Transforming gene symbol to genomic position

gene_symbol2locus.rb

#!/usr/bin/env ruby

require "rubygems"
require "biomart"
require "pp"

htgt = Biomart::Server.new( "http://www.sanger.ac.uk/htgt/biomart" )
ensmus = htgt.datasets["mmusculus_gene_ensembl"]
# pp ensmus.list_filters

gene_symbol = ARGF.each do |line|
  line.chomp!
  refseqid, gene_symbol, ensg = line.split(/,/)
  res = ensmus.search(
    :filters => { "ensembl_gene_id" => ensg },
    :attributes => ["ensembl_gene_id", "chromosome_name", "start", "end"]
  )
  ensg, chr, start_bp, end_bp = res[:data].flatten
  puts [gene_symbol, ensg, "chr#{chr}:#{start_bp}-#{end_bp}"].join("\t")
end