+# Copyright (C) 2007-2011 Martin A. Hansen.
+
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
require 'seq'
-require 'zlib'
+require 'filesys'
# Error class for all exceptions to do with FASTA.
class FastaError < StandardError; end
-class Fasta
- include Enumerable
-
- # Class method allowing open to be used on (zipped) files.
- # See File.open.
- def self.open(*args)
- ios = self.zopen(*args)
-
- if block_given?
- begin
- yield ios
- ensure
- ios.close
- end
- else
- return ios
- end
- end
-
- def initialize(io, type=nil)
- @io = io
- @type = type
- end
-
- # Method to close ios.
- def close
- @io.close
- end
-
- # Iterator method for parsing FASTA enries.
- def each
- while entry = get_entry do
- yield entry
- end
- end
-
+class Fasta < Filesys
# Method to get the next FASTA entry form an ios and return this
# as a Seq object. If no entry is found or eof then nil is returned.
def get_entry
@io.print "#{record[:SEQ]}\n"
end
end
-
- private
-
- # Helper method to return an ios to a file that may be zipped in which case
- # the ios is unzipped on the fly. See File.open.
- def self.zopen(*args)
- ios = File.open(*args)
-
- begin
- ios = Zlib::GzipReader.new(ios)
- rescue
- ios.rewind
- end
-
- self.new(ios)
- end
end