primer3.rb in bio-polyploid-tools-0.4.4

- old
+ new

@@ -1,6 +1,6 @@
-
+require 'pp'
 module Bio::DB::Primer3
   class Primer3Exception < RuntimeError 
   end
 
   def self.read_primer_preferences(file, defaults)
@@ -156,16 +156,20 @@
           values << primer3_line_2.shortest_pair.left.tm
           values << primer3_line_2.shortest_pair.right.tm
           values << "second"
           values << primer3_line_2.shortest_pair.product_size
         else
+
           first_candidate = find_primer_pair_first
           second_candidate = find_primer_pair_second
 
           if first_candidate
+
+            #puts "input to search #{first_candidate.left_coordinates}"
             primer_2 = primer3_line_2.left_primer_with_coordinates(first_candidate.left_coordinates, first_candidate.orientation)
             primer_2_tm = find_left_primer_temp(primer_2)
+            #puts "In the funky if #{primer_2}"
           end
           if second_candidate
             primer_1 = primer3_line_1.left_primer_with_coordinates(second_candidate.left_coordinates, second_candidate.orientation) 
             primer_1_tm = find_left_primer_temp(primer_1)
           end
@@ -281,11 +285,11 @@
         case
         when primer3record.line == @line_1
           primers_line_1 << primer3record
           @primer3_line_1 = primer3record if not @primer3_line_1  or @primer3_line_1 > primer3record
         when primer3record.line == @line_2
-          primers_line_1 << primer3record
+          primers_line_2 << primer3record
           @primer3_line_2 = primer3record if not @primer3_line_2 or @primer3_line_2 > primer3record
         else
           raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
         end
       end
@@ -417,17 +421,18 @@
       elsif tmp_primer[-1] == base_snp
         tmp_primer[-1] = base_original  
       else
         raise Primer3Exception.new "#{tmp_primer} doesnt end in a base in the SNP #{snp.to_s}"
       end
+      #puts "tmp_primer: #{tmp_primer}"
       return tmp_primer
     end
 
     def left_primer_with_coordinates(coordinates, other_orientation)
 
       seq = self.sequence_template
-
+      #puts "Left coordinates: #{seq}"
       seq = reverse_complement_string(seq) if self.orientation != other_orientation
 
       seq[coordinates[0],coordinates[1]] 
     end
 
@@ -685,10 +690,10 @@
 
     def add_primers_file(filename)
       Primer3Record.parse_file(filename) do | primer3record |
         current_snp = @snp_hash["#{primer3record.snp.to_s}:#{primer3record.chromosome}"]
         current_snp.add_record(primer3record)
-        #puts current_snp.inspect
+
       end
     end
 
     def print_primers
       str = ""