Method: Bio::EMBOSS#initialize

Defined in:
lib/bio/appl/emboss.rb

#initialize(cmd_line) ⇒ EMBOSS

WARNING: Bio::EMBOSS.new will be changed in the future because Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options…) is strongly recommended.

Initializes a new Bio::EMBOSS object. This provides a holder that can subsequently be executed (see Bio::EMBOSS.exec). The object does not hold any actual data when initialized.

e = Bio::EMBOSS.new('seqret embl:xlrhodop')

For e to actually hold data, it has to be executed:

puts e.exec

For an overview of commands that can be used with this method, see the emboss website.

Arguments:

  • (required) command: emboss command

Returns

Bio::EMBOSS object



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# File 'lib/bio/appl/emboss.rb', line 132

def initialize(cmd_line)
  warn 'Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options...) is strongly recommended.'
  @cmd_line = cmd_line + ' -stdout -auto'
end