bin/polymarker.rb in bio-polyploid-tools-0.4.7 vs bin/polymarker.rb in bio-polyploid-tools-0.5.0

@@ -33,23 +33,21 @@
 options[:chunks] = 1
 options[:bucket_size] = 0
 options[:bucket] = 1
 options[:model] = "est2genome"
 options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
-options[:flanking_size] = 100;
+options[:flanking_size] = 150;
 options[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
       :primer_lib_ambiguity_codes_consensus => 1,
       :primer_liberal_base => 1, 
       :primer_num_return=>5,
+      :primer_explain_flag => 1,
       :primer_thermodynamic_parameters_path=>File.expand_path(File.dirname(__FILE__) + '../../conf/primer3_config/') + '/'
-
     }
 
-
-
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
   opts.on("-c", "--contigs FILE", "File with contigs to use as database") do |o|
     options[:path_to_contigs] = o
@@ -79,10 +77,11 @@
     options[:arm_selection] = arm_selection_functions[o.to_sym];
    end
   
   opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
     options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
+
   end
     
 end.parse!
 
 if options[:primer_3_preferences][:primer_product_size_range]
@@ -212,16 +211,16 @@
 target=filename
 
 fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
 fasta_file.load_fai_entries
 
-found_cointigs = Set.new
+found_contigs = Set.new
 Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
   if aln.identity > min_identity
     exo_f.puts aln.line
-    unless found_cointigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
-      found_cointigs.add(aln.target_id)
+    unless found_contigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
+      found_contigs.add(aln.target_id)
       entry = fasta_file.index.region_for_entry(aln.target_id)
       raise ExonerateException.new,  "Entry not found! #{aln.target_id}. Make sure that the #{target_id}.fai was generated properly." if entry == nil
       region = entry.get_full_region
       seq = fasta_file.fetch_sequence(region)
       contigs_f.puts(">#{aln.target_id}\n#{seq}")
@@ -257,16 +256,10 @@
 file = File.open(exons_filename, "w")
 container.print_fasta_snp_exones(file)
 file.close
 
 file = File.open(primer_3_input, "w")
-#file.puts("PRIMER_PRODUCT_SIZE_RANGE=50-150")
-#file.puts("PRIMER_MAX_SIZE=25")
-#file.puts("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1")
-#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])
 added_exons = container.print_primer_3_exons(file, nil, snp_in)
 file.close
 
@@ -282,10 +275,10 @@
 snps.each do |snp|
   kasp_container.add_snp(snp) 
 end
 
 kasp_container.add_primers_file(primer_3_output) if added_exons > 0
-header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size"
+header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
 
 write_status "DONE"
 rescue StandardError => e
   write_status "ERROR\t#{e.message}"
\ No newline at end of file