From af545a8962b7fd47682a11852bb752e4b9bad50f Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 19 Mar 2011 08:20:17 +0000
Subject: [PATCH] cleanup of Filsys in ruby code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1296 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_python/Cjung/Args.pyc        | Bin 5601 -> 5375 bytes
 code_ruby/Maasha/lib/biopieces.rb |   2 +-
 code_ruby/Maasha/lib/fasta.rb     |  55 ++----------------------------
 code_ruby/Maasha/lib/fastq.rb     |   8 ++---
 code_ruby/Maasha/lib/filesys.rb   |   2 +-
 code_ruby/Maasha/lib/genbank.rb   |  41 ++--------------------
 6 files changed, 10 insertions(+), 98 deletions(-)

diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index 66b245e94a16f34c4cd693215c8322410309cd50..c22941cdaa6b72f2e8e900a946250984191f6325 100644
GIT binary patch
delta 612
zcmaE;{a=&g;wN6NDKhT98#yxA1PvJ&81zGnQ;UlAa}yJbGZH5!@~TeW$!5w}JNZ4E
zql_g3V+lJ$CI>?%Cqpv>Lp~P+V+u2ayGIHuL-1sO_Ln#eXyj0~VP)iG<N@MjMxY%`
zK+Fcj&Olsz4oFn2XD9)hx152ohJhiIks*@_WPU9pLk%NCzVhS;94edHIWrh>n7@Nd
zo{@F(4K7W_xXDc1nldsBEI`wMW@K?O<nuBx0znER$eBz)XL@lz#$rq$kBuW6#Bm@8
zvcepv4`ft|Fo0YIb{No{W=4kK@H`Qq9S{pRAQphkzQ~h<#q31hKz&fiRth4_0s0PT
zh$P$)bXPv%EyiL}Adl+i1$_26!eO(9Kmc|r&B;dv<+<P?ZZP?spac&vaDiT8W&nE0
kY_f<@7Iyn49~Tm2l$(50C>y){=3e0w*ez9^JWtda004lG2LJ#7

delta 809
zcmeyb`B0l<^Cw=e8#j}EHgaUJskksOFz6ST<QFBTryA<#CRUWE=HvkB#Nv!Zeb2n&
zlEj>x$&GALj180TusO=xFff*|Gh}iwWO6bzGce@yGBBnvGq`)CurdVaF)~cHWPeGl
zkvfy(Ib;|)Cf9IC@>~SEqGA(63DCq<lNWM`GOA79&Y{8#G;#B7jtoX(jZ~dn$t4do
zaweB1W8&n)T$=Lo3@kuHGnp8&xES&U7#M*dg%RXlCZKzn7$$RYKPJ|2mB|V`5~7@p
z$&5h9f-ox(I|FgC(PUp932||tRS<i)A@)G6sN~5Z)(X|h(!4rGCO|VQ1sQ69?gk=8
zP&fyN=gGj0$Ks7L-eO|yP}wZU=RkajZl1y)K)mY7Qi93`?C@{_GC-lv$lwK`SU`Sa
yV#r`%0JE4Gn1GRCGdWu@i)hzR<`NQORG2I)lufjj&3lDT672;Q#^T9)M4SN+Cg7+5

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("//" + $/)
-- 
2.39.2