Module: EnsemblREST::Comparative

Defined in:
lib/ensemblrest/comparativegenomics.rb

Class Method Summary collapse

Class Method Details

.genetree(id, options = {}) ⇒ JSON

Retrieves a gene tree dump for a gene tree stable identifier



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# File 'lib/ensemblrest/comparativegenomics.rb', line 23

def genetree(id, options = {})
  return EnsemblREST.get("genetree/id/#{id}", {format: 'json'}.merge(options))
end

.genetree_member_id(id, options = {}) ⇒ JSON

Retrieves a gene tree that contains the stable identifier



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# File 'lib/ensemblrest/comparativegenomics.rb', line 32

def genetree_member_id(id, options = {})
  return EnsemblREST.get("genetree/member/id/#{id}", {format: 'json'}.merge(options))
end

.genetree_member_symbol(symbol, species = 'human', options = {}) ⇒ JSON

Retrieves a gene tree containing the gene identified by a symbol



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# File 'lib/ensemblrest/comparativegenomics.rb', line 42

def genetree_member_symbol(symbol, species = 'human', options = {})
  return EnsemblREST.get("genetree/member/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
end

.genomic_alignment_region(region, species = 'human', options = {}) ⇒ JSON

Retrieves genomic alignments as separate blocks based on a region and species



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# File 'lib/ensemblrest/comparativegenomics.rb', line 52

def genomic_alignment_region(region, species = 'human', options = {})
  return EnsemblREST.get("alignment/region/#{species}/#{region}", {format: 'json'}.merge(options))
end

.homology_ensemblgene(id, options = {}) ⇒ JSON

Retrieves homology information (orthologs) by Ensembl gene id



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# File 'lib/ensemblrest/comparativegenomics.rb', line 61

def homology_ensemblgene(id, options = {})
  return EnsemblREST.get("homology/id/#{id}", {format: 'json'}.merge(options))
end

.homology_symbol(symbol, species = 'human', options = {}) ⇒ JSON

Retrieves homology information (orthologs) by symbol



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# File 'lib/ensemblrest/comparativegenomics.rb', line 71

def homology_symbol(symbol, species = 'human', options = {})
  return EnsemblREST.get("homology/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
end