mizlab 0.1.0

checksums.yaml

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+SHA256:
+  metadata.gz: 894a3675ba2feea2a673e352e900a2000805b0fc6d44b413e912fc17a65d4b09
+  data.tar.gz: 26b8765e6ef006ff1bcf12dc9d93a8293a4c52b9b8cf6c84093a22ca94009dd1
+SHA512:
+  metadata.gz: 4d9284a55408dd8bfd122313c47c5a762a5c41ab419c12e619e5b68938d578846a4c265e3c9b0e619d5b4dec388453077aa982db92d00ce998f663b793544f10
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data/.github/workflows/deploy.yml

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+name: Publish-gem
+
+on:
+  push:
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+"
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Publish gem
+        uses: dawidd6/action-publish-gem@v1
+        with:
+          # Optional, will publish to RubyGems if specified
+          api_key: ${{secrets.RUBYGEMS_API_KEY}}
+          # Optional, will publish to GitHub Packages if specified
+          github_token: ${{secrets.GITHUB_TOKEN}}

data/.github/workflows/minitest.yml

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+name: Test
+
+on: [push,pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: 3.0.1
+    - name: Run test
+      run: |
+        gem install bundler -v 2.2.15
+        bundle install
+        bundle exec rake test

data/.github/workflows/yardoc.yml

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+name: Build page
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: 3.0.1
+    - name: Run yardoc
+      run: |
+        gem install bundler -v 2.2.15
+        bundle install
+        bundle exec rake yard
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: ${{ github.ref == 'refs/heads/main' }}
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./doc

data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/Gemfile

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in mizlab.gemspec
+gemspec
+
+gem "rake", "~> 13.0"
+
+gem "minitest", "~> 5.0"
+
+gem "yard", "~> 0.9"
+
+gem "bio"

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2021 mochi-MizLab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

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)
+[![Build page](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml/badge.svg)](https://github.com/MizLab/Mizlab-ruby/actions/workflows/yardoc.yml)
+
+# Mizlab-ruby
+
+This gem is for easy handling of the processes used in our labolatory.
+
+
+## Installation
+
+Install it yourself as:
+
+```sh
+gem install mizlab
+```
+
+or add below to your application's Gemfile:
+
+```ruby
+gem 'mizlab'
+```
+
+And then execute:
+
+```sh
+bundle install
+```
+
+## Usage
+
+See [document](https://mizlab.github.io/Mizlab-ruby).
+
+## Development
+
+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.
+
+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).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/mizlab.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

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+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rake/testtask"
+require "yard"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList["test/**/*_test.rb"]
+end
+
+YARD::Rake::YardocTask.new do |t|
+  t.files = ["lib/**/*.rb"]
+  t.options = []
+  t.stats_options = ["--list-undoc"]
+end
+
+task default: :test

data/bin/console

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "bundler/setup"
+require "mizlab"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/mizlab/version.rb

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+# frozen_string_literal: true
+
+module Mizlab
+  VERSION = "0.1.0"
+end

data/lib/mizlab.rb

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+# frozen_string_literal: true
+
+require_relative "mizlab/version"
+require "set"
+require "bio"
+
+module Mizlab
+  class << self
+    # Fetch data via genbank
+    # @param  [String] accession Accession number Like "NC_012920".
+    # @param  [Bool] is_protein wheather the accession is protein. Default to true.
+    # @return [Bio::GenBank] GenBank object.
+    def getobj(accession, is_protein = false)
+      ret = is_protein ? fetch_protein(accession) : fetch_nucleotide(accession)
+      parse(ret) do |o|
+        return o
+      end
+    end
+
+    # Fetch multiple data via genbank
+    # @param  [Array] accessions Array of accession string.
+    # @param  [Bool] is_protein wheather the accession is protein. Default to true.
+    # @yield  [Bio::GenBank] GenBank object.
+    def getobjs(accessions, is_protein = false)
+      ret = is_protein ? fetch_protein(accessions) : fetch_nucleotide(accessions)
+      parse(ret) do |o|
+        yield o
+      end
+    end
+
+    # Calculate coordinates from sequence
+    # @param  [Bio::Sequence] sequence sequence
+    # @param  [Hash] mappings Hash formated {String => [Float...]}. All of [Float...] must be have same dimention.
+    # @param  [Hash] weights Weights for some base combination.
+    # @param  [Integer] Size of window when scanning sequence. If not give this, will use `mappings.keys[0].length -1`.
+    # @return [Array] coordinates like [[dim1...], [dim2...]...].
+    def calculate_coordinates(sequence, mappings,
+                              weights = nil, window_size = nil)
+      # error detections
+      if weights.is_a?(Hash) && window_size.nil?
+        keys = weights.keys
+        expect_window_size = keys[0].length
+        if keys.any? { |k| k.length != expect_window_size }
+          raise TypeError, "When not give `window_size`, `weights` must have same length keys"
+        end
+      end
+      n_dimention = mappings.values[0].length
+      if mappings.values.any? { |v| v.length != n_dimention }
+        raise TypeError, "All of `mappings`.values must have same size"
+      end
+
+      mappings.each do |k, v|
+        mappings[k] = v.map(&:to_f)
+      end
+
+      window_size = (if window_size.nil?
+        unless weights.nil?
+          weights.keys[0].length
+        else
+          3 # default
+        end
+      else
+        window_size
+      end)
+      window_size -= 1
+      weights = weights.nil? ? {} : weights
+      weights.default = 1.0
+      coordinates = Array.new(n_dimention) { [0.0] }
+      sequence.length.times do |idx|
+        start = idx < window_size ? 0 : idx - window_size
+        vector = mappings[sequence[idx]].map { |v| v * weights[sequence[start..idx]] }
+        vector.each_with_index do |v, j|
+          coordinates[j].append(coordinates[j][-1] + v)
+        end
+      end
+      return coordinates
+    end
+
+    # Compute local patterns from coordinates.
+    # @param  [Array] x_coordinates coordinates on x.
+    # @param  [Array] y_coordinates coordinates on y.
+    # @return [Array] Local pattern histgram (unnormalized).
+    def local_patterns(x_coordinates, y_coordinates)
+      length = x_coordinates.length
+      if length != y_coordinates.length
+        raise TypeError, "The arguments must have same length."
+      end
+
+      filled_pixs = Set.new
+      0.upto(length - 2) do |idx|
+        filled_pixs += bresenham(x_coordinates[idx].truncate, y_coordinates[idx].truncate,
+                                 x_coordinates[idx + 1].truncate, y_coordinates[idx + 1].truncate)
+      end
+
+      local_pattern_list = [0] * 512
+      get_patterns(filled_pixs) do |pix|
+        local_pattern_list[convert(pix)] += 1
+      end
+      return local_pattern_list
+    end
+
+    private
+
+    def fetch_protein(accession)
+      return Bio::NCBI::REST::EFetch.protein(accession)
+    end
+
+    def fetch_nucleotide(accession)
+      return Bio::NCBI::REST::EFetch.protein(accession)
+    end
+
+    # get patterns from filled pixs.
+    # @param [Set] filleds filled pix's coordinates.
+    # @yield [binaries] Array like [t, f, t...].
+    def get_patterns(filleds)
+      unless filleds.is_a?(Set)
+        raise TypeError, "The argument must be Set"
+      end
+
+      centers = Set.new()
+      filleds.each do |focused|
+        get_centers(focused) do |center|
+          if centers.include?(center)
+            next
+          end
+          centers.add(center)
+          binaries = []
+          -1.upto(1) do |dy|
+            1.downto(-1) do |dx|
+              binaries.append(filleds.include?([center[0] + dx, center[1] + dy]))
+            end
+          end
+          yield binaries
+        end
+      end
+    end
+
+    # get center coordinates of all window that include focused pixel
+    # @param  [Array] focused coordinate of focused pixel
+    # @yield [Array] center coordinates of all window
+    def get_centers(focused)
+      -1.upto(1) do |dy|
+        1.downto(-1) do |dx|
+          yield [focused[0] + dx, focused[1] + dy]
+        end
+      end
+    end
+
+    # Convert binary array to interger
+    # @param  [Array] binaries Array of binaries
+    # @return [Integer] converted integer
+    def convert(binaries)
+      unless binaries.all? { |v| v.is_a?(TrueClass) || v.is_a?(FalseClass) }
+        raise TypeError, "The argument must be Boolean"
+      end
+      rst = 0
+      binaries.reverse.each_with_index do |b, i|
+        if b
+          rst += 2 ** i
+        end
+      end
+      return rst
+    end
+
+    # Compute fill pixels by bresenham algorithm
+    # @param  [Interger] x0 the start point on x.
+    # @param  [Interger] y0 the start point on y.
+    # @param  [Interger] x1 the end point on x.
+    # @param  [Interger] x1 the end point on y.
+    # @return [Array] filled pixels
+    def bresenham(x0, y0, x1, y1)
+      if ![x0, y0, x1, y1].all? { |v| v.is_a?(Integer) }
+        raise TypeError, "All of arguments must be Integer"
+      end
+      dx = (x1 - x0).abs
+      dy = (y1 - y0).abs
+      sx = x0 < x1 ? 1 : -1
+      sy = y0 < y1 ? 1 : -1
+      err = dx - dy
+      lines = []
+      while true
+        lines.append([x0, y0])
+        if (x0 == x1 && y0 == y1)
+          break
+        end
+        e2 = 2 * err
+        if e2 > -dy
+          err = err - dy
+          x0 = x0 + sx
+        end
+        if e2 < dx
+          err = err + dx
+          y0 = y0 + sy
+        end
+      end
+      return lines
+    end
+
+    # Parse fetched data.
+    # @param  [String] entries Entries as string
+    # @yield  [Object] Object that match entry format.
+    def parse(entries)
+      tmp_file_name = ".mizlab_fetch_tmpfile"
+      File.open(tmp_file_name, "w") do |f|
+        f.puts entries
+      end
+      Bio::FlatFile.auto(tmp_file_name).each_entry do |e|
+        yield e
+      end
+      File.delete(tmp_file_name)
+    end
+  end
+end

data/mizlab.gemspec

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+# frozen_string_literal: true
+
+require_relative "lib/mizlab/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "mizlab"
+  spec.version       = Mizlab::VERSION
+  spec.authors       = ["Omochice"]
+  spec.email         = ["mochice.mls.ntl@gmail.com"]
+
+  spec.summary       = "The tools for our laboratory"
+  spec.description   = "The tools for our laboratory"
+  spec.homepage      = "https://mizlab.github.io/Mizlab-ruby"
+  spec.license       = "MIT"
+  spec.required_ruby_version = Gem::Requirement.new(">= 2.4.0")
+
+  # spec.metadata["allowed_push_host"] = "TODO: Set to 'http://mygemserver.com'"
+
+  spec.metadata["homepage_uri"] = spec.homepage
+  spec.metadata["source_code_uri"] = "https://github.com/MizLab/Mizlab-ruby"
+  # spec.metadata["changelog_uri"] = "TODO: Put your gem's CHANGELOG.md URL here."
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{\A(?:test|spec|features)/}) }
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  # Uncomment to register a new dependency of your gem
+  # spec.add_dependency "example-gem", "~> 1.0"
+
+  # For more information and examples about making a new gem, checkout our
+  # guide at: https://bundler.io/guides/creating_gem.html
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: mizlab
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Omochice
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2021-10-22 00:00:00.000000000 Z
+dependencies: []
+description: The tools for our laboratory
+email:
+- mochice.mls.ntl@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".github/workflows/deploy.yml"
+- ".github/workflows/minitest.yml"
+- ".github/workflows/yardoc.yml"
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/mizlab.rb
+- lib/mizlab/version.rb
+- mizlab.gemspec
+homepage: https://mizlab.github.io/Mizlab-ruby
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://mizlab.github.io/Mizlab-ruby
+  source_code_uri: https://github.com/MizLab/Mizlab-ruby
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.4.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.2
+signing_key: 
+specification_version: 4
+summary: The tools for our laboratory
+test_files: []