module VepHgvs

Public Class Methods

consequences_for_transcript(json_object,tscript) click to toggle source
# 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

Public Instance Methods

vep(species="human",reference_type=nil) click to toggle source
# 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