X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq.rb;h=c22ecec8948a0230079aacd05af1e552a168819e;hb=eb15b4040e0ceba1c3df40b7f0a597c469771cee;hp=a2d5bbac3462d44401d0e1d97a70101f1b7d3af4;hpb=a30677c14f1738f6a76e8c12f2e732cdef9958d6;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index a2d5bba..c22ecec 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -136,7 +136,7 @@ class Seq
     @type     = options[:type]
     @qual     = options[:qual]
 
-    if @qual and @seq.length != @qual.length
+    if @seq and @qual and @seq.length != @qual.length
       raise SeqError, "Sequence length and score length mismatch: #{@seq.length} != #{@qual.length}"
     end
   end
@@ -294,8 +294,8 @@ class Seq
     raise SeqError, "Missing seq_name" if self.seq_name.nil? or self.seq_name == ''
     raise SeqError, "Missing seq"      if self.seq.nil?      or self.seq.empty?
 
-    seq_name = self.seq_name.to_s
-    seq      = self.seq.to_s
+    seq_name = self.seq_name
+    seq      = self.seq.dup
 
     unless wrap.nil?
       seq.gsub!(/(.{#{wrap}})/) do |match|
@@ -343,12 +343,14 @@ class Seq
 
   # Method to reverse the sequence.
   def reverse
-    Seq.new(
+    entry = Seq.new(
       seq_name: self.seq_name,
       seq:      self.seq.reverse,
       type:     self.type,
       qual:     (self.qual ? self.qual.reverse : self.qual)
     )
+
+    entry
   end
 
   # Method to reverse the sequence.
@@ -667,22 +669,26 @@ 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
+
+          break
         end
 
-        pos_beg += 1
+        pos_end += 1
       end
+
+      pos_beg += 1
     end
 
     if pick_longest