Method: Bio::FlatFile.open

Defined in:
lib/bio/io/flatfile.rb

.open(*arg, &block) ⇒ Object

Bio::FlatFile.open(file, *arg)

Bio::FlatFile.open(dbclass, file, *arg)

Creates a new Bio::FlatFile object to read a file or a stream which contains dbclass data.

dbclass should be a class (or module) or nil. e.g. Bio::GenBank, Bio::FastaFormat.

If file is a filename (which doesn’t have gets method), the method opens a local file named file with File.open(filename, *arg).

When dbclass is omitted or nil is given to dbclass, the method tries to determine database class (file format) automatically. When it fails to determine, dbclass is set to nil and FlatFile#next_entry would fail. You can still set dbclass using FlatFile#dbclass= method.

  • Example 1

    Bio::FlatFile.open(Bio::GenBank, "genbank/gbest40.seq")

  • Example 2

    Bio::FlatFile.open(nil, "embl/est_hum17.dat")

  • Example 3

    Bio::FlatFile.open("genbank/gbest40.seq")

  • Example 4

    Bio::FlatFile.open(Bio::GenBank, $stdin)

If it is called with a block, the block will be executed with a new Bio::FlatFile object. If filename is given, the file is automatically closed when leaving the block.

  • Example 5

    Bio::FlatFile.open(nil, 'test4.fst') do |ff|
    ff.each { |e| print e.definition, "\n" }
end

  • Example 6

    Bio::FlatFile.open('test4.fst') do |ff|
    ff.each { |e| print e.definition, "\n" }
end

Compatibility Note: *arg is completely passed to the File.open and you cannot specify “:raw => true” or “:raw => false”.



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# File 'lib/bio/io/flatfile.rb', line 80

def self.open(*arg, &block)
  # FlatFile.open(dbclass, file, mode, perm)
  # FlatFile.open(file, mode, perm)
  if arg.size <= 0
    raise ArgumentError, 'wrong number of arguments (0 for 1)'
  end
  x = arg.shift
  if x.is_a?(Module) then
    # FlatFile.open(dbclass, filename_or_io, ...)
    dbclass = x
  elsif x.nil? then
    # FlatFile.open(nil, filename_or_io, ...)
    dbclass = nil
  else
    # FlatFile.open(filename, ...)
    dbclass = nil
    arg.unshift(x)
  end
  if arg.size <= 0
    raise ArgumentError, 'wrong number of arguments (1 for 2)'
  end
  file = arg.shift
  # check if file is filename or IO object
  unless file.respond_to?(:gets)
    # 'file' is a filename
    _open_file(dbclass, file, *arg, &block)
  else
    # 'file' is a IO object
    ff = self.new(dbclass, file)
    block_given? ? (yield ff) : ff
  end
end