Rereferences

Combines the initialization and execution for the emboss entret command.

 puts Bio::EMBOSS.entret('embl:xlrhodop')

is equivalent to:

 object = Bio::EMBOSS.new('entret embl:xlrhodop')
 puts object.exec

Arguments:

• (required) arg: argument given to the emboss entret command

[Source]

     # File lib/bio/appl/emboss.rb, line 109
109:   def self.entret(arg)
110:     str = self.retrieve('entret', arg)
111:   end

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

[Source]

     # File lib/bio/appl/emboss.rb, line 132
132:   def initialize(cmd_line)
133:     warn 'Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options...) is strongly recommended.'
134:     @cmd_line = cmd_line + ' -stdout -auto'
135:   end

Runs an emboss program and get the result as string. Note that "-auto -stdout" are automatically added to the options.

Example 1:

  result = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')

Example 2:

  result = Bio::EMBOSS.run('water',
                            '-asequence', 'swissprot:slpi_human',
                            '-bsequence', 'swissprot:slpi_mouse')

Example 3:

  options = %w( -asequence swissprot:slpi_human
                -bsequence swissprot:slpi_mouse )
  result = Bio::EMBOSS.run('needle', *options)

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

Arguments:

• (required) program: command name, or filename of an emboss program
• options: options given to the emboss program

[Source]

     # File lib/bio/appl/emboss.rb, line 187
187:   def self.run(program, *options)
188:     cmd = [ program, *options ]
189:     cmd.push '-auto'
190:     cmd.push '-stdout'
191:     return Bio::Command.query_command(cmd)
192:   end

Combines the initialization and execution for the emboss seqret command.

 puts Bio::EMBOSS.seqret('embl:xlrhodop')

is equivalent to:

 object = Bio::EMBOSS.new('seqret embl:xlrhodop')
 puts object.exec

Arguments:

• (required) arg: argument given to the emboss seqret command

[Source]

    # File lib/bio/appl/emboss.rb, line 93
93:   def self.seqret(arg)
94:     str = self.retrieve('seqret', arg)
95:   end

A Bio::EMBOSS object has to be executed before it can return any result.

  obj_A = Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop')
  puts obj_A.result                   #=> nil
  obj_A.exec
  puts obj_A.result                   #=> a FASTA-formatted sequence

  obj_B = Bio::EMBOSS.new('showfeat embl:xlrhodop')
  obj_B.exec
  puts obj_B.result

[Source]

     # File lib/bio/appl/emboss.rb, line 146
146:   def exec
147:     begin
148:       @io = IO.popen(@cmd_line, "w+")
149:       @result = @io.read
150:       return @result
151:     ensure
152:       @io.close
153:     end
154:   end