[BioRuby] Problem running HMMER from bioruby

[George Githinji]

Hi!
What could possibly be wrong with this code for running a hmm search the
bioruby way?

hmmfile = "/home/george/NetBeansProjects/pfvsa/public/hmms/pfVSAs.hmm"

   #the bioruby way
seq_to_search ="/home/george/sequences/sequences.fasta"
  factory = Bio::HMMER.new('hmmpfam',hmmfile,seq_to_search)
  report = factory.query
  puts report.class

I am getting this error

/usr/lib/ruby/1.8/shellwords.rb:30:in `shellwords': Argument must be a
string (ArgumentError)
        from
/usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/hmmer.rb:70:in
`initialize'
        from /home/george/NetBeansProjects/bio_test/lib/blasting.rb:27:in
`new'
        from /home/george/NetBeansProjects/bio_test/lib/blasting.rb:27

closer inspection of shellwords shows this code
def shellwords(line)
    line = String.new(line) rescue
      raise(ArgumentError, "Argument must be a string")
    line.lstrip!
    words = []
    until line.empty?
      field = ''
      loop do
    if line.sub!(/\A"(([^"\\]|\\.)*)"/, '') then
      snippet = $1.gsub(/\\(.)/, '\1')
    elsif line =~ /\A"/ then
      raise ArgumentError, "Unmatched double quote: #{line}"
    elsif line.sub!(/\A'([^']*)'/, '') then
      snippet = $1
    elsif line =~ /\A'/ then
      raise ArgumentError, "Unmatched single quote: #{line}"
    elsif line.sub!(/\A\\(.)?/, '') then
      snippet = $1 || '\\'
    elsif line.sub!(/\A([^\s\\'"]+)/, '') then
      snippet = $1
    else
      line.lstrip!
      break
    end
    field.concat(snippet)
      end
      words.push(field)
    end
    words
  end
-- 
---------------
Sincerely
George

Skype: george_g2
Website: http://biorelated.wordpress.com/