polymarker.rb in bio-polyploid-tools-0.4.1

- old
+ new

@@ -264,14 +264,14 @@
 #file.puts("PRIMER_LIBERAL_BASE=1")
 #file.puts("PRIMER_NUM_RETURN=5")
 #file.puts("PRIMER_THERMODYNAMIC_PARAMETERS_PATH=#{primer_3_config}/")
 
 Bio::DB::Primer3.prepare_input_file(file, options[:primer_3_preferences])
-container.print_primer_3_exons(file, nil, snp_in)
+added_exons = container.print_primer_3_exons(file, nil, snp_in)
 file.close
 
-Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output})
+Bio::DB::Primer3.run({:in=>primer_3_input, :out=>primer_3_output}) if added_exons > 0
 
 
 #5. Pick the best primer and make the primer3 output
 write_status "Selecting best primers"
 kasp_container=Bio::DB::Primer3::KASPContainer.new
@@ -280,10 +280,10 @@
 
 snps.each do |snp|
   kasp_container.add_snp(snp) 
 end
 
-kasp_container.add_primers_file(primer_3_output)
+kasp_container.add_primers_file(primer_3_output) if added_exons > 0
 header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{snp_in},#{original_name},common,primer_type,orientation,#{snp_in}_TM,#{original_name}_TM,common_TM,selected_from,product_size"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
 
 write_status "DONE"
 rescue StandardError => e
\ No newline at end of file