Module: VepHgvs

Included in:
Bio::Mutation, Bio::MutationArray
Defined in:
lib/bio-sam-mutation/bio/vephgvs.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.consequences_for_transcript(json_object, tscript) ⇒ Object 



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# File 'lib/bio-sam-mutation/bio/vephgvs.rb', line 12

def self.consequences_for_transcript (json_object,tscript)
  if json_object.length > 0
    if json_object.first["transcript_consequences"]
      consequences = json_object.first["transcript_consequences"]
      consequences.keep_if{|a| a["transcript_id"] == tscript}
      consequences.map{|a| {"Allele" => json_object.first["allele_string"], "CDS position" => a["cds_start"], "Protein start" => a["protein_start"], "Mutation" => a["amino_acids"], "Consequence" => a["consequence_terms"]}}
    end
  end
end

Instance Method Details

#vep(species = "human", reference_type = nil) ⇒ Object 



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# File 'lib/bio-sam-mutation/bio/vephgvs.rb', line 3

def vep(species="human",reference_type=nil)
  return unless self.first.to_hgvs
  if reference_type.nil?
    reference_type = self.first.seqname.match(/^ENS/) ? "c" : "g"
  end
  EnsemblRest.connect_db
  JSON.parse(EnsemblRest::Variation.vep_hgvs(species,self.to_hgvs(reference_type)))
end