tree_clusters 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +12 -0
- data/.rspec +2 -0
- data/.travis.yml +10 -0
- data/CODE_OF_CONDUCT.md +74 -0
- data/Gemfile +6 -0
- data/LICENSE +21 -0
- data/README.md +63 -0
- data/Rakefile +6 -0
- data/bin/console +14 -0
- data/bin/setup +8 -0
- data/lib/tree_clusters.rb +168 -0
- data/lib/tree_clusters/version.rb +3 -0
- data/test_files/test.rb +15 -0
- data/test_files/test.tre +1 -0
- data/tree_clusters.gemspec +33 -0
- metadata +162 -0
checksums.yaml
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data/.gitignore
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data/.rspec
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data/.travis.yml
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data/CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, gender identity and expression, level of experience,
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nationality, personal appearance, race, religion, or sexual identity and
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orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at moorer@udel.edu. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at [http://contributor-covenant.org/version/1/4][version]
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[homepage]: http://contributor-covenant.org
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[version]: http://contributor-covenant.org/version/1/4/
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data/Gemfile
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data/LICENSE
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MIT License
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Copyright (c) 2017 Ryan Moore
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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 all
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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 THE
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SOFTWARE.
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data/README.md
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# TreeClusters
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[](http://badge.fury.io/rb/tree_clusters) [](https://travis-ci.org/mooreryan/tree_clusters) [](https://coveralls.io/r/mooreryan/tree_clusters)
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Wanna do something with every cluster in a Newick tree? So do we!
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem 'tree_clusters'
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```
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install tree_clusters
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## Documentation
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Checkout
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[TreeClusters docs](http://rubydoc.info/gems/tree_clusters)
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for the full api documentation.
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## Usage
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Here is a small example.
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```ruby
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# Require the library
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require "tree_clusters"
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# Make the TreeClusters methods available under the namespace
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# TreeClusters
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TreeClusters.extend TreeClusters
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# Read in the Newick formatted tree
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tree = NewickTree.fromFile ARGV.first
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# Iterate through all the clades
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TreeClusters.all_clades(tree).each do |clade|
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# Print out the clade name and the names of all leaves in that clade
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printf "%s\t%s\n", clade.name, clade.all_leaves.join(", ")
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end
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```
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## Development
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After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` 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 tags, 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]/tree_clusters. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
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## Code of Conduct
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Everyone interacting in the TreeClusters project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/tree_clusters/blob/master/CODE_OF_CONDUCT.md).
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data/Rakefile
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data/bin/console
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#!/usr/bin/env ruby
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require "bundler/setup"
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require "tree_clusters"
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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
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require "abort_if"
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require "Newick"
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require "set"
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require "tree_clusters/version"
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include AbortIf
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include AbortIf::Assert
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# Monkey patch of the NewickTree class
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class NewickTree
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# Like NewickTree.clades but returns NewickNodes instead of taxa
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# names.
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#
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# @return [Array<NewickNode>] array of NewickNodes representing the
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# tree clades
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def clade_nodes
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clades = []
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@root.descendants.each do |clade|
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clades.push(clade) if (!clade.children.empty?)
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end
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return clades
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end
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end
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# Top level namespace of the Gem.
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module TreeClusters
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# Given a NewickTree, return an array of all Clades in that tree.
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#
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# @param tree [NewickTree] a NewickTree object
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#
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# @return [Array<Clade>] array of Clade objects
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def all_clades tree
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tree.clade_nodes.reverse.map do |node|
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Clade.new node, tree
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end
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end
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# A Hash table for genome/leaf/taxa attributes
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class Attrs < Hash
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# Returns the an AttrArray of Sets for the given genomes and
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# attribute.
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#
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# @note If a genome is in the leaves array, but is not in the hash
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# table, NO error will be raised. Rather that genome will be
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# skipped. This is for cases in which not all genomes have
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# attributes.
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#
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# @param leaves [Array<String>] names of the leaves for which you
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# need attributes
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# @param attr [Symbol] the attribute you are interested in eg,
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# :genes
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#
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# @return [AttrArray<Set>] an AttrArray of Sets of
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# attributes
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#
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# @raise [AbortIf::Exit] if they leaf is present but doesn't have
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# the requested attr
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def attrs leaves, attr
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ary = leaves.map do |leaf|
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if self.has_key? leaf
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abort_unless self[leaf].has_key?(attr),
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"Missing attr #{attr.inspect} for leaf '#{leaf}'"
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self[leaf][attr]
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else
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nil
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end
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end.compact
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TreeClusters::AttrArray.new ary
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end
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end
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# Provides convenience methods for working with Arrays of Sets
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class AttrArray < Object::Array
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# Takes the union of all sets in the AttrArray
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#
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# @return [Set]
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def union
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self.reduce(&:union)
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end
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# Takes the intersection of all sets in the AttrArray
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#
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# @return [Set]
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def intersection
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self.reduce(&:intersection)
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end
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end
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# Represents a clade in a NewickTree
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class Clade
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attr_accessor :name,
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:all_leaves,
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:left_leaves,
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:right_leaves,
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:sibling_leaves,
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:parent_leaves,
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:other_leaves
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# @param node [NewickNode] a NewickNode from a NewickTree
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# @param tree [NewickTree] a NewickTree
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def initialize node, tree
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@name = node.name
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@all_leaves = descendant_leaves node
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children = node.children
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assert children.count == 2,
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"Not a bifurcating tree (See: #{node.name})"
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lchild, rchild = node.children
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@left_leaves = descendant_leaves lchild
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@right_leaves = descendant_leaves rchild
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siblings = node.siblings
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assert siblings.count == 1,
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"Node #{node.name} has more than one sibling."
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@sibling_leaves = descendant_leaves siblings.first
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parent = node.parent
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assert parent,
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"Noge #{node.name} has no parent. Is it the root?"
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@parent_leaves = descendant_leaves parent
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@other_leaves =
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Object::Set.new(tree.taxa) - Object::Set.new(all_leaves)
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end
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# Compares two Clades field by field.
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#
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# If all instance variables are == than the two clades are == as
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# well.
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def == clade
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(
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self.name == clade.name &&
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self.all_leaves == clade.all_leaves &&
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self.left_leaves == clade.left_leaves &&
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self.right_leaves == clade.right_leaves &&
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self.sibling_leaves == clade.sibling_leaves &&
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self.parent_leaves == clade.parent_leaves &&
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self.other_leaves == clade.other_leaves
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)
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end
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# Alias for ==
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def eql? clade
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self == clade
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end
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private
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def descendant_leaves node
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if node.leaf?
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[node.name]
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else
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node.
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descendants.
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flatten.
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uniq.
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select { |node| node.leaf? }.map(&:name)
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end
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end
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end
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end
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data/test_files/test.rb
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# Require the library
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require "tree_clusters"
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# Make the TreeClusters methods available under the namespace
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# TreeClusters
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TreeClusters.extend TreeClusters
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# Read in the Newick formatted tree
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tree = NewickTree.fromFile ARGV.first
|
10
|
+
|
11
|
+
# Iterate through all the clades
|
12
|
+
TreeClusters.all_clades(tree).each do |clade|
|
13
|
+
# Print out the clade name and the names of all leaves in that clade
|
14
|
+
printf "%s\t%s\n", clade.name, clade.all_leaves.join(", ")
|
15
|
+
end
|
data/test_files/test.tre
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
((((((g1:1, g2:1)cluster1:1, g3:2)cluster4:1, (g4a:1, g4b:1)cluster7:2)cluster6:1, ((g5:2, g6:2)cluster11:1, g7:3)cluster14:1)cluster10:1, g8:5)cluster16:1, ((g9:1, g10:1)cluster19:1, g11:2)cluster22:4)cluster18:1;
|
@@ -0,0 +1,33 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path("../lib", __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require "tree_clusters/version"
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "tree_clusters"
|
8
|
+
spec.version = TreeClusters::VERSION
|
9
|
+
spec.authors = ["Ryan Moore"]
|
10
|
+
spec.email = ["moorer@udel.edu"]
|
11
|
+
|
12
|
+
spec.summary = %q{Snazzy code for working with each cluster in a tree.}
|
13
|
+
spec.description = spec.summary
|
14
|
+
spec.homepage = "https://github.com/mooreryan/tree_clusters"
|
15
|
+
|
16
|
+
spec.files = `git ls-files -z`.split("\x0").reject do |f|
|
17
|
+
f.match(%r{^(test|spec|features)/})
|
18
|
+
end
|
19
|
+
spec.bindir = "exe"
|
20
|
+
spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
|
21
|
+
spec.require_paths = ["lib"]
|
22
|
+
|
23
|
+
spec.required_ruby_version = ">= 2"
|
24
|
+
|
25
|
+
spec.add_development_dependency "bundler", "~> 1.15"
|
26
|
+
spec.add_development_dependency "coveralls", "~> 0.8.21"
|
27
|
+
spec.add_development_dependency "rake", "~> 10.0"
|
28
|
+
spec.add_development_dependency "rspec", "~> 3.0"
|
29
|
+
spec.add_development_dependency "yard", "~> 0.9.9"
|
30
|
+
|
31
|
+
spec.add_runtime_dependency "abort_if", "~> 0.2.0"
|
32
|
+
spec.add_runtime_dependency "newick-ruby", "~> 1.0", ">= 1.0.4"
|
33
|
+
end
|
metadata
ADDED
@@ -0,0 +1,162 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: tree_clusters
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Ryan Moore
|
8
|
+
autorequire:
|
9
|
+
bindir: exe
|
10
|
+
cert_chain: []
|
11
|
+
date: 2017-10-29 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.15'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.15'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: coveralls
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - "~>"
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: 0.8.21
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - "~>"
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: 0.8.21
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rake
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - "~>"
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '10.0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - "~>"
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '10.0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: rspec
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - "~>"
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '3.0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - "~>"
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '3.0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: yard
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - "~>"
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 0.9.9
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - "~>"
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 0.9.9
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: abort_if
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - "~>"
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: 0.2.0
|
90
|
+
type: :runtime
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - "~>"
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: 0.2.0
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: newick-ruby
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - "~>"
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: '1.0'
|
104
|
+
- - ">="
|
105
|
+
- !ruby/object:Gem::Version
|
106
|
+
version: 1.0.4
|
107
|
+
type: :runtime
|
108
|
+
prerelease: false
|
109
|
+
version_requirements: !ruby/object:Gem::Requirement
|
110
|
+
requirements:
|
111
|
+
- - "~>"
|
112
|
+
- !ruby/object:Gem::Version
|
113
|
+
version: '1.0'
|
114
|
+
- - ">="
|
115
|
+
- !ruby/object:Gem::Version
|
116
|
+
version: 1.0.4
|
117
|
+
description: Snazzy code for working with each cluster in a tree.
|
118
|
+
email:
|
119
|
+
- moorer@udel.edu
|
120
|
+
executables: []
|
121
|
+
extensions: []
|
122
|
+
extra_rdoc_files: []
|
123
|
+
files:
|
124
|
+
- ".gitignore"
|
125
|
+
- ".rspec"
|
126
|
+
- ".travis.yml"
|
127
|
+
- CODE_OF_CONDUCT.md
|
128
|
+
- Gemfile
|
129
|
+
- LICENSE
|
130
|
+
- README.md
|
131
|
+
- Rakefile
|
132
|
+
- bin/console
|
133
|
+
- bin/setup
|
134
|
+
- lib/tree_clusters.rb
|
135
|
+
- lib/tree_clusters/version.rb
|
136
|
+
- test_files/test.rb
|
137
|
+
- test_files/test.tre
|
138
|
+
- tree_clusters.gemspec
|
139
|
+
homepage: https://github.com/mooreryan/tree_clusters
|
140
|
+
licenses: []
|
141
|
+
metadata: {}
|
142
|
+
post_install_message:
|
143
|
+
rdoc_options: []
|
144
|
+
require_paths:
|
145
|
+
- lib
|
146
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
147
|
+
requirements:
|
148
|
+
- - ">="
|
149
|
+
- !ruby/object:Gem::Version
|
150
|
+
version: '2'
|
151
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
152
|
+
requirements:
|
153
|
+
- - ">="
|
154
|
+
- !ruby/object:Gem::Version
|
155
|
+
version: '0'
|
156
|
+
requirements: []
|
157
|
+
rubyforge_project:
|
158
|
+
rubygems_version: 2.6.14
|
159
|
+
signing_key:
|
160
|
+
specification_version: 4
|
161
|
+
summary: Snazzy code for working with each cluster in a tree.
|
162
|
+
test_files: []
|