: {}
)
  body = {
    'features' => features,
    'path' => path
  }
  response = @client.request(
    method: :post,
    path: '/v1/genomes/variants/nearby',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantNearbyData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#variantsNormalize(path:, assembly: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeVariantNormalizeData

POST /v1/genomes/variants/normalize

Parameters:

  • assembly (Rafflesia::Types::VariantNormalizeRequestAssembly, nil) (defaults to: nil) —

    Reference assembly id, e.g. GRCh38.

  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • output_format (Rafflesia::Types::VariantNormalizeRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • path (String) —

    Path to a VCF file readable by the server.

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 352

def variantsNormalize(
  path:,
  assembly: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'assembly' => assembly,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'path' => path,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/variants/normalize',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantNormalizeData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#variantsQuery(chrom:, end_:, file:, start:, region: nil, request_options: {}) ⇒ Rafflesia::EnvelopeVariantQueryData

POST /v1/genomes/variants/query

Parameters:

  • chrom (String) —

    Sequence/contig name to query, e.g. chr1 or 1

  • end (Integer) —

    1-based inclusive end coordinate

  • file (String) —

    Local bgzipped, tabix-indexed VCF path (.vcf.gz); its .tbi/.csi index must sit beside it

  • region (String, nil) (defaults to: nil) —

    Optional combined region string :-; chrom/start/end take precedence when set

  • start (Integer) —

    1-based inclusive start coordinate

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 397

def variantsQuery(
  chrom:,
  end_:,
  file:,
  start:,
  region: nil,
  request_options: {}
)
  body = {
    'chrom' => chrom,
    'end' => end_,
    'file' => file,
    'region' => region,
    'start' => start
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/genomes/variants/query',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantQueryData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#variantsSplit(path:, request_options: {}) ⇒ Rafflesia::EnvelopeVariantSplitData

POST /v1/genomes/variants/split

Parameters:

  • path (String) —

    Path to a VCF file readable by the server.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/genomes.rb', line 428

def variantsSplit(
  path:,
  request_options: {}
)
  body = {
    'path' => path
  }
  response = @client.request(
    method: :post,
    path: '/v1/genomes/variants/split',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantSplitData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end