blat.rb

require 'formula'

class Blat < Formula
  homepage 'http://genome.ucsc.edu/FAQ/FAQblat.html'
  url 'http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip'
  sha1 'a2cae7407e512166bf7b1ed300db9be6649693bd'

  def install
    bin.mkpath
    system "make", "MACHTYPE=darwin", "BINDIR=#{bin}"
  end

  def test
    mktemp do
      Pathname.new('db.fa').write <<-EOF.undent
        >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
        LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
      EOF
      Pathname.new('query.fa').write <<-EOF.undent
        >spam
        CLYTHIGRNIYYGSY
      EOF
      system "#{bin}/blat", "-prot", "db.fa", "query.fa", "out.fa"
      system "cat out.fa | grep spam"
    end
  end
end