primer3.rb in bio-polyploid-tools-0.9.6

- old
+ new

@@ -59,10 +59,11 @@
     attr_accessor :snp_from
     attr_accessor :regions
     attr_accessor :primer3_errors
     attr_accessor :repetitive
     attr_accessor :hit_count
+    attr_accessor :snp_type
     
     def line_1_name
       "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
     end
 
@@ -123,13 +124,12 @@
       @values << "#{original}#{position}#{snp}"
       @values << template_length
       @values << snp_from.chromosome
       @values << regions.size
       @values << regions.join("|")
+      @values << snp_type
       if primer3_line_1 and primer3_line_2
-        @values <<  primer3_line_1.polymorphism
-
         #Block that searches both if both pairs have a TM
         primer_2 = primer3_line_2.left_primer_with_coordinates(primer3_line_1.left_coordinates, primer3_line_1.orientation)
         primer_2_tm = find_left_primer_temp(primer_2)
         primer_1 = primer3_line_1.left_primer_with_coordinates(primer3_line_2.left_coordinates, primer3_line_2.orientation) 
         primer_1_tm = find_left_primer_temp(primer_1)
@@ -211,11 +211,10 @@
             @values << first_candidate.best_pair.product_size
           end
         end
 
       elsif primer3_line_1 
-        @values << primer3_line_1.polymorphism
         @values << primer3_line_1.left_primer
         @values << primer3_line_1.left_primer_snp(self) 
         @values << primer3_line_1.right_primer 
         @values << primer3_line_1.type.to_s 
         @values << primer3_line_1.orientation.to_s      
@@ -224,11 +223,10 @@
         @values << primer3_line_1.best_pair.right.tm
 
         @values << "first+"
         @values << primer3_line_1.best_pair.product_size
       elsif primer3_line_2 
-        @values << primer3_line_2.polymorphism
         @values << primer3_line_2.left_primer_snp(self) 
         @values << primer3_line_2.left_primer
         @values << primer3_line_2.right_primer
         @values << primer3_line_2.type.to_s
         @values << primer3_line_2.orientation.to_s
@@ -767,9 +765,10 @@
       snp.position = snp_in.position
       snp.snp = snp_in.snp
       snp.repetitive = snp_in.repetitive
       #puts snp_in.inspect
       snp.hit_count = snp_in.hit_count
+      snp.snp_type  = snp_in.snp_type
       snp.line_1 = @line_1
       snp.line_2 = @line_2 
       snp.snp_from = snp_in
       snp.regions = snp_in.exon_list.values.collect { |x|  x.collect {|y| y.target_region.to_s }}
       @snp_hash[snp.to_s] = snp