polymarker.rb in bio-polyploid-tools-0.6.1

- old
+ new

@@ -26,10 +26,23 @@
 arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
   ret = contig_name.split(':')[0].split("_")[1];       
   return ret
 end
 
+def validate_files(o)
+
+  [
+    o[:path_to_contigs], 
+    o[:marker_list], 
+    o[:snp_list], 
+    o[:mutant_list],
+    o[:reference]
+  ].flatten.compact.each do |f|  
+        raise IOError "Unable to read #{f}" unless File.exists? f 
+    end
+end 
+
 options = {}
 options[:path_to_contigs] = "/tgac/references/external/projects/iwgsc/css/IWGSC_CSS_all_scaff_v1.fa"
 options[:chunks] = 1
 options[:bucket_size] = 0
 options[:bucket] = 1
@@ -102,10 +115,12 @@
   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("-")
   min = range_arr[0].to_i
   max = range_arr[1].to_i
@@ -265,10 +280,10 @@
 
 
 container= Bio::PolyploidTools::ExonContainer.new
 container.flanking_size=options[:flanking_size] 
 container.gene_models(temp_fasta_query)
-container.chromosomes(fasta_reference)
+container.chromosomes(target)
 container.add_parental({:name=>snp_in})
 container.add_parental({:name=>original_name})
 snps.each do |snp|
   snp.container = container
   snp.flanking_size = container.flanking_size
\ No newline at end of file