lib/bio/db/primer3.rb in bio-polyploid-tools-0.10.1 vs lib/bio/db/primer3.rb in bio-polyploid-tools-1.0.0

@@ -127,16 +127,16 @@
       @values << regions.size
       @values << regions.join("|")
       @values << snp_type
       if primer3_line_1 and primer3_line_2
         #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    = 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)
-        #  $stderr.puts primer_1
-        #  $stderr.puts primer_2
+
+        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)
+
         if primer3_line_1 < primer3_line_2 and primer_2_tm != "NA"
           @values << primer3_line_1.left_primer
           @values << primer_2
           @values << primer3_line_1.right_primer 
           @values << primer3_line_1.type.to_s 
@@ -157,11 +157,11 @@
           @values << primer3_line_2.best_pair.right.tm
           @values << "second"
           @values << primer3_line_2.best_pair.product_size
         else
 
-          first_candidate = find_primer_pair_first
+          first_candidate  = find_primer_pair_first
           second_candidate = find_primer_pair_second
 
           if first_candidate
             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)
@@ -181,11 +181,11 @@
             @values << first_candidate.type.to_s 
             @values << first_candidate.orientation.to_s 
             @values << first_candidate.best_pair.left.tm 
             @values << primer_2_tm
             @values << first_candidate.best_pair.right.tm
-            @values << "first" 
+            @values << "first-" 
             @values << first_candidate.best_pair.product_size
           elsif  second_candidate 
             #puts "B"
             @values << primer_1
             @values << second_candidate.left_primer
@@ -193,11 +193,11 @@
             @values << second_candidate.type.to_s
             @values << second_candidate.orientation.to_s
             @values << primer_1_tm
             @values << second_candidate.best_pair.left.tm
             @values << second_candidate.best_pair.right.tm
-            @values << "second"
+            @values << "second-"
             @values << second_candidate.best_pair.product_size
           elsif  first_candidate 
             #puts "C"
             @values << first_candidate.left_primer
             @values << primer_2
@@ -205,11 +205,11 @@
             @values << first_candidate.type.to_s
             @values << first_candidate.orientation.to_s
             @values << primer_2_tm
             @values << first_candidate.best_pair.left.tm
             @values << first_candidate.best_pair.right.tm
-            @values << "first"
+            @values << "first/"
             @values << first_candidate.best_pair.product_size
           end
         end
 
       elsif primer3_line_1 
@@ -275,11 +275,10 @@
       return self.values[16].to_i if self.values[16]&& self.values[16] != nil 
       return 0
     end
 
     def orientation
-      puts "insideOrientation: #{self.values[11]}"
       return self.values[11] if self.values[11]&& self.values[11] != nil 
       return 'unknown'
     end
 
 
@@ -383,11 +382,11 @@
           primers_line_1 << primer3record
           #puts primer3record.inspect
           @primer3_line_1 = primer3record if not @primer3_line_1  or @primer3_line_1 > primer3record
         when primer3record.line == @line_2
           primers_line_2 << primer3record
-          @primer3_line_2 = primer3record if not @primer3_line_2 or @primer3_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
       else
         primer3_errors << "#{primer3record.line}(#{primer3record.orientation}):#{primer3record.primer_left_explain.gsub!(',',';')}"
@@ -506,13 +505,11 @@
     end
 
     def left_primer_with_coordinates(coordinates, other_orientation)
 
       seq = self.sequence_template
-      #puts "Left coordinates: #{seq}"
-      seq = Primer3Record.reverse_complement_string(seq) if self.orientation != other_orientation
-
+      seq = Primer3Record.reverse_complement_string(seq) if self.orientation != other_orientation    
       seq[coordinates[0],coordinates[1]] 
     end
 
     def self.reverse_complement_string(sequenc_str)
       complement = sequenc_str.tr('atgcrymkdhvbswnATGCRYMKDHVBSWN', 'tacgyrkmhdbvswnTACGYRKMHDBVSWN')
@@ -805,12 +802,12 @@
 
     def print_primers_with_tails(tail_a: "GAAGGTCGGAGTCAACGGATT", tail_b: "GAAGGTGACCAAGTTCATGCT")
       str = ""
       snp_hash.each do |k, snp|  
         if snp.found_primers?
-          str << snp.gene << snp.original << "\t" << tail_a << snp.first_primer << "\n"
-          str << snp.gene << snp.snp      << "\t" << tail_b << snp.second_primer << "\n"
-          str << snp.gene                 << "\t"           << snp.common_primer << "\n"
+          str << snp.gene << snp.original << "_1st\t" << tail_a << snp.first_primer  << "\n"
+          str << snp.gene << snp.snp      << "_2nd\t" << tail_b << snp.second_primer << "\n"
+          str << snp.gene                 << "_common\t"        << snp.common_primer << "\n"
         end
       end
       return str
     end