From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 29 Nov 2013 20:14:12 +0000 (+0000)
Subject: fixed bug in find_orfs
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=801e0b96e0ac9ffb02f193e8432c021c92cbf78c

fixed bug in find_orfs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2260 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index b291803..5e4d1b5 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -669,22 +669,24 @@ class Seq
     regex_start = Regexp.new(start_codons.join('|'), true)
     regex_stop  = Regexp.new(stop_codons.join('|'), true)
 
-    while pos_beg and pos_beg < self.length - size_min
-      if pos_beg = self.seq.index(regex_start, pos_beg)
-        if pos_end = self.seq.index(regex_stop, pos_beg)
-          length = (pos_end - pos_beg) + 3
+    while pos_beg = self.seq.index(regex_start, pos_beg)
+      pos_end = pos_beg + 3
+       
+      while pos_end = self.seq.index(regex_stop, pos_end)
+        length = (pos_end - pos_beg) + 3
 
-          if (length % 3) == 0
-            if size_min <= length and length <= size_max
-              subseq = self.subseq(pos_beg, length)
+        if (length % 3) == 0
+          if size_min <= length and length <= size_max
+            subseq = self.subseq(pos_beg, length)
 
-              orfs << [subseq, pos_beg, pos_end + 3]
-            end
+            orfs << [subseq, pos_beg, pos_end + 3]
           end
         end
 
-        pos_beg += 1
+        pos_end += 1
       end
+
+      pos_beg += 1
     end
 
     if pick_longest