bio-tm_hmm 0.2.2 → 0.2.3

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Files changed (6) hide show
  1. checksums.yaml +7 -0
  2. data/Gemfile +3 -2
  3. data/VERSION +1 -1
  4. data/bin/bio-tm_hmm +0 -1
  5. data/bio-tm_hmm.gemspec +33 -29
  6. metadata +47 -48
@@ -0,0 +1,7 @@
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+ ---
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+ SHA1:
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+ metadata.gz: a63ec466bfd78426f0c588a4fa930cc83ef1b017
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+ data.tar.gz: 016f3310e83507e7a8c43d5f4980495990299ee9
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+ SHA512:
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+ metadata.gz: cab26f0526b1d1858251b9c7db940b0b79aa8d9f2e1a051060d24463337d63124ccdcaddbbcf550f01fc041afa160f3df19eba5449b424decdd4397a5c2d5d16
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+ data.tar.gz: 68a9f82aaafb5723ee217405872bababd8c458a7ecb77e09c704f4a5303ba3033be3d1127deb3ff66642d4e5f7259fe201f0bbfd01ad94841b3e963776af45e2
data/Gemfile CHANGED
@@ -2,13 +2,14 @@ source "http://rubygems.org"
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2
  # Add dependencies required to use your gem here.
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3
  # Example:
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  # gem "activesupport", ">= 2.3.5"
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+ gem "bio", ">= 1.4.2"
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+ gem "test-unit", "~>3.2"
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  # Add dependencies to develop your gem here.
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  # Include everything needed to run rake, tests, features, etc.
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  group :development do
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  gem "shoulda", ">= 0"
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  gem "rdoc", "~> 3.12"
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- gem "jeweler", "~> 1.8.3"
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+ gem "jeweler", "~> 2.3"
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  gem "bundler", ">= 1.0.21"
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- gem "bio", ">= 1.4.2"
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  end
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.2.2
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+ 0.2.3
@@ -45,7 +45,6 @@ Bio::FlatFile.auto(ARGF).each do |seq|
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  # Default output - a description of the TMDs for each input aaseq
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  if options[:filter_in] == false and options[:filter_out] == false
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- p result
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  if result.has_domain?
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  # At least one TMD found. Output each on a separate line
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  result.transmembrane_domains.each do |tmd|
@@ -2,17 +2,19 @@
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  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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+ # stub: bio-tm_hmm 0.2.3 ruby lib
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  Gem::Specification.new do |s|
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- s.name = "bio-tm_hmm"
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- s.version = "0.2.2"
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+ s.name = "bio-tm_hmm".freeze
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+ s.version = "0.2.3"
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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 = ["Ben J. Woodcroft"]
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- s.date = "2012-12-01"
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- s.description = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
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- s.email = "donttrustben@gmail.com"
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- s.executables = ["bio-tm_hmm"]
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+ s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
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+ s.require_paths = ["lib".freeze]
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+ s.authors = ["Ben J. Woodcroft".freeze]
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+ s.date = "2017-04-06"
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+ s.description = "A bioruby plugin for interaction with the transmembrane predictor TMHMM".freeze
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+ s.email = "donttrustben@gmail.com".freeze
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+ s.executables = ["bio-tm_hmm".freeze]
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  s.extra_rdoc_files = [
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  "LICENSE.txt",
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  "README.md"
@@ -36,34 +38,36 @@ Gem::Specification.new do |s|
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  "test/test_tm_hmm_wrapper.rb",
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  "test/test_transmembrane.rb"
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  ]
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- s.homepage = "http://github.com/wwood/bioruby-tm_hmm"
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- s.licenses = ["MIT"]
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- s.require_paths = ["lib"]
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- s.rubygems_version = "1.8.24"
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- s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
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+ s.homepage = "http://github.com/wwood/bioruby-tm_hmm".freeze
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+ s.licenses = ["MIT".freeze]
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+ s.rubygems_version = "2.5.2".freeze
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+ s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM".freeze
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45
 
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  if s.respond_to? :specification_version then
46
- s.specification_version = 3
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+ s.specification_version = 4
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48
 
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  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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- s.add_development_dependency(%q<shoulda>, [">= 0"])
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- s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
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- s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
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- s.add_development_dependency(%q<bundler>, [">= 1.0.21"])
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- s.add_development_dependency(%q<bio>, [">= 1.4.2"])
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+ s.add_runtime_dependency(%q<bio>.freeze, [">= 1.4.2"])
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+ s.add_runtime_dependency(%q<test-unit>.freeze, ["~> 3.2"])
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+ s.add_development_dependency(%q<shoulda>.freeze, [">= 0"])
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+ s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
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+ s.add_development_dependency(%q<jeweler>.freeze, ["~> 2.3"])
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+ s.add_development_dependency(%q<bundler>.freeze, [">= 1.0.21"])
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  else
55
- s.add_dependency(%q<shoulda>, [">= 0"])
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- s.add_dependency(%q<rdoc>, ["~> 3.12"])
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- s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
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- s.add_dependency(%q<bundler>, [">= 1.0.21"])
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- s.add_dependency(%q<bio>, [">= 1.4.2"])
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+ s.add_dependency(%q<bio>.freeze, [">= 1.4.2"])
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+ s.add_dependency(%q<test-unit>.freeze, ["~> 3.2"])
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+ s.add_dependency(%q<shoulda>.freeze, [">= 0"])
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+ s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
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+ s.add_dependency(%q<jeweler>.freeze, ["~> 2.3"])
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+ s.add_dependency(%q<bundler>.freeze, [">= 1.0.21"])
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  end
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  else
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- s.add_dependency(%q<shoulda>, [">= 0"])
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- s.add_dependency(%q<rdoc>, ["~> 3.12"])
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- s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
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- s.add_dependency(%q<bundler>, [">= 1.0.21"])
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- s.add_dependency(%q<bio>, [">= 1.4.2"])
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+ s.add_dependency(%q<bio>.freeze, [">= 1.4.2"])
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+ s.add_dependency(%q<test-unit>.freeze, ["~> 3.2"])
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+ s.add_dependency(%q<shoulda>.freeze, [">= 0"])
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+ s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
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+ s.add_dependency(%q<jeweler>.freeze, ["~> 2.3"])
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+ s.add_dependency(%q<bundler>.freeze, [">= 1.0.21"])
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  end
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  end
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metadata CHANGED
@@ -1,96 +1,99 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: bio-tm_hmm
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  version: !ruby/object:Gem::Version
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- version: 0.2.2
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- prerelease:
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+ version: 0.2.3
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  platform: ruby
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  authors:
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  - Ben J. Woodcroft
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-12-01 00:00:00.000000000 Z
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+ date: 2017-04-06 00:00:00.000000000 Z
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  dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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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: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.4.2
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+ - !ruby/object:Gem::Dependency
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+ name: test-unit
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '3.2'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '3.2'
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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  requirement: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
19
- - - ! '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: '0'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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- none: false
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51
  requirements:
27
- - - ! '>='
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+ - - ">="
28
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  - !ruby/object:Gem::Version
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  version: '0'
30
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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  requirement: !ruby/object:Gem::Requirement
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- none: false
34
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  requirements:
35
- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '3.12'
38
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  type: :development
39
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  prerelease: false
40
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  version_requirements: !ruby/object:Gem::Requirement
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- none: false
42
65
  requirements:
43
- - - ~>
66
+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '3.12'
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  - !ruby/object:Gem::Dependency
47
70
  name: jeweler
48
71
  requirement: !ruby/object:Gem::Requirement
49
- none: false
50
72
  requirements:
51
- - - ~>
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+ - - "~>"
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74
  - !ruby/object:Gem::Version
53
- version: 1.8.3
75
+ version: '2.3'
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76
  type: :development
55
77
  prerelease: false
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78
  version_requirements: !ruby/object:Gem::Requirement
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- none: false
58
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  requirements:
59
- - - ~>
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+ - - "~>"
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81
  - !ruby/object:Gem::Version
61
- version: 1.8.3
82
+ version: '2.3'
62
83
  - !ruby/object:Gem::Dependency
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84
  name: bundler
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  requirement: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
67
- - - ! '>='
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+ - - ">="
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  - !ruby/object:Gem::Version
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89
  version: 1.0.21
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  type: :development
71
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  prerelease: false
72
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  version_requirements: !ruby/object:Gem::Requirement
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- none: false
74
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  requirements:
75
- - - ! '>='
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+ - - ">="
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95
  - !ruby/object:Gem::Version
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96
  version: 1.0.21
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- - !ruby/object:Gem::Dependency
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- name: bio
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- requirement: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
83
- - - ! '>='
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- - !ruby/object:Gem::Version
85
- version: 1.4.2
86
- type: :development
87
- prerelease: false
88
- version_requirements: !ruby/object:Gem::Requirement
89
- none: false
90
- requirements:
91
- - - ! '>='
92
- - !ruby/object:Gem::Version
93
- version: 1.4.2
94
97
  description: A bioruby plugin for interaction with the transmembrane predictor TMHMM
95
98
  email: donttrustben@gmail.com
96
99
  executables:
@@ -100,8 +103,8 @@ extra_rdoc_files:
100
103
  - LICENSE.txt
101
104
  - README.md
102
105
  files:
103
- - .document
104
- - .travis.yml
106
+ - ".document"
107
+ - ".travis.yml"
105
108
  - Gemfile
106
109
  - LICENSE.txt
107
110
  - README.md
@@ -120,29 +123,25 @@ files:
120
123
  homepage: http://github.com/wwood/bioruby-tm_hmm
121
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  licenses:
122
125
  - MIT
126
+ metadata: {}
123
127
  post_install_message:
124
128
  rdoc_options: []
125
129
  require_paths:
126
130
  - lib
127
131
  required_ruby_version: !ruby/object:Gem::Requirement
128
- none: false
129
132
  requirements:
130
- - - ! '>='
133
+ - - ">="
131
134
  - !ruby/object:Gem::Version
132
135
  version: '0'
133
- segments:
134
- - 0
135
- hash: 24340783
136
136
  required_rubygems_version: !ruby/object:Gem::Requirement
137
- none: false
138
137
  requirements:
139
- - - ! '>='
138
+ - - ">="
140
139
  - !ruby/object:Gem::Version
141
140
  version: '0'
142
141
  requirements: []
143
142
  rubyforge_project:
144
- rubygems_version: 1.8.24
143
+ rubygems_version: 2.5.2
145
144
  signing_key:
146
- specification_version: 3
145
+ specification_version: 4
147
146
  summary: A bioruby plugin for interaction with the transmembrane predictor TMHMM
148
147
  test_files: []