From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 19 Mar 2011 08:20:17 +0000 (+0000)
Subject: cleanup of Filsys in ruby code
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=af545a8962b7fd47682a11852bb752e4b9bad50f;p=biopieces.git

cleanup of Filsys in ruby code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1296 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index 66b245e..c22941c 100644
Binary files a/code_python/Cjung/Args.pyc and b/code_python/Cjung/Args.pyc differ
diff --git a/code_ruby/Maasha/lib/biopieces.rb b/code_ruby/Maasha/lib/biopieces.rb
index 05658e4..2f98fe9 100644
--- a/code_ruby/Maasha/lib/biopieces.rb
+++ b/code_ruby/Maasha/lib/biopieces.rb
@@ -571,7 +571,7 @@ class Stream < IO
   # specified in options[:stream_out] or options[:data_out].
   def self.open(options, mode, stdio)
     if mode == "r"
-      if options[:data_in].first == "-"
+      if options[:data_in] and options[:data_in].first == "-"
         self.nread(["-"])
       else
         $stdin.tty? ? read(options[:stream_in]) : stdio
diff --git a/code_ruby/Maasha/lib/fasta.rb b/code_ruby/Maasha/lib/fasta.rb
index 26e6d73..e972751 100644
--- a/code_ruby/Maasha/lib/fasta.rb
+++ b/code_ruby/Maasha/lib/fasta.rb
@@ -23,47 +23,12 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 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
@@ -94,22 +59,6 @@ class Fasta
       @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/fastq.rb b/code_ruby/Maasha/lib/fastq.rb
index 82c242e..a1eb86c 100644
--- a/code_ruby/Maasha/lib/fastq.rb
+++ b/code_ruby/Maasha/lib/fastq.rb
@@ -33,10 +33,10 @@ class Fastq < Filesys
   # as a Seq object. If no entry is found or eof then nil is returned.
   def get_entry
     begin
-      seq_name  = @io.gets.chomp!
-      seq       = @io.gets.chomp!
-      qual_name = @io.gets.chomp!
-      qual      = @io.gets.chomp!
+      seq_name       = @io.gets.chomp!
+      seq            = @io.gets.chomp!
+      qual_name      = @io.gets.chomp!
+      qual           = @io.gets.chomp!
 
       entry          = Seq.new
       entry.type     = @type.nil? ? nil : @type.downcase
diff --git a/code_ruby/Maasha/lib/filesys.rb b/code_ruby/Maasha/lib/filesys.rb
index 6f6d8cc..7e0deaa 100644
--- a/code_ruby/Maasha/lib/filesys.rb
+++ b/code_ruby/Maasha/lib/filesys.rb
@@ -65,7 +65,7 @@ class Filesys
     @io.close
   end
 
-  # Iterator method for parsing FASTQ enries.
+  # Iterator method for parsing entries.
   def each
     while entry = get_entry do
       yield entry
diff --git a/code_ruby/Maasha/lib/genbank.rb b/code_ruby/Maasha/lib/genbank.rb
index 7abed69..beff0ed 100644
--- a/code_ruby/Maasha/lib/genbank.rb
+++ b/code_ruby/Maasha/lib/genbank.rb
@@ -23,40 +23,17 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'seq'
-require 'zlib'
+require 'filesys'
 
 # Error class for all exceptions to do with Genbank.
 class GenbankError < StandardError; end
 
-class Genbank
-  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
-
+class Genbank < Filesys
   def initialize(io)
     @io      = io
     @entry   = []
   end
 
-  # Method to close ios.
-  def close
-    @io.close
-  end
-
   # Iterator method for parsing Genbank entries.
   def each(hash_keys, hash_feats, hash_quals)
     while @entry = get_entry do
@@ -82,20 +59,6 @@ class Genbank
 
   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
-
   # Method to get the next Genbank entry form an ios and return this.
   def get_entry
     block = @io.gets("//" + $/)