snp-search in snp-search-0.30.0

- old
+ new
@@ -9,60 +9,60 @@
 opts = Slop.new :help do
   banner "ruby snp-search [OPTIONS]"
 
   on :V, :verbose, 'Enable verbose mode'
   on :n, :name=, 'Name of database, Required', true 
-  on :r, :reference_file=, 'Reference genome file, in gbk or embl file format, Required', true
+  on :d, :database_reference_file=, 'Reference genome file, in gbk or embl file format, Required', true
   on :v, :vcf_file=, '.vcf file, Required', true
   on :c, :cuttoff_snp=, 'SNP quality cutoff, (default = 90)', :default => 90 
   on :t, :cuttoff_genotype=, 'Genotype quality cutoff (default = 30)', :default => 30
    
 end
 opts.parse
 
   error_msg = ""
 
   error_msg += "You must supply the -n option, it's a required field\n" unless opts[:name]
-  error_msg += "You must supply the -r option, it's a required field\n" unless opts[:reference_file]
+  error_msg += "You must supply the -d option, it's a required field\n" unless opts[:database_reference_file]
   error_msg += "You must supply the -v option, it's a required field" unless opts[:vcf_file]
   
   unless error_msg == "" 
     puts error_msg
     puts opts.help unless opts.empty?
     exit
   end
    
-  abort "#{opts[:reference_file]} file does not exist!" unless File.exist?(opts[:reference_file])
+  abort "#{opts[:database_reference_file]} file does not exist!" unless File.exist?(opts[:database_reference_file])
   
   abort "#{opts[:vcf_file]} file does not exist!" unless File.exist?(opts[:vcf_file])
 
 
 # Name of your database 
 establish_connection(opts[:name])
 
 # Schema will run here
 db_schema
 
-ref = opts[:reference_file]
+ref = opts[:database_reference_file]
 
 sequence_format = guess_sequence_format(ref)
 
       case sequence_format
       when :genbank
-        sequence_flatfile = Bio::FlatFile.open(Bio::GenBank,opts[:reference_file]).next_entry
+        sequence_flatfile = Bio::FlatFile.open(Bio::GenBank,opts[:database_reference_file]).next_entry
       when :embl
-        sequence_flatfile = Bio::FlatFile.open(Bio::EMBL,opts[:reference_file]).next_entry
+        sequence_flatfile = Bio::FlatFile.open(Bio::EMBL,opts[:database_reference_file]).next_entry
       else
         puts "All sequence files should be of genbank or embl format"
         exit
       end
 
 
 # path for vcf file here
 vcf_mpileup_file = opts[:vcf_file]
 
 # The populate_features_and_annotations method populates the features and annotations.  It uses the embl/gbk file.
-# populate_features_and_annotations(sequence_flatfile)
+populate_features_and_annotations(sequence_flatfile)
 
 #The populate_snps_alleles_genotypes method populates the snps, alleles and genotypes.  It uses the vcf file, and if specified, the SNP quality cutoff and genotype quality cutoff
 populate_snps_alleles_genotypes(vcf_mpileup_file, opts[:cuttoff_snp].to_i, opts[:cuttoff_genotype].to_i)
 