module EnsemblRest::ComparativeGenomics

Public Class Methods

alignment_block(species, region, opts = {}) click to toggle source

Retrieves genomic alignments as separate blocks based on its location

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 6
def self.alignment_block(species, region, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/alignment/block/region/#{species}/#{region}", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    return JSON.parse ComparativeGenomics.alignment_block species, region, plain_opts
  end

  return EnsemblRest.fetch_data path, opts, 'compara'
end
alignment_slice(species, region, opts = {}) click to toggle source

Retrieves genomic alignments as a single slice based on its location

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 21
def self.alignment_slice(species, region, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/alignment/slice/region/#{species}/#{region}", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    return JSON.parse ComparativeGenomics.alignment_slice species, region, plain_opts
  end

  return EnsemblRest.fetch_data path, opts, 'compara'
end
genetree_id(id, opts = {}) click to toggle source

Retrieves Gene Tree dumps for a given Gene Tree stable identifier

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 38
def self.genetree_id(id, opts = {})
  return _genetree_generic id, 'id', opts
end
genetree_member_id(id, opts = {}) click to toggle source

Retrieves the Gene Tree that contains the given stable identifier

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 44
def self.genetree_member_id(id, opts = {})
  return _genetree_generic id, 'member', opts
end
genetree_member_symbol(species, symbol, opts = {}) click to toggle source

Retrieves a Gene Tree containing the Gene identified by the given symbol

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 66
def self.genetree_member_symbol(species, symbol, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/genetree/member/symbol/#{species}/#{symbol}", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'text/x-phyloxml+xml'
    return Bio::PhyloXML::Parser.new genetree_member_symbol(species, symbol, plain_opts)
  end

  return EnsemblRest.fetch_data path, opts, 'compara'
end
homology_id(id, opts = {}) click to toggle source

Retrieves homology information by ensembl gene id

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 82
def self.homology_id(id, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/homology/id/#{id}", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    data = JSON.parse ComparativeGenomics.homology_id id, plain_opts
    return build_homology_class data
  end

  return EnsemblRest.fetch_data path, opts, 'compara'
end
homology_symbol(species, symbol, opts = {}) click to toggle source

Retrieves homology information by symbol

# File lib/bio-ensembl-rest/comparative-genomics.rb, line 99
def self.homology_symbol(species, symbol, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/homology/symbol/#{species}/#{symbol}", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    data = JSON.parse ComparativeGenomics.homology_symbol species, symbol, plain_opts
    return build_homology_class data
  end

  return EnsemblRest.fetch_data path, opts, 'compara'      

end