polymarker.rb in bio-polyploid-tools-0.7.0

- old
+ new

@@ -49,10 +49,11 @@
 options[:model] = "est2genome"
 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[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
       :primer_lib_ambiguity_codes_consensus => 1,
       :primer_liberal_base => 1, 
@@ -69,10 +70,14 @@
   end
   
   opts.on("-m", "--marker_list FILE", "File with the list of markers to search from") do |o|
     options[:marker_list] = o
   end
+
+  opts.on("-g", "--genomes_count INT", "Number of genomes (default 3, for hexaploid)") do |o|
+    options[:genomes_count] = o.to_i
+  end
   
   opts.on("-s", "--snp_list FILE", "File with the list of snps to search from, requires --reference to get the sequence using a position") do |o|
     options[:snp_list] = o
   end
 
@@ -122,11 +127,11 @@
 if options[:primer_3_preferences][:primer_product_size_range]
   range = options[:primer_3_preferences][:primer_product_size_range]
   range_arr = range.split("-")
   min = range_arr[0].to_i
   max = range_arr[1].to_i
-  raise  Bio::DB::Exonerate::ExonerateException.new "Ragne #{range} is invalid!" unless max > min
+  raise  Bio::DB::Exonerate::ExonerateException.new "Range #{range} is invalid!" unless max > min
   options[:flanking_size] = max
 end
 
 p options
 p ARGV
@@ -212,10 +217,11 @@
       end
     else
       rise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. " 
     end
     rise Bio::DB::Exonerate::ExonerateException.new "No SNP for line '#{line}'" if snp == nil
-  
+
+    snp.genomes_count = options[:genomes_count]
     snp.snp_in = snp_in
     snp.original_name = original_name
     if snp.position 
       snps << snp
     else
\ No newline at end of file