get_rnaseq_number_for_species.rb

#!/nfs/users/nfs_m/mh6/.linuxbrew/homebrew/bin/ruby
# usage:  ruby get_rnaseq_number_for_species.rb "Xestospongia muta"

require "net/http"
require "uri"
require "cgi"

species = ARGV[0]

species = CGI.escapeURIComponent(species)

uri = URI("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=#{species}%5borgn%5d+AND+biomol_rna%5bProp%5d&usehistory=y")
r = Net::HTTP.get_response(uri)

spots = 0 
if r.body =~ /\<Count\>\d+\<\/Count\>/
  spots = r.body.to_enum(:scan,/\<Count\>(\d+)\<\/Count\>/).map{|r| $1.to_i }.sum
end

puts "#{ARGV[0]}\t#{spots}"