polymarker.rb in bio-polyploid-tools-0.9.10

- old
+ new

@@ -122,11 +122,11 @@
 
   opts.on("-H", "--het_dels", "If present, change the scoring to give priority to: semi-specific, specific, non-specific")  do
     options[:scoring] = :het_dels
   end
 
-  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: exonerate") do |o|
+  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: #{options[:aligner]}") do |o|
     raise "Invalid aligner" unless o == "exonerate" or o == "blast" 
     options[:aligner] = o.to_sym
   end
 
   opts.on("-d", "--database PREFIX", "Path to the blast database. Only used if the aligner is blast. The default is the name of the contigs file without extension.") do |o|
@@ -135,11 +135,11 @@
 end.parse!
 
 
 validate_files(options)
 
- options[:database] = options[:path_to_contigs] unless  options[:database] 
+options[:database] = options[:path_to_contigs] unless  options[:database] 
 
 
 if options[:primer_3_preferences][:primer_product_size_range]
   range = options[:primer_3_preferences][:primer_product_size_range]
   range_arr = range.split("-")
@@ -167,10 +167,10 @@
 test_file=options[:snp_list] if options[:snp_list]
 test_file=options[:mutant_list] if options[:mutant_list]
 fasta_reference = options[:reference]
 output_folder="#{test_file}_primer_design_#{Time.now.strftime('%Y%m%d-%H%M%S')}" 
 output_folder= options[:output_folder] if  options[:output_folder]
-Dir.mkdir(output_folder)
+Dir.mkdir(output_folder) unless Dir.exist?(output_folder)
 #TODO Make this tmp files
 temp_fasta_query="#{output_folder}/to_align.fa"
 temp_contigs="#{output_folder}/contigs_tmp.fa"
 exonerate_file="#{output_folder}/exonerate_tmp.tab"
 primer_3_input="#{output_folder}/primer_3_input_temp"