snp-search 0.23.0 → 0.26.0

data/Gemfile

@@ -7,6 +7,7 @@ source "http://rubygems.org"
  gem "bio", "~> 1.4.2"
  gem "slop", "~> 2.4.0"
  gem 'sqlite3', "~> 1.3.4"
+ gem 'activerecord-import', "~> 0.2.8"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/Gemfile.lock

@@ -10,6 +10,9 @@ GEM
       activesupport (= 3.1.3)
       arel (~> 2.2.1)
       tzinfo (~> 0.3.29)
+    activerecord-import (0.2.8)
+      activerecord (~> 3.0pre)
+      activerecord (~> 3.0pre)
     activesupport (3.1.3)
       multi_json (~> 1.0)
     arel (2.2.1)
@@ -42,6 +45,7 @@ PLATFORMS
 
 DEPENDENCIES
   activerecord (~> 3.1.3)
+  activerecord-import (~> 0.2.8)
   bio (~> 1.4.2)
   bundler (~> 1.0.0)
   jeweler (~> 1.6.4)

data/VERSION

@@ -1 +1 @@
-0.23.0
+0.26.0

data/bin/snp-search

@@ -22,17 +22,25 @@ opts = Slop.new :help do
 end
 opts.parse
 
-  puts "You must supply the -n option, it's a required field" and exit unless opts[:name]
-  puts "You must supply the -r option, it's a required field" and exit unless opts[:reference_file]
-  puts "You must supply the -v option, it's a required field" and exit unless opts[:vcf_file] 
+  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 -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
    
   begin 
-  puts "#{opts[:reference_file]} file does not exist!" and exit unless File.exist?(opts[:reference_file])
+  abort "#{opts[:reference_file]} file does not exist!" unless File.exist?(opts[:reference_file])
   rescue
   end
   
   begin
-  puts "#{opts[:vcf_file]} file does not exist!" and exit unless File.exist?(opts[:vcf_file])
+  abort "#{opts[:vcf_file]} file does not exist!" unless File.exist?(opts[:vcf_file])
   rescue
   end
 
@@ -62,7 +70,7 @@ sequence_format = guess_sequence_format(ref)
 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)

data/lib/snp-search.rb

@@ -2,10 +2,9 @@ require 'rubygems'
 gem "bio", "~> 1.4.2"
 require 'bio'
 require  'snp_db_models'
+require 'activerecord-import'
 #establish_connection
 
-GC.disable
-
 def guess_sequence_format(reference_genome)
   file_extension = File.extname(reference_genome).downcase
   file_format = nil
@@ -22,29 +21,30 @@ end
 # We include all features that are not 'source' or 'gene' as they are repetitive info.  'CDS' is the gene.
 # The annotation table includes also the start and end coordinates of the CDS.  The strand is also included.  the 'locations' method is defined in bioruby under genbank.  It must be required at the top (bio).
 # Also, the qualifier and value are extracted from the embl file and added to the database.
-def populate_features_and_annotations(sequence_file)
-	sequence_file.features.each do |feature|
-		unless feature.feature == "source" || feature.feature == "gene"
-			db_feature = Feature.new
-			db_feature.start = feature.locations.first.from
-			db_feature.end = feature.locations.first.to
-			db_feature.strand = feature.locations.first.strand
-			db_feature.name = feature.feature
-			db_feature.save
-			puts "populating #{db_feature.name}, start: #{db_feature.start}, end: #{db_feature.end}, strand: #{db_feature.strand} for feature: #{db_feature.id}"
-			# Populate the Annotation table with qualifier information from the genbank file
-			feature.qualifiers.each do |qualifier|
-				a = Annotation.new
-				a.qualifier = qualifier.qualifier
-				a.value = qualifier.value
-				a.save
-				db_feature.annotations << a
-				puts "populating #{a.qualifier} for feature: #{db_feature.id}"
-			end
-		end
-	end
-end
-
+# def populate_features_and_annotations(sequence_file)
+# 	 ActiveRecord::Base.transaction do
+# 		sequence_file.features.each do |feature|
+# 			unless feature.feature == "source" || feature.feature == "gene"
+# 				db_feature = Feature.new
+# 				db_feature.start = feature.locations.first.from
+# 				db_feature.end = feature.locations.first.to
+# 				db_feature.strand = feature.locations.first.strand
+# 				db_feature.name = feature.feature
+# 				db_feature.save
+# 				puts "populating #{db_feature.name}, start: #{db_feature.start}, end: #{db_feature.end}, strand: #{db_feature.strand} for feature: #{db_feature.id}"
+# 				# Populate the Annotation table with qualifier information from the genbank file
+# 				feature.qualifiers.each do |qualifier|
+# 					a = Annotation.new
+# 					a.qualifier = qualifier.qualifier
+# 					a.value = qualifier.value
+# 					a.save
+# 					db_feature.annotations << a
+# 					puts "populating #{a.qualifier} for feature: #{db_feature.id}"
+# 				end
+# 			end
+# 		end
+# 	end
+# end
 
 #This method populates the rest of the information, i.e. SNP information, Alleles and Genotypes.
 # It requires the strain_names as array and the output (vcf file) from mpileup-snp identification algorithm.
@@ -134,23 +134,31 @@ def populate_snps_alleles_genotypes(vcf_file, cuttoff_snp, cuttoff_genotype)
 			        snp_allele.save
 
 			        puts "Adding SNP base: #{snp_base}"
-
 			        
-
-			        genotypes.each_with_index do |gt, index|
-			          genotype = Genotype.new
-			          genotype.strain = strains[index]
-			          puts index if strains[index].nil?
-			          # print "#{gt}(#{genotypes_qualities[index]}) "
-			          if gt == "0/0" # wild type
-			            genotype.allele = ref_allele
-			          elsif gt == "1/1" # snp type
-			            genotype.allele = snp_allele
-			          else
-			            puts "Strange SNP #{gt}"
-			          end
-			          genotype.save
-			        end
+			        a = Time.now
+
+			        puts "Adding Genotype information..."
+			     	ActiveRecord::Base.transaction do
+					     genotypes.each_with_index do |gt, index|
+					          genotype = Genotype.new
+					          genotype.strain = strains[index]
+					          puts index if strains[index].nil?
+					          # print "#{gt}(#{genotypes_qualities[index]}) "
+					          if gt == "0/0" # wild type
+					            genotype.allele = ref_allele
+					          elsif gt == "1/1" # snp type
+					            genotype.allele = snp_allele
+					          else
+					            puts "Strange SNP #{gt}"
+					          end
+					         	#genotype.save
+
+					     end
+					end
+					b = Time.now
+					mm, ss = (b-a).divmod(60)
+					puts "Time taken:  #{mm} minutes #{ss} seconds"
+ 					a = Time.now 
 		      	end
 		    end
 

data/snp-search.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.23.0"
+  s.version = "0.26.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
-  s.date = "2011-12-08"
+  s.date = "2011-12-13"
   s.description = "Use the snp-search toolset to query the SNP database"
   s.email = "ali.al-shahib@hpa.org.uk"
   s.executables = ["snp-search"]
@@ -55,6 +55,7 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<bio>, ["~> 1.4.2"])
       s.add_runtime_dependency(%q<slop>, ["~> 2.4.0"])
       s.add_runtime_dependency(%q<sqlite3>, ["~> 1.3.4"])
+      s.add_runtime_dependency(%q<activerecord-import>, ["~> 0.2.8"])
       s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
@@ -64,6 +65,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<bio>, ["~> 1.4.2"])
       s.add_dependency(%q<slop>, ["~> 2.4.0"])
       s.add_dependency(%q<sqlite3>, ["~> 1.3.4"])
+      s.add_dependency(%q<activerecord-import>, ["~> 0.2.8"])
       s.add_dependency(%q<rspec>, ["~> 2.3.0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
@@ -74,6 +76,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<bio>, ["~> 1.4.2"])
     s.add_dependency(%q<slop>, ["~> 2.4.0"])
     s.add_dependency(%q<sqlite3>, ["~> 1.3.4"])
+    s.add_dependency(%q<activerecord-import>, ["~> 0.2.8"])
     s.add_dependency(%q<rspec>, ["~> 2.3.0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 0.23.0
+  version: 0.26.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-08 00:00:00.000000000Z
+date: 2011-12-13 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2158724720 !ruby/object:Gem::Requirement
+  requirement: &2153046460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2158724720
+  version_requirements: *2153046460
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2158724140 !ruby/object:Gem::Requirement
+  requirement: &2153045960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,10 +33,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2158724140
+  version_requirements: *2153045960
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2158723560 !ruby/object:Gem::Requirement
+  requirement: &2153045420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *2158723560
+  version_requirements: *2153045420
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2158722980 !ruby/object:Gem::Requirement
+  requirement: &2153044880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,21 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2158722980
+  version_requirements: *2153044880
+- !ruby/object:Gem::Dependency
+  name: activerecord-import
+  requirement: &2153044340 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.2.8
+  type: :runtime
+  prerelease: false
+  version_requirements: *2153044340
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2158722400 !ruby/object:Gem::Requirement
+  requirement: &2153043800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +77,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2158722400
+  version_requirements: *2153043800
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2158693340 !ruby/object:Gem::Requirement
+  requirement: &2153043300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +88,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2158693340
+  version_requirements: *2153043300
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2158692760 !ruby/object:Gem::Requirement
+  requirement: &2153042820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +99,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2158692760
+  version_requirements: *2153042820
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2158692180 !ruby/object:Gem::Requirement
+  requirement: &2153042340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,7 +110,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2158692180
+  version_requirements: *2153042340
 description: Use the snp-search toolset to query the SNP database
 email: ali.al-shahib@hpa.org.uk
 executables:
@@ -146,7 +157,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 802966617095520080
+      hash: -2048575630589609763
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: