changed fasta parse to allow leading empty lines

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 5e4d1b528027b9af8c2a4d80b9a26696f71ceb12..9a8816dc53b47b60e764a98c184a44375dd36bff 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -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|
@@ -305,7 +305,7 @@ class Seq
       seq.chomp!
     end
 
-    ">" + seq_name + $/ + seq + $/
+    ">" + seq_name.to_s + $/ + seq + $/
   end
 
   # Method that given a Seq entry returns a FASTQ entry (a string).
@@ -681,6 +681,8 @@ class Seq
 
             orfs << [subseq, pos_beg, pos_end + 3]
           end
+
+          break
         end
 
         pos_end += 1