added filesys

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1294 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/fastq.rb b/code_ruby/Maasha/lib/fastq.rb
index 44a9013fe5c5b4747dd0c531f01cbf8aa0e077e6..82c242e62fe34d664faba1e81f53a74e271976b0 100644 (file)
--- a/code_ruby/Maasha/lib/fastq.rb
+++ b/code_ruby/Maasha/lib/fastq.rb
@@ -23,54 +23,12 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'seq'
-require 'zlib'
+require 'filesys'
 
 # Error class for all exceptions to do with FASTQ.
 class FastqError < StandardError; end
 
-class Fastq
-  include Enumerable
-
-  # Class method allowing open to be used on (zipped) files.
-  # See File.open.
-  def self.open(*args)
-    tyt = *args
-    if tyt.first == "-"
-      ios = self.new(STDIN)
-    elsif File.pipe? *args.first
-      ios = self.new(File.open(*args))
-    else
-      ios = self.zopen(*args)
-    end
-
-    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 FASTQ enries.
-  def each
-    while entry = get_entry do
-      yield entry
-    end
-  end
-
+class Fastq < Filesys
   # Method to get the next FASTQ 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
@@ -99,22 +57,6 @@ class Fastq
       @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
 
 

diff --git a/code_ruby/Maasha/lib/filesys.rb b/code_ruby/Maasha/lib/filesys.rb
new file mode 100644 (file)
index 0000000..f7d2b9b
--- /dev/null
+++ b/code_ruby/Maasha/lib/filesys.rb
@@ -0,0 +1,92 @@
+# 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
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'zlib'
+
+# Error class for all exceptions to do with Filesys.
+class FilesysError < StandardError; end
+
+class Filesys
+  include Enumerable
+
+  # Class method allowing open to be used on (zipped) files.
+  # See File.open.
+  def self.open(*args)
+    pp *args
+
+    tyt = *args
+    if tyt.first == "-"
+      ios = self.new(STDIN)
+    elsif File.pipe? *args.first
+      ios = self.new(File.open(*args))
+    else
+      ios = self.zopen(*args)
+    end
+
+    if block_given?
+      puts "BLOCK"
+      begin
+        puts "YIELD"
+        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 FASTQ enries.
+  def each
+    while entry = get_entry do
+      yield entry
+    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