Top Level Namespace

Defined Under Namespace

Modules: Bio

Instance Method Summary collapse

Instance Method Details

#process(string) ⇒ Object 



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# File 'bin/biohello.rb', line 118

def process(string)
  if $opts[:decode]
    puts $hello.decode(string)
  else # default incl. $opts[:encode]
    puts $hello.encode(string)
  end
  if $opts[:helix]
    puts
    puts $hello.helix(string)
  end
  if $opts[:code]
    puts
    puts %Q[% ruby -rubygems -r bio -e 'p Bio::Sequence::NA.new("#{$hello.na}").translate']
    puts %Q[ ==> "#{$hello.aa}"]
    puts
  end
end

#show_usage ⇒ Object 



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# File 'bin/biohello.rb', line 52

def show_usage
  prog  = File.basename($0)
  usage = %Q[
Usage:
    % #{prog} \[options...\] string
    % #{prog} \[options...\] file

Options:
    -e or --encode
       Encode the given string or file contents as a DNA sequence. (default)
    -d or --decode
       Decode a DNA encoded string.
    -x or --helix
       Show a DNA double strand helix in ASCII art.
    -c or --code
       Show the BioRuby code snippet.
    -h or --help
       Print this help message.

Examples:
    % #{prog} file
    % #{prog} -e file
    % #{prog} -d file

    % #{prog} "BioRuby is fun"
    % #{prog} -e "BIORUBY*IS*FUN"
    % #{prog} -d "nacatatagagatganactattaaataagttaattttgaaat"

    % #{prog} -x "I love you"
    % #{prog} -x -e "I*LOVE*YOU"
    % #{prog} -x -d "atataattataggtagaataatattagtga"

    % #{prog} -c "A happy new year"
    % #{prog} -c -e "A*HAPPY*NEW*YEAR"
    % #{prog} -c -d "gcataacatgcacctccttattaaaatgaatggtaatatgaagcaaga"

]
  puts usage
  exit
end