From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 18 Aug 2010 11:20:24 +0000 (+0000)
Subject: read_fasta now reads zipped fasta fails again
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=4be853d0dc4a89f01d1816a294ffb0ec2e4fe021;p=biopieces.git

read_fasta now reads zipped fasta fails again

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1065 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/Maasha/lib/fasta.rb b/code_ruby/Maasha/lib/fasta.rb
index 23bad26..b0db2c8 100644
--- a/code_ruby/Maasha/lib/fasta.rb
+++ b/code_ruby/Maasha/lib/fasta.rb
@@ -21,6 +21,8 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'seq'
+require 'zlib'
+require 'pp'
 
 # Error class for all exceptions to do with FASTA.
 class FastaError < StandardError; end
@@ -28,10 +30,17 @@ class FastaError < StandardError; end
 class Fasta
   include Enumerable
 
-  # Class method allowing open to be used on files.
-  # See File.open.
+  # Class method allowing open to be used on (zipped) files.
+  # See File.open and Zlib::GzipReader.
   def self.open(*args)
-    ios   = File.open(*args)
+    ios = File.open(*args)
+
+    begin
+      ios = Zlib::GzipReader.new(ios)
+    rescue
+      ios.rewind
+    end
+
     fasta = self.new(ios)
 
     if block_given?