Class: Genfrag::App

Inherits:
Object
  • Object
show all
Defined in:
lib/genfrag/app.rb,
lib/genfrag/app/command.rb,
lib/genfrag/app/index_command.rb,
lib/genfrag/app/search_command.rb,
lib/genfrag/app/index_command/db.rb,
lib/genfrag/app/search_command/trim.rb,
lib/genfrag/app/search_command/match.rb,
lib/genfrag/app/search_command/process_file.rb

Defined Under Namespace

Classes: Command, IndexCommand, SearchCommand

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(out = STDOUT, err = STDERR) ⇒ App

Create a new main instance using io for standard output and err for error messages.



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# File 'lib/genfrag/app.rb', line 30

def initialize( out = STDOUT, err = STDERR )
  @out = out
  @err = err
end

Class Method Details

.cli_run(args) ⇒ Object

Create a new instance of App, and run the genfrag application given the command line args.



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# File 'lib/genfrag/app.rb', line 23

def self.cli_run( args )
  self.new.cli_run args
end

Instance Method Details

#cli_run(args) ⇒ Object

Parse the desired user command and run that command object.



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# File 'lib/genfrag/app.rb', line 37

def cli_run( args )
  cmd_str = args.shift
  cmd = case cmd_str
    when 'index';     IndexCommand.new(@out, @err)
    when 'search';    SearchCommand.new(@out, @err)
    when 'info';      InfoCommand.new(@out, @err)
    when nil, '-h', '--help'
      help
    when '-V', '--version'
      @out.puts "Genfrag #{::Genfrag::VERSION}"
      nil
    else
      @err.puts "Unknown command #{cmd_str.inspect}"
      help
      nil
    end

  cmd.cli_run args if cmd

rescue StandardError => err
  @err.puts "ERROR:  While executing genfrag ... (#{err.class})"
  @err.puts "    #{err.to_s}"
  @err.puts %Q(    #{err.backtrace.join("\n\t")})
  exit 1
end

#help ⇒ Object

Show the toplevel help message.



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# File 'lib/genfrag/app.rb', line 65

def help
  @out.puts "\nGenFrag allows for rapid in-silico searching of fragments cut by\ndifferent restriction enzymes in large nucleotide acid databases,\nfollowed by matching specificity adapters which allow a further data\nreduction when looking for differential expression of genes and\nmarkers.\n  \nUsage:\n  genfrag -h/--help\n  genfrag -V/--version\n  genfrag command [options] [arguments]\n\nExamples:\n  genfrag index -f example.fasta --RE5 BstYI --RE3 MseI\n  genfrag search -f example.fasta --RE5 BstYI --RE3 MseI --adapter5 ct\n\nCommands:\n  genfrag index           initialize the index\n  genfrag search          search FIXME\n  genfrag info            show information about FIXME\n\nFurther Help:\n  Each command has a '--help' option that will provide detailed\n  information for that command.\n\n  http://genfrag.rubyforge.org/\n\n  MSG\n  nil\nend\n"