gistfile1.rbx

#!/usr/bin/env ruby

# hackery to simulate a file
require 'stringio'
RealFile = File
Object.send(:remove_const, :File)
File = StringIO
def StringIO.open(data); x=new(data);x.rewind; x; end
# end of hackery

data = <<EODATA
SEQ_NAME: test1
SEQ: ATCG
---
SEQ_NAME: test2
SEQ: ATCGA---
---
SEQ_NAME: test3
SEQ: ATCGAT
---
SEQ_NAME: test4
SEQ: --------
---
EODATA

class BioPieces
  RECORD_DELIMITER = "\n---\n"
  
  class Record
    attr_reader :__hash__

    def initialize(data)
      @__hash__ = data
    end
    
    def method_missing(name, *a, &b)
      if a.empty? && @__hash__.has_key?(name) then
        @__hash__[name]
      else
        super # get the original exception
      end
    end
    
    def to_s
      @__hash__.map { |key, value|
        "#{key}: #{value}"
      }.join("\n")+RECORD_DELIMITER
    end
    
    def to_hash
      @__hash__.dup
    end
  end

  def self.file(path)
    bp = new(File.open(path))
    yield bp if block_given?
    bp
  ensure
    # if no block was given, the user wants the BioPieces instance
    # with a still open File so he can read it, so only close if a block
    # had been given.
    bp.close if block_given?
  end

  def initialize( file )
    @stream = file
  end

  def close
    @stream.close if @stream.respond_to? :close
  end

  def record_get
    return unless block = @stream.gets(RECORD_DELIMITER)

    block.chomp!(RECORD_DELIMITER)
    data = Hash[*block.scan(/(\w+):\s+(.*)/).flatten]
    Record.new(data)
  end
  
  def each
    yield record_get until @stream.eof?
    self # not to have a messy return value
  end
end

#path = "test.stream"
path = data # using the hack

BioPieces.file(path) do |bp|
  bp.each { |record|
    puts record
  }
end