primer3.rb in bio-polyploid-tools-0.8.5

- old
+ new

@@ -57,10 +57,11 @@
     attr_accessor :primers_line_1, :primers_line_2
     attr_accessor :used_contigs
     attr_accessor :snp_from
     attr_accessor :regions
     attr_accessor :primer3_errors
+    attr_accessor :repetitive
     
     def line_1_name
       "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
     end
 
@@ -110,21 +111,22 @@
       return @values if @values
       left_start = 0
       left_end = 0
       right_start = 0
       right_end = 0
-      total_columns_before_messages=17
+      total_columns_before_messages=18
       #puts "Values in primer3"
       #puts snp_from.inspect
       @values = Array.new
       #@values << "#{gene},,#{template_length},"
       @values << gene
       @values << "#{original}#{position}#{snp}"
       @values << template_length
       @values << snp_from.chromosome
       @values << regions.size
       @values << regions.join("|")
+      @values << repetitive
       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)
@@ -653,12 +655,11 @@
     attr_accessor :pair
     def initialize
       @values = Hash.new
     end
 
-    def method_missing(m, *args, &block)  
-
+    def method_missing(m, *args, &block)
       return @values[m.to_s] if @values[m.to_s] != nil
       raise NoMethodError.new(), "There's no method called #{m}, available: #{@values.keys.to_s}."  
     end
 
     def set_value(key, value)
@@ -752,16 +753,18 @@
         snp.line_2 = @line_2
       end
     end
 
     def add_snp(snp_in) 
+      #TODO: Here we need to also copy the errors that will be printed. 
       @snp_hash=Hash.new unless @snp_hash
       snp = SNP.new
       snp.gene = snp_in.gene
       snp.original = snp_in.original
-
+      snp.primer3_errors = Set.new snp_in.errors
       snp.position = snp_in.position
       snp.snp = snp_in.snp
+      snp.repetitive = snp_in.repetitive
 
       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 }}