polymarker.rb in bio-polyploid-tools-0.7.2

- old
+ new

@@ -59,10 +59,12 @@
 options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
 options[:flanking_size] = 150;
 options[:variation_free_region] = 0 
 options[:extract_found_contigs] = false
 options[:genomes_count] = 3
+options[:min_identity] = 90
+
 options[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
       :primer_lib_ambiguity_codes_consensus => 1,
       :primer_liberal_base => 1, 
@@ -96,10 +98,14 @@
   end
   
   opts.on("-r", "--reference FILE", "Fasta file with the sequence for the markers (to complement --snp_list)") do |o|
     options[:reference] = o
   end
+
+  opts.on("-i", "--min_identity INT", "Minimum identity to consider a hit (default 90)") do |o|
+    options[:min_identity] = o.to_i
+  end
   
   opts.on("-o", "--output FOLDER", "Output folder") do |o|
     options[:output_folder] = o
   end
   
@@ -121,18 +127,19 @@
 
   opts.on("-x", "--extract_found_contigs", "If present, save in a separate file the contigs with matches. Useful to debug.") do |o|
     options[:extract_found_contigs] = true
   end
 
-  opts.on("-P", "--primers_to_order")do
+  opts.on("-P", "--primers_to_order", "If present, save a separate file with the primers with the KASP tails")do
     #TODO: have a string with the tails, optional. 
     options[:primers_to_order] = true
   end
 
   
 end.parse!
 
+
 validate_files(options)
 
 if options[:primer_3_preferences][:primer_product_size_range]
   range = options[:primer_3_preferences][:primer_product_size_range]
   range_arr = range.split("-")
@@ -170,10 +177,12 @@
 primer_3_input="#{output_folder}/primer_3_input_temp"
 primer_3_output="#{output_folder}/primer_3_output_temp"
 exons_filename="#{output_folder}/exons_genes_and_contigs.fa"
 output_primers="#{output_folder}/primers.csv"
 output_to_order="#{output_folder}/primers_to_order.csv"
+min_identity= options[:min_identity]
+
 @status_file="#{output_folder}/status.txt"
 
 primer_3_config=File.expand_path(File.dirname(__FILE__) + '/../conf/primer3_config')
 model=options[:model] 
 
@@ -181,10 +190,10 @@
   f=File.open(@status_file, "a")
   f.puts "#{Time.now.to_s},#{status}"
   f.close
 end
 
-min_identity= 90
+
 snps = Array.new
 
 begin
   
 write_status "Loading Reference"
\ No newline at end of file