Class: Genfrag::App::Command

Inherits:
Object
  • Object
show all
Defined in:
lib/genfrag/app/command.rb

Direct Known Subclasses

IndexCommand, SearchCommand

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

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

Returns a new instance of Command.



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# File 'lib/genfrag/app/command.rb', line 10

def initialize( out = STDOUT, err = STDERR )
  @out = out
  @err = err
  @options = {
  #  :skeleton_dir => File.join(mrbones_dir, 'data'),
  #  :with_tasks => false,
  #  :verbose => false,
  #  :name => nil,
  #  :output_dir => nil
  }
  @ops = OpenStruct.new
  #@options[:skeleton_dir] = ::Bones.path('data') unless test(?d, skeleton_dir)
end

Instance Attribute Details

#ops ⇒ Object

an OpenStruct of the options



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# File 'lib/genfrag/app/command.rb', line 8

def ops
  @ops
end

#options ⇒ Object

a Hash used by optparse



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# File 'lib/genfrag/app/command.rb', line 7

def options
  @options
end

Instance Method Details

#cli_p(cli = true, str = '') ⇒ Object

Print running output when used in command-line mode



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# File 'lib/genfrag/app/command.rb', line 34

def cli_p(cli=true, str='')
  return false if !cli or @ops.quiet
  @out.puts str
end

#cli_run(args) ⇒ Object

Raises:

  • (NotImplementedError) 


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# File 'lib/genfrag/app/command.rb', line 24

def cli_run( args )
  raise NotImplementedError
end

#clierr_p(str) ⇒ Object

Print an error from the command-line options



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# File 'lib/genfrag/app/command.rb', line 41

def clierr_p(str)
  @out.puts
  @err.puts "Error: #{str}"
  @out.puts
  @out.puts opt_parser
end

#run(args) ⇒ Object

Raises:

  • (NotImplementedError) 


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# File 'lib/genfrag/app/command.rb', line 28

def run( args )
  raise NotImplementedError
end

#standard_options ⇒ Object

Define the command-line option available



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# File 'lib/genfrag/app/command.rb', line 50

def standard_options
  {
    :verbose => ['-v', '--verbose', 'enable verbose output',
        lambda { |ruby19bug|
          options[:verbose] = true
        }],
    :tracktime => ['-m', '--tracktime', 'track execution time',
        lambda { |ruby19bug|
          options[:tracktime] = true
        }],
    :quiet => ['-q', '--quiet', 'silence output',
        lambda { |ruby19bug|
          options[:quiet] = true
        }],
    :indir => ['-i', '--in DIR', String, 'input directory', "(default #{Dir.pwd})",
        lambda{ |value|
          options[:indir] = value
        }],
    :outdir => ['-o', '--out DIR', String, 'output directory', "(default #{Dir.pwd})",
        lambda{ |value|
          options[:outdir] = value
        }],
    :re5 => ['-5', '--re5 ENZYME', String, "5' restriction enzyme",
        lambda { |value|
          options[:re5] = value
        }],
    :re3 => ['-3', '--re3 ENZYME', String, "3' restriction enzyme",
        lambda { |value|
          options[:re3] = value
        }],
    :sqlite => ['-t', '--sqlite', 'use sqlite', '(default is tab-delimited)',
        lambda { |ruby19bug|
          options[:sqlite] = true
        }],
    :filelookup => ['-l', '--lookup FILE', String, "name of the frequency lookup file generated by 'index'",
        lambda { |value|
          options[:filelookup] = value
        }],
    :filefasta => ['-f', '--fasta FILE', String, 'name of the Fasta sequences file',
        lambda { |value|
          options[:filefasta] = value
        }],
    :seqsize => ['-s', '--seqsize SIZE', Array, '',
        lambda { |value|
          options[:seqsize] = value
        }],
        
    :adapter5 => ['-y', '--adapter5 ADAPTER', String, '',
        lambda { |value|
          options[:adapter5] = value
        }],
    :adapter3 => ['-z', '--adapter3 ADAPTER', String, '',
        lambda { |value|
          options[:adapter3] = value
        }],
        
    :named_adapter5 => ['-b', '--named-adapter5 NAME', String, '',
        lambda { |value|
          options[:named_adapter5] = value
        }],
    :named_adapter3 => ['-c', '--named-adapter3 NAME', String, '',
        lambda { |value|
          options[:named_adapter3] = value
        }],
        
    :adapter5_size => ['-d', '--adapter5-size SIZE', Integer, '',
        lambda { |value|
          options[:adapter5_size] = value
        }],
    :adapter3_size => ['-e', '--adapter3-size SIZE', Integer, '',
        lambda { |value|
          options[:adapter3_size] = value
        }],
        
    :adapter5_sequence => ['-w', '--adapter5-sequence SEQUENCE', String, '',
        lambda { |value|
          options[:adapter5_sequence] = value
        }],
    :adapter3_sequence => ['-x', '--adapter3-sequence SEQUENCE', String, '',
        lambda { |value|
          options[:adapter3_sequence] = value
        }],
        
    :fileadapters => ['-a', '--adapters FILE', String, '',
        lambda { |value|
          options[:fileadapters] = value
        }]

  }
end