temporary fix of bzip2 read problem

[biopieces.git] / code_ruby / lib / maasha / filesys.rb

diff --git a/code_ruby/lib/maasha/filesys.rb b/code_ruby/lib/maasha/filesys.rb
index 2ee775760fa36faabcabcbac99f193bdbc4524dc..6a6067fbc859bb3df62a7f4eda547c0f44d8070c 100644 (file)
--- a/code_ruby/lib/maasha/filesys.rb
+++ b/code_ruby/lib/maasha/filesys.rb
@@ -23,6 +23,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'zlib'
+require 'bzip2'
 
 # Error class for all exceptions to do with Filesys.
 class FilesysError < StandardError; end
@@ -40,43 +41,61 @@ class Filesys
     path
   end
 
-  # Class method allowing open to be used on (zipped) files.
-  # See File.open.
   def self.open(*args)
-    args = *args
-    file = args.first
-
-    if file == "-"
-      ios = self.new(STDIN)
-    elsif File.pipe? file
-      ios = self.new(File.open(*args))
+    file    = args.shift
+    mode    = args.shift
+    options = args.shift || {}
+
+    if mode == 'w'
+      case options[:compress]
+      when :gzip
+        ios = Zlib::GzipWriter.new File.open(file, mode, options)
+      when :bzip, :bzip2
+        ios = Bzip2::Writer.new File.open(file, mode, options)
+      else 
+        ios = File.open(file, mode, options)
+      end
     else
-      ios = self.zopen(*args)
+      if file == '-'
+        ios = STDIN
+      else
+        case `file #{file}`
+        when /gzip/
+          ios = Zlib::GzipReader.new File.open(file, mode, options)
+        when /bzip/
+          # ios = Bzip2::Reader.new File.open(file, mode, options)   # TODO this method is buggy, investigate
+          ios = IO.popen("bzcat #{file}")
+        else
+          ios = File.open(file, mode, options)
+        end
+      end
     end
 
     if block_given?
       begin
-        yield ios
+        yield self.new(ios)
       ensure
         ios.close
       end
     else
-      return ios
+      return self.new(ios)
     end
   end
 
-  def initialize(io)
-    @io = io
+  def initialize(ios)
+    @io = ios
+  end
+
+  def puts(*args)
+    @io.puts(*args)
   end
 
-  # Method to close ios.
   def close
     @io.close
   end
 
-  # Method to check if io is closed.
-  def closed?
-    @io.closed?
+  def eof?
+    @io.eof?
   end
 
   # Iterator method for parsing entries.
@@ -85,26 +104,5 @@ class Filesys
       yield entry
     end
   end
-
-  # Method to puts directoy on Filesys objects.
-  def puts(*args)
-    @io.puts(*args)
-  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