snp-search 0.31.0 → 0.32.0

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Files changed (4) hide show
  1. data/VERSION +1 -1
  2. data/lib/snp-search.rb +13 -10
  3. data/snp-search.gemspec +2 -2
  4. metadata +21 -21
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.31.0
1
+ 0.32.0
data/lib/snp-search.rb CHANGED
@@ -54,8 +54,9 @@ puts "Adding SNPs........"
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  # open vcf file and parse each line
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  File.open(vcf_file) do |f|
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  # header names
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- while line = f.gets.chomp!
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+ while line = f.gets
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  if line =~ /CHROM/
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+ line.chomp
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  column_headings = line.split("\t")
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  strain_names = column_headings[9..-1]
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  strain_names.map!{|name| name.sub(/\..*/, '')}
@@ -129,22 +130,25 @@ puts "Adding SNPs........"
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  snp_allele.base = snp_base
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  snp_allele.snp = s
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  snp_allele.save
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-
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+
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  ActiveRecord::Base.transaction do
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+ genos = []
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  genotypes.each_with_index do |gt, index|
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- genotype = Genotype.new
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- genotype.strain = strains[index]
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- puts index if strains[index].nil?
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+ genotype = Genotype.new
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+ genotype.strain = strains[index]
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+ puts index if strains[index].nil?
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  if gt == "0/0" # wild type
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- genotype.allele = ref_allele
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+ genotype.allele = ref_allele
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  elsif gt == "1/1" # snp type
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- genotype.allele = snp_allele
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+ genotype.allele = snp_allele
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  else
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  puts "Strange SNP #{gt}"
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  end
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- genotype.save
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+ genos << genotype
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  end
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- puts "Total SNPs added so far: #{good_snps}" if good_snps % 100 == 0
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+ # Using activerecord-import to speed up importing
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+ Genotype.import genos, :validate => false
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+ puts "Total SNPs added so far: #{good_snps}" if good_snps % 100 == 0
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  end
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  end
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  end
@@ -159,4 +163,3 @@ puts "Adding SNPs........"
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  snp.save
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  end
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  end
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-
data/snp-search.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "snp-search"
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- s.version = "0.31.0"
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+ s.version = "0.32.0"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
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- s.date = "2012-01-05"
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+ s.date = "2012-01-09"
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  s.description = "Use the snp-search tool to create, import, manipulate and query your SNP database"
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  s.email = "ali.al-shahib@hpa.org.uk"
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  s.executables = ["snp-search"]
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: snp-search
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  version: !ruby/object:Gem::Version
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- version: 0.31.0
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+ version: 0.32.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -10,11 +10,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-01-05 00:00:00.000000000Z
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+ date: 2012-01-09 00:00:00.000000000Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: activerecord
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- requirement: &2166762680 !ruby/object:Gem::Requirement
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+ requirement: &2168842620 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -22,10 +22,10 @@ dependencies:
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  version: 3.1.3
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  type: :runtime
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  prerelease: false
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- version_requirements: *2166762680
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+ version_requirements: *2168842620
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &2166762200 !ruby/object:Gem::Requirement
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+ requirement: &2168842040 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -33,10 +33,10 @@ dependencies:
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  version: 1.4.2
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  type: :runtime
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  prerelease: false
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- version_requirements: *2166762200
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+ version_requirements: *2168842040
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  - !ruby/object:Gem::Dependency
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  name: slop
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- requirement: &2166761700 !ruby/object:Gem::Requirement
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+ requirement: &2168841440 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -44,10 +44,10 @@ dependencies:
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  version: 2.4.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *2166761700
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+ version_requirements: *2168841440
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  - !ruby/object:Gem::Dependency
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  name: sqlite3
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- requirement: &2166761140 !ruby/object:Gem::Requirement
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+ requirement: &2168840820 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -55,10 +55,10 @@ dependencies:
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  version: 1.3.4
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  type: :runtime
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  prerelease: false
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- version_requirements: *2166761140
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+ version_requirements: *2168840820
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  - !ruby/object:Gem::Dependency
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  name: activerecord-import
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- requirement: &2166760640 !ruby/object:Gem::Requirement
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+ requirement: &2168839800 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -66,10 +66,10 @@ dependencies:
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  version: 0.2.8
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  type: :runtime
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  prerelease: false
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- version_requirements: *2166760640
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+ version_requirements: *2168839800
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &2166760160 !ruby/object:Gem::Requirement
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+ requirement: &2168839320 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -77,10 +77,10 @@ dependencies:
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  version: 2.3.0
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  type: :development
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  prerelease: false
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- version_requirements: *2166760160
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+ version_requirements: *2168839320
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2166759680 !ruby/object:Gem::Requirement
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+ requirement: &2168838760 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -88,10 +88,10 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *2166759680
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+ version_requirements: *2168838760
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2166759180 !ruby/object:Gem::Requirement
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+ requirement: &2168838280 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -99,10 +99,10 @@ dependencies:
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  version: 1.6.4
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  type: :development
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  prerelease: false
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- version_requirements: *2166759180
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+ version_requirements: *2168838280
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  - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &2166758660 !ruby/object:Gem::Requirement
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+ requirement: &2168837800 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -110,7 +110,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2166758660
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+ version_requirements: *2168837800
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  description: Use the snp-search tool to create, import, manipulate and query your
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  SNP database
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  email: ali.al-shahib@hpa.org.uk
@@ -156,7 +156,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: 2364715720088994534
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+ hash: 4420329220307997884
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: