Method: Bio::EMBL#ft

Defined in:
lib/bio/db/embl/embl.rb

#ft ⇒ Object Also known as: features

returns contents in the feature table (FT) lines.

  • Bio::EMBL#ft -> Bio::Features

  • Bio::EMBL#ft {} -> {|Bio::Feature| }

same as features method in bio/db/genbank.rb

FT Line; feature table data (>=0)



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# File 'lib/bio/db/embl/embl.rb', line 247

def ft
  unless @data['FT']
    @data['FT'] = Array.new
    ary = Array.new
    in_quote = false
    @orig['FT'].each_line do |line|
      next if line =~ /^FEATURES/

      head = line[0,20].strip  # feature key (source, CDS, ...)
      body = line[20,60].chomp # feature value (position, /qualifier=)
      if line =~ /^FT {3}(\S+)/
        ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
      elsif body =~ /^ \// and not in_quote
        ary.last.push(body)    # /q="data..., /q=data, /q

        if body =~ /=" / and body !~ /"$/
          in_quote = true
        end

      else
        ary.last.last << body # ...data..., ...data..."

        if body =~ /"$/
          in_quote = false
        end
      end
    end

    ary.map! do |subary|
      parse_qualifiers(subary)
    end

    @data['FT'] = Features.new(ary)
  end
  if block_given?
    @data['FT'].each do |feature|
      yield feature
    end
  else
    @data['FT']
  end
end