snp-search.rb in snp-search-0.32.0

- old
+ new

@@ -52,12 +52,13 @@
 def populate_snps_alleles_genotypes(vcf_file, cuttoff_snp, cuttoff_genotype)
 puts "Adding SNPs........"
 # open vcf file and parse each line
 	File.open(vcf_file) do |f|
 	  # header names
-		while line = f.gets.chomp!
+		while line = f.gets
 	  		if  line =~ /CHROM/
+	  			line.chomp
 				column_headings = line.split("\t")
 				strain_names = column_headings[9..-1]
 				strain_names.map!{|name| name.sub(/\..*/, '')}
 					
 				strain_names.each do |str|
@@ -127,26 +128,29 @@
 					        # create snp allele
 					        snp_allele = Allele.new
 					        snp_allele.base = snp_base
 					        snp_allele.snp = s
 					        snp_allele.save
-
+					        
 					     	ActiveRecord::Base.transaction do
+						    	genos = []
 							    genotypes.each_with_index do |gt, index|
-							        genotype = Genotype.new
-							        genotype.strain = strains[index]
-							        puts index if strains[index].nil?
+							         genotype = Genotype.new
+							         genotype.strain = strains[index]
+							    	 puts index if strains[index].nil?
 							          if gt == "0/0" # wild type
-							            genotype.allele = ref_allele
+							             genotype.allele = ref_allele
 							          elsif gt == "1/1" # snp type
-							            genotype.allele = snp_allele
+							             genotype.allele = snp_allele
 							          else
 							            puts "Strange SNP #{gt}"
 							          end
-							        genotype.save
+							          genos << genotype
 								end
-								puts "Total SNPs added so far: #{good_snps}" if good_snps % 100 == 0
+								# Using activerecord-import to speed up importing
+						        Genotype.import genos, :validate => false 
+								 puts "Total SNPs added so far: #{good_snps}" if good_snps % 100 == 0
 							end
 				      	end
 			    	end
 			    end
 			end
@@ -157,6 +161,5 @@
 		x = Feature.where("features.start <= ? AND features.end >= ?", snp.ref_pos, snp.ref_pos).first
 		snp.feature = x
 		snp.save
 	end
 end
-