From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 31 Jan 2012 10:55:06 +0000 (+0000)
Subject: add ustar method to usearch.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b573d2ab7a95ff03226d7f7851173274640061bb;p=biopieces.git

add ustar method to usearch.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1737 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/usearch.rb b/code_ruby/lib/maasha/usearch.rb
index 129cfce..9f09751 100644
--- a/code_ruby/lib/maasha/usearch.rb
+++ b/code_ruby/lib/maasha/usearch.rb
@@ -83,6 +83,25 @@ class Usearch
 		execute
   end
 
+  # Method to execute ustar alignment.
+  def ustar
+    @command << %Q{grep "^[SH]" #{@outfile} > #{@outfile}.sub}
+
+    execute
+
+    File.rename "#{@outfile}.sub", @outfile
+
+    @command << "usearch --uc2fastax #{@outfile} --input #{@infile} --output #{@infile}.sub"
+
+    execute
+
+    @command << "usearch --staralign #{@infile}.sub --output #{@outfile}"
+
+    execute
+
+    File.delete "#{@infile}.sub"
+  end
+
 	# Method to parse a Uclust .uc file and for each line of data
 	# yield a Biopiece record.
   def each_cluster