mizlab 0.1.0
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- checksums.yaml +7 -0
- data/.github/workflows/deploy.yml +21 -0
- data/.github/workflows/minitest.yml +18 -0
- data/.github/workflows/yardoc.yml +27 -0
- data/.gitignore +8 -0
- data/Gemfile +14 -0
- data/LICENSE.txt +21 -0
- data/README.md +45 -0
- data/Rakefile +19 -0
- data/bin/console +15 -0
- data/bin/setup +8 -0
- data/lib/mizlab/version.rb +5 -0
- data/lib/mizlab.rb +213 -0
- data/mizlab.gemspec +37 -0
- metadata +58 -0
checksums.yaml
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---
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SHA256:
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metadata.gz: 894a3675ba2feea2a673e352e900a2000805b0fc6d44b413e912fc17a65d4b09
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data.tar.gz: 26b8765e6ef006ff1bcf12dc9d93a8293a4c52b9b8cf6c84093a22ca94009dd1
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SHA512:
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metadata.gz: 4d9284a55408dd8bfd122313c47c5a762a5c41ab419c12e619e5b68938d578846a4c265e3c9b0e619d5b4dec388453077aa982db92d00ce998f663b793544f10
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data.tar.gz: 81024dcb6542d7b269ee0ef0339fade2d3f4d8fa5467b0edf31f4c17c9ddd2dd9b3587a1b6b457700910624728197a5c14ca429dcc4fd7dec6f03d9d9fc555a1
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name: Publish-gem
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on:
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push:
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tags:
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- "v[0-9]+.[0-9]+.[0-9]+"
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Publish gem
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uses: dawidd6/action-publish-gem@v1
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with:
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# Optional, will publish to RubyGems if specified
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api_key: ${{secrets.RUBYGEMS_API_KEY}}
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# Optional, will publish to GitHub Packages if specified
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github_token: ${{secrets.GITHUB_TOKEN}}
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name: Test
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on: [push,pull_request]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: 3.0.1
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- name: Run test
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run: |
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gem install bundler -v 2.2.15
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bundle install
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bundle exec rake test
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name: Build page
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on:
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push:
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branches:
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- main
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: 3.0.1
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- name: Run yardoc
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run: |
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gem install bundler -v 2.2.15
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bundle install
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bundle exec rake yard
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3
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if: ${{ github.ref == 'refs/heads/main' }}
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./doc
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data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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The MIT License (MIT)
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Copyright (c) 2021 mochi-MizLab
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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data/README.md
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[![Test](https://github.com/MizLab/Mizlab-ruby/actions/workflows/minitest.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/minitest.yml)
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[![Build page](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml)
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# Mizlab-ruby
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This gem is for easy handling of the processes used in our labolatory.
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## Installation
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Install it yourself as:
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```sh
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gem install mizlab
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```
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or add below to your application's Gemfile:
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```ruby
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gem 'mizlab'
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```
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And then execute:
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```sh
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bundle install
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```
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## Usage
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See [document](https://mizlab.github.io/Mizlab-ruby).
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## Development
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After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
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To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
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## Contributing
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Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/mizlab.
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## License
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The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
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data/Rakefile
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# frozen_string_literal: true
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require "bundler/gem_tasks"
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require "rake/testtask"
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require "yard"
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Rake::TestTask.new(:test) do |t|
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t.libs << "test"
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t.libs << "lib"
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t.test_files = FileList["test/**/*_test.rb"]
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end
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YARD::Rake::YardocTask.new do |t|
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t.files = ["lib/**/*.rb"]
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t.options = []
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t.stats_options = ["--list-undoc"]
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end
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task default: :test
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data/bin/console
ADDED
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#!/usr/bin/env ruby
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# frozen_string_literal: true
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require "bundler/setup"
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require "mizlab"
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# You can add fixtures and/or initialization code here to make experimenting
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# with your gem easier. You can also use a different console, if you like.
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# (If you use this, don't forget to add pry to your Gemfile!)
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# require "pry"
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# Pry.start
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require "irb"
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IRB.start(__FILE__)
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data/bin/setup
ADDED
data/lib/mizlab.rb
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# frozen_string_literal: true
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require_relative "mizlab/version"
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require "set"
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require "bio"
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module Mizlab
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class << self
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# Fetch data via genbank
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# @param [String] accession Accession number Like "NC_012920".
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# @param [Bool] is_protein wheather the accession is protein. Default to true.
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# @return [Bio::GenBank] GenBank object.
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def getobj(accession, is_protein = false)
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ret = is_protein ? fetch_protein(accession) : fetch_nucleotide(accession)
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parse(ret) do |o|
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return o
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end
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end
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# Fetch multiple data via genbank
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# @param [Array] accessions Array of accession string.
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# @param [Bool] is_protein wheather the accession is protein. Default to true.
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# @yield [Bio::GenBank] GenBank object.
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def getobjs(accessions, is_protein = false)
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ret = is_protein ? fetch_protein(accessions) : fetch_nucleotide(accessions)
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parse(ret) do |o|
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yield o
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end
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end
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# Calculate coordinates from sequence
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# @param [Bio::Sequence] sequence sequence
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# @param [Hash] mappings Hash formated {String => [Float...]}. All of [Float...] must be have same dimention.
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# @param [Hash] weights Weights for some base combination.
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# @param [Integer] Size of window when scanning sequence. If not give this, will use `mappings.keys[0].length -1`.
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# @return [Array] coordinates like [[dim1...], [dim2...]...].
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def calculate_coordinates(sequence, mappings,
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weights = nil, window_size = nil)
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# error detections
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if weights.is_a?(Hash) && window_size.nil?
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keys = weights.keys
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expect_window_size = keys[0].length
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if keys.any? { |k| k.length != expect_window_size }
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raise TypeError, "When not give `window_size`, `weights` must have same length keys"
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end
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end
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n_dimention = mappings.values[0].length
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if mappings.values.any? { |v| v.length != n_dimention }
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raise TypeError, "All of `mappings`.values must have same size"
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end
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mappings.each do |k, v|
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mappings[k] = v.map(&:to_f)
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end
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window_size = (if window_size.nil?
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unless weights.nil?
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weights.keys[0].length
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else
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3 # default
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end
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else
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window_size
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end)
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window_size -= 1
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weights = weights.nil? ? {} : weights
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weights.default = 1.0
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coordinates = Array.new(n_dimention) { [0.0] }
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sequence.length.times do |idx|
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start = idx < window_size ? 0 : idx - window_size
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vector = mappings[sequence[idx]].map { |v| v * weights[sequence[start..idx]] }
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vector.each_with_index do |v, j|
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coordinates[j].append(coordinates[j][-1] + v)
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end
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end
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return coordinates
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end
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# Compute local patterns from coordinates.
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# @param [Array] x_coordinates coordinates on x.
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# @param [Array] y_coordinates coordinates on y.
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# @return [Array] Local pattern histgram (unnormalized).
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def local_patterns(x_coordinates, y_coordinates)
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length = x_coordinates.length
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if length != y_coordinates.length
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raise TypeError, "The arguments must have same length."
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end
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filled_pixs = Set.new
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0.upto(length - 2) do |idx|
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filled_pixs += bresenham(x_coordinates[idx].truncate, y_coordinates[idx].truncate,
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x_coordinates[idx + 1].truncate, y_coordinates[idx + 1].truncate)
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end
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local_pattern_list = [0] * 512
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get_patterns(filled_pixs) do |pix|
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local_pattern_list[convert(pix)] += 1
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end
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return local_pattern_list
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end
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private
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def fetch_protein(accession)
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return Bio::NCBI::REST::EFetch.protein(accession)
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end
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def fetch_nucleotide(accession)
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return Bio::NCBI::REST::EFetch.protein(accession)
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end
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# get patterns from filled pixs.
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# @param [Set] filleds filled pix's coordinates.
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# @yield [binaries] Array like [t, f, t...].
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def get_patterns(filleds)
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unless filleds.is_a?(Set)
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raise TypeError, "The argument must be Set"
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end
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centers = Set.new()
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filleds.each do |focused|
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get_centers(focused) do |center|
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if centers.include?(center)
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next
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end
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centers.add(center)
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binaries = []
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-1.upto(1) do |dy|
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1.downto(-1) do |dx|
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binaries.append(filleds.include?([center[0] + dx, center[1] + dy]))
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end
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end
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yield binaries
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end
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end
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end
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# get center coordinates of all window that include focused pixel
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# @param [Array] focused coordinate of focused pixel
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# @yield [Array] center coordinates of all window
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def get_centers(focused)
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-1.upto(1) do |dy|
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1.downto(-1) do |dx|
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yield [focused[0] + dx, focused[1] + dy]
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145
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end
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146
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end
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147
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end
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|
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# Convert binary array to interger
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# @param [Array] binaries Array of binaries
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# @return [Integer] converted integer
|
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def convert(binaries)
|
153
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unless binaries.all? { |v| v.is_a?(TrueClass) || v.is_a?(FalseClass) }
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154
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raise TypeError, "The argument must be Boolean"
|
155
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end
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rst = 0
|
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binaries.reverse.each_with_index do |b, i|
|
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if b
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rst += 2 ** i
|
160
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end
|
161
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end
|
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return rst
|
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+
end
|
164
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+
|
165
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# Compute fill pixels by bresenham algorithm
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# @param [Interger] x0 the start point on x.
|
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# @param [Interger] y0 the start point on y.
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# @param [Interger] x1 the end point on x.
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# @param [Interger] x1 the end point on y.
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# @return [Array] filled pixels
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def bresenham(x0, y0, x1, y1)
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if ![x0, y0, x1, y1].all? { |v| v.is_a?(Integer) }
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raise TypeError, "All of arguments must be Integer"
|
174
|
+
end
|
175
|
+
dx = (x1 - x0).abs
|
176
|
+
dy = (y1 - y0).abs
|
177
|
+
sx = x0 < x1 ? 1 : -1
|
178
|
+
sy = y0 < y1 ? 1 : -1
|
179
|
+
err = dx - dy
|
180
|
+
lines = []
|
181
|
+
while true
|
182
|
+
lines.append([x0, y0])
|
183
|
+
if (x0 == x1 && y0 == y1)
|
184
|
+
break
|
185
|
+
end
|
186
|
+
e2 = 2 * err
|
187
|
+
if e2 > -dy
|
188
|
+
err = err - dy
|
189
|
+
x0 = x0 + sx
|
190
|
+
end
|
191
|
+
if e2 < dx
|
192
|
+
err = err + dx
|
193
|
+
y0 = y0 + sy
|
194
|
+
end
|
195
|
+
end
|
196
|
+
return lines
|
197
|
+
end
|
198
|
+
|
199
|
+
# Parse fetched data.
|
200
|
+
# @param [String] entries Entries as string
|
201
|
+
# @yield [Object] Object that match entry format.
|
202
|
+
def parse(entries)
|
203
|
+
tmp_file_name = ".mizlab_fetch_tmpfile"
|
204
|
+
File.open(tmp_file_name, "w") do |f|
|
205
|
+
f.puts entries
|
206
|
+
end
|
207
|
+
Bio::FlatFile.auto(tmp_file_name).each_entry do |e|
|
208
|
+
yield e
|
209
|
+
end
|
210
|
+
File.delete(tmp_file_name)
|
211
|
+
end
|
212
|
+
end
|
213
|
+
end
|
data/mizlab.gemspec
ADDED
@@ -0,0 +1,37 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
require_relative "lib/mizlab/version"
|
4
|
+
|
5
|
+
Gem::Specification.new do |spec|
|
6
|
+
spec.name = "mizlab"
|
7
|
+
spec.version = Mizlab::VERSION
|
8
|
+
spec.authors = ["Omochice"]
|
9
|
+
spec.email = ["mochice.mls.ntl@gmail.com"]
|
10
|
+
|
11
|
+
spec.summary = "The tools for our laboratory"
|
12
|
+
spec.description = "The tools for our laboratory"
|
13
|
+
spec.homepage = "https://mizlab.github.io/Mizlab-ruby"
|
14
|
+
spec.license = "MIT"
|
15
|
+
spec.required_ruby_version = Gem::Requirement.new(">= 2.4.0")
|
16
|
+
|
17
|
+
# spec.metadata["allowed_push_host"] = "TODO: Set to 'http://mygemserver.com'"
|
18
|
+
|
19
|
+
spec.metadata["homepage_uri"] = spec.homepage
|
20
|
+
spec.metadata["source_code_uri"] = "https://github.com/MizLab/Mizlab-ruby"
|
21
|
+
# spec.metadata["changelog_uri"] = "TODO: Put your gem's CHANGELOG.md URL here."
|
22
|
+
|
23
|
+
# Specify which files should be added to the gem when it is released.
|
24
|
+
# The `git ls-files -z` loads the files in the RubyGem that have been added into git.
|
25
|
+
spec.files = Dir.chdir(File.expand_path(__dir__)) do
|
26
|
+
`git ls-files -z`.split("\x0").reject { |f| f.match(%r{\A(?:test|spec|features)/}) }
|
27
|
+
end
|
28
|
+
spec.bindir = "exe"
|
29
|
+
spec.executables = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
|
30
|
+
spec.require_paths = ["lib"]
|
31
|
+
|
32
|
+
# Uncomment to register a new dependency of your gem
|
33
|
+
# spec.add_dependency "example-gem", "~> 1.0"
|
34
|
+
|
35
|
+
# For more information and examples about making a new gem, checkout our
|
36
|
+
# guide at: https://bundler.io/guides/creating_gem.html
|
37
|
+
end
|
metadata
ADDED
@@ -0,0 +1,58 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: mizlab
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Omochice
|
8
|
+
autorequire:
|
9
|
+
bindir: exe
|
10
|
+
cert_chain: []
|
11
|
+
date: 2021-10-22 00:00:00.000000000 Z
|
12
|
+
dependencies: []
|
13
|
+
description: The tools for our laboratory
|
14
|
+
email:
|
15
|
+
- mochice.mls.ntl@gmail.com
|
16
|
+
executables: []
|
17
|
+
extensions: []
|
18
|
+
extra_rdoc_files: []
|
19
|
+
files:
|
20
|
+
- ".github/workflows/deploy.yml"
|
21
|
+
- ".github/workflows/minitest.yml"
|
22
|
+
- ".github/workflows/yardoc.yml"
|
23
|
+
- ".gitignore"
|
24
|
+
- Gemfile
|
25
|
+
- LICENSE.txt
|
26
|
+
- README.md
|
27
|
+
- Rakefile
|
28
|
+
- bin/console
|
29
|
+
- bin/setup
|
30
|
+
- lib/mizlab.rb
|
31
|
+
- lib/mizlab/version.rb
|
32
|
+
- mizlab.gemspec
|
33
|
+
homepage: https://mizlab.github.io/Mizlab-ruby
|
34
|
+
licenses:
|
35
|
+
- MIT
|
36
|
+
metadata:
|
37
|
+
homepage_uri: https://mizlab.github.io/Mizlab-ruby
|
38
|
+
source_code_uri: https://github.com/MizLab/Mizlab-ruby
|
39
|
+
post_install_message:
|
40
|
+
rdoc_options: []
|
41
|
+
require_paths:
|
42
|
+
- lib
|
43
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ">="
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: 2.4.0
|
48
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
49
|
+
requirements:
|
50
|
+
- - ">="
|
51
|
+
- !ruby/object:Gem::Version
|
52
|
+
version: '0'
|
53
|
+
requirements: []
|
54
|
+
rubygems_version: 3.1.2
|
55
|
+
signing_key:
|
56
|
+
specification_version: 4
|
57
|
+
summary: The tools for our laboratory
|
58
|
+
test_files: []
|