snp-search 0.31.0 → 0.32.0

data/VERSION

@@ -1 +1 @@
-0.31.0
+0.32.0

data/lib/snp-search.rb

@@ -54,8 +54,9 @@ 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(/\..*/, '')}
@@ -129,22 +130,25 @@ puts "Adding SNPs........"
 					        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
@@ -159,4 +163,3 @@ puts "Adding SNPs........"
 		snp.save
 	end
 end
-

data/snp-search.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.31.0"
+  s.version = "0.32.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
-  s.date = "2012-01-05"
+  s.date = "2012-01-09"
   s.description = "Use the snp-search tool to create, import, manipulate and query your SNP database"
   s.email = "ali.al-shahib@hpa.org.uk"
   s.executables = ["snp-search"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 0.31.0
+  version: 0.32.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-05 00:00:00.000000000Z
+date: 2012-01-09 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2166762680 !ruby/object:Gem::Requirement
+  requirement: &2168842620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2166762680
+  version_requirements: *2168842620
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2166762200 !ruby/object:Gem::Requirement
+  requirement: &2168842040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,10 +33,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2166762200
+  version_requirements: *2168842040
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2166761700 !ruby/object:Gem::Requirement
+  requirement: &2168841440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *2166761700
+  version_requirements: *2168841440
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2166761140 !ruby/object:Gem::Requirement
+  requirement: &2168840820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2166761140
+  version_requirements: *2168840820
 - !ruby/object:Gem::Dependency
   name: activerecord-import
-  requirement: &2166760640 !ruby/object:Gem::Requirement
+  requirement: &2168839800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 0.2.8
   type: :runtime
   prerelease: false
-  version_requirements: *2166760640
+  version_requirements: *2168839800
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2166760160 !ruby/object:Gem::Requirement
+  requirement: &2168839320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2166760160
+  version_requirements: *2168839320
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2166759680 !ruby/object:Gem::Requirement
+  requirement: &2168838760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2166759680
+  version_requirements: *2168838760
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2166759180 !ruby/object:Gem::Requirement
+  requirement: &2168838280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +99,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2166759180
+  version_requirements: *2168838280
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2166758660 !ruby/object:Gem::Requirement
+  requirement: &2168837800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,7 +110,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2166758660
+  version_requirements: *2168837800
 description: Use the snp-search tool to create, import, manipulate and query your
   SNP database
 email: ali.al-shahib@hpa.org.uk
@@ -156,7 +156,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2364715720088994534
+      hash: 4420329220307997884
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: