virust-locator-ruby 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 61b36ab571a54c1e758d9f472016c7ceb2fb3b89f40a52caa9752cfcb1906303
+  data.tar.gz: f8ec24020b4a78766e5674190822ec2caf15374d446a849115612136013aa154
+SHA512:
+  metadata.gz: 298fdbe81f8304553f257a6aadb393b2895e986ff72a6075bc5c6ce7833389053abd7e0499234e8632c68f617e5b77c9f322351c77c16dea0fb2dbf10038d912
+  data.tar.gz: 7ee8da59a5ce256b81700659bc50f93ac288704c1299842a80b320a9a4b6a421af1038f6c7d981995a4615ef49a31c80a3f4a6b3c6b07b2791fb0f7840187dba

data/.rspec

@@ -0,0 +1,3 @@
+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

@@ -0,0 +1,8 @@
+AllCops:
+  TargetRubyVersion: 3.1
+
+Style/StringLiterals:
+  EnforcedStyle: double_quotes
+
+Style/StringLiteralsInInterpolation:
+  EnforcedStyle: double_quotes

data/CHANGELOG.md

@@ -0,0 +1,5 @@
+## [Unreleased]
+
+## [0.1.0] - 2025-04-08
+
+- Initial release

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,132 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2025 Shuntai Zhou
+
+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

@@ -0,0 +1,53 @@
+# Virust::Locator::Ruby
+
+Wrapper for viRust-locator, a Rust API for simplied LANL HIV Locator tool.
+
+## Installation
+
+```bash
+bundle add virust-locator-ruby
+```
+
+If bundler is not being used to manage dependencies, install the gem by executing:
+
+```bash
+gem install virust-locator-ruby
+```
+
+## Usage
+
+VirustLocator::Locator.exec("GAAAGCATAGTAATATGGGGAAAGACTCCTAAA")
+
+=>
+
+"3681\t3713\t100\tfalse\tGAAAGCATAGTAATATGGGGAAAGACTCCTAAA\tGAAAGCATAGTAATATGGGGAAAGACTCCTAAA"
+
+More options for `virust-locator`
+
+Usage: virust-locator [OPTIONS] --query <QUERY>
+
+Options:
+
+-q, --query <QUERY> Query sequence
+
+-r, --reference <REFERENCE> Reference genome, either HXB2 or SIVmm239 [default: HXB2]
+
+-t, --type-query <TYPE_QUERY> Type of query, either nt or aa [default: nt]
+
+-a, --algorithm <ALGORITHM> algorithm for locator, 1 is accurate but slower, 2 is fast but less accurate, suitable for smaller query sequences [default: 1]
+
+-h, --help Print help
+
+-V, --version Print version
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/virust-locator-ruby. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/[USERNAME]/virust-locator-ruby/blob/main/CODE_OF_CONDUCT.md).
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the Virust::Locator::Ruby project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/virust-locator-ruby/blob/main/CODE_OF_CONDUCT.md).

data/Rakefile

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+require "rubocop/rake_task"
+
+RuboCop::RakeTask.new
+
+task default: %i[spec rubocop]

data/lib/virust_locator/locator.rb

@@ -0,0 +1,36 @@
+# Module to run the Locator executable
+# frozen_string_literal: true
+
+module VirustLocator
+  # This module provides a method to run the Locator executable based on the platform
+  # and architecture of the system. It determines the appropriate executable file
+  # to use and constructs the command to run it with the provided arguments.
+  #
+  # @example
+  #   Locator.exec("GAAAGCATAGTAATATGGGGAAAGACTCCTAAA")
+  #   => "3681\t3713\t100\tfalse\tGAAAGCATAGTAATATGGGGAAAGACTCCTAAA\tGAAAGCATAGTAATATGGGGAAAGACTCCTAAA"
+  module Locator
+    def self.exec(query, type = "nt", algorithm = "1", ref = "HXB2") # rubocop:disable Metrics/MethodLength
+      file = case RUBY_PLATFORM
+             when /arm64-darwin/
+               "virust-locator-aarch64-apple-darwin"
+             when /x86.*darwin/
+               "virust-locator-x86_64-apple-darwin"
+             when /cygwin|mswin|mingw|bccwin|wince|emx/
+               "virust-locator-x86_64-pc-windows-gnu.exe"
+             when /x86.*linux/
+               "virust-locator-x86_64-unknown-linux-gnu"
+             when /aarch64.*linux/
+               "virust-locator-aarch64-unknown-linux-gnu"
+             else
+               raise "Unsupported platform: #{RUBY_PLATFORM}"
+             end
+
+      file = File.join(File.dirname(__FILE__), "runnable", file)
+      safe_file = Shellwords.escape(file)
+      raise "Excecutable file not found: #{file}" unless File.exist?(file)
+
+      `#{safe_file} -q #{Shellwords.escape(query)} -t #{Shellwords.escape(type)} -a #{Shellwords.escape(algorithm)} -r #{Shellwords.escape(ref)}`.strip # rubocop:disable Layout/LineLength
+    end
+  end
+end

data/lib/virust_locator/version.rb

@@ -0,0 +1,7 @@
+# lib/virust_locator/version.rb
+# frozen_string_literal: true
+
+module VirustLocator
+  # The version of the virust-locator-ruby gem.
+  VERSION = "0.1.0"
+end

data/lib/virust_locator.rb

@@ -0,0 +1,29 @@
+# Copyright (c) 2020 Shuntai Zhou (shuntai.zhou@gmail.com)
+#
+# 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.
+#
+# frozen_string_literal: true
+
+# Main module for virust-locator-ruby gem.
+module VirustLocator end
+
+require_relative "virust_locator/version"
+require_relative "virust_locator/locator"
+
+require "shellwords"

data/sig/virust/locator/ruby.rbs

@@ -0,0 +1,8 @@
+module Virust
+  module Locator
+    module Ruby
+      VERSION: String
+      # See the writing guide of rbs: https://github.com/ruby/rbs#guides
+    end
+  end
+end

metadata

@@ -0,0 +1,73 @@
+--- !ruby/object:Gem::Specification
+name: virust-locator-ruby
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Shuntai Zhou
+bindir: exe
+cert_chain: []
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shellwords
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+description: virust-locator provides API for HIV/SIV sequence locating, as in the
+  LANL HIV tools. This is the Ruby wrapper for the virust-locator cmd tool.
+email:
+- shunta.zhou@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".rspec"
+- ".rubocop.yml"
+- CHANGELOG.md
+- CODE_OF_CONDUCT.md
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/virust_locator.rb
+- lib/virust_locator/locator.rb
+- lib/virust_locator/runnable/virust-locator-aarch64-apple-darwin
+- lib/virust_locator/runnable/virust-locator-aarch64-unknown-linux-gnu
+- lib/virust_locator/runnable/virust-locator-x86_64-apple-darwin
+- lib/virust_locator/runnable/virust-locator-x86_64-pc-windows-gnu.exe
+- lib/virust_locator/runnable/virust-locator-x86_64-unknown-linux-gnu
+- lib/virust_locator/version.rb
+- sig/virust/locator/ruby.rbs
+homepage: https://github.com/ViralSeq/virust-locator-ruby
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org/
+  homepage_uri: https://github.com/ViralSeq/virust-locator-ruby
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.1.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.6.7
+specification_version: 4
+summary: Wrapper for viRust-locator, a Rust API for simplied LANL HIV Locator tool.
+test_files: []