module VepHgvs
Public Class Methods
consequences_for_transcript(json_object,tscript)
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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
Public Instance Methods
vep(species="human",reference_type=nil)
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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