tree_clusters 0.1.0

checksums.yaml

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+  data.tar.gz: cefdde1e0149b0ccd30b44ae0ae1e2c3646548c9
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color

data/.travis.yml

@@ -0,0 +1,10 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.0
+  - 2.1
+  - 2.2
+  - 2.3
+  - 2.4
+  - 2.4.1
+before_install: gem install bundler -v 1.15.4

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at moorer@udel.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in tree_clusters.gemspec
+gemspec

data/LICENSE

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+MIT License
+
+Copyright (c) 2017 Ryan Moore
+
+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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+# TreeClusters
+
+[![Gem Version](https://badge.fury.io/rb/tree_clusters.svg)](http://badge.fury.io/rb/tree_clusters) [![Build Status](https://travis-ci.org/mooreryan/tree_clusters.svg?branch=master)](https://travis-ci.org/mooreryan/tree_clusters) [![Coverage Status](https://coveralls.io/repos/mooreryan/tree_clusters/badge.svg)](https://coveralls.io/r/mooreryan/tree_clusters)
+
+Wanna do something with every cluster in a Newick tree? So do we!
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'tree_clusters'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install tree_clusters
+
+## Documentation
+
+Checkout
+[TreeClusters docs](http://rubydoc.info/gems/tree_clusters)
+for the full api documentation.
+
+## Usage
+
+Here is a small example.
+
+```ruby
+# Require the library
+require "tree_clusters"
+
+# Make the TreeClusters methods available under the namespace
+# TreeClusters
+TreeClusters.extend TreeClusters
+
+# Read in the Newick formatted tree
+tree = NewickTree.fromFile ARGV.first
+
+# Iterate through all the clades
+TreeClusters.all_clades(tree).each do |clade|
+  # Print out the clade name and the names of all leaves in that clade
+  printf "%s\t%s\n", clade.name, clade.all_leaves.join(", ")
+end
+```
+
+## Development
+
+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.
+
+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).
+
+## Contributing
+
+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.
+
+## Code of Conduct
+
+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).

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "tree_clusters"
+
+# 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/tree_clusters.rb

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+require "abort_if"
+require "Newick"
+require "set"
+require "tree_clusters/version"
+
+include AbortIf
+include AbortIf::Assert
+
+# Monkey patch of the NewickTree class
+class NewickTree
+  # Like NewickTree.clades but returns NewickNodes instead of taxa
+  # names.
+  #
+  # @return [Array<NewickNode>] array of NewickNodes representing the
+  #   tree clades
+  def clade_nodes
+    clades = []
+    @root.descendants.each do |clade|
+      clades.push(clade) if (!clade.children.empty?)
+    end
+    return clades
+  end
+end
+
+# Top level namespace of the Gem.
+module TreeClusters
+
+  # Given a NewickTree, return an array of all Clades in that tree.
+  #
+  # @param tree [NewickTree] a NewickTree object
+  #
+  # @return [Array<Clade>] array of Clade objects
+  def all_clades tree
+    tree.clade_nodes.reverse.map do |node|
+      Clade.new node, tree
+    end
+  end
+
+  # A Hash table for genome/leaf/taxa attributes
+  class Attrs < Hash
+
+    # Returns the an AttrArray of Sets for the given genomes and
+    # attribute.
+    #
+    # @note If a genome is in the leaves array, but is not in the hash
+    #   table, NO error will be raised. Rather that genome will be
+    #   skipped. This is for cases in which not all genomes have
+    #   attributes.
+    #
+    # @param leaves [Array<String>] names of the leaves for which you
+    #   need attributes
+    # @param attr [Symbol] the attribute you are interested in eg,
+    #   :genes
+    #
+    # @return [AttrArray<Set>] an AttrArray of Sets of
+    #   attributes
+    #
+    # @raise [AbortIf::Exit] if they leaf is present but doesn't have
+    #   the requested attr
+    def attrs leaves, attr
+      ary = leaves.map do |leaf|
+
+        if self.has_key? leaf
+          abort_unless self[leaf].has_key?(attr),
+                       "Missing attr #{attr.inspect} for leaf '#{leaf}'"
+
+          self[leaf][attr]
+        else
+          nil
+        end
+      end.compact
+
+      TreeClusters::AttrArray.new ary
+    end
+  end
+
+  # Provides convenience methods for working with Arrays of Sets
+  class AttrArray < Object::Array
+    # Takes the union of all sets in the AttrArray
+    #
+    # @return [Set]
+    def union
+      self.reduce(&:union)
+    end
+
+    # Takes the intersection of all sets in the AttrArray
+    #
+    # @return [Set]
+    def intersection
+      self.reduce(&:intersection)
+    end
+  end
+
+  # Represents a clade in a NewickTree
+  class Clade
+    attr_accessor :name,
+                  :all_leaves,
+                  :left_leaves,
+                  :right_leaves,
+                  :sibling_leaves,
+                  :parent_leaves,
+                  :other_leaves
+
+    # @param node [NewickNode] a NewickNode from a NewickTree
+    # @param tree [NewickTree] a NewickTree
+    def initialize node, tree
+      @name = node.name
+      @all_leaves = descendant_leaves node
+
+      children = node.children
+      assert children.count == 2,
+             "Not a bifurcating tree (See: #{node.name})"
+      lchild, rchild = node.children
+
+      @left_leaves = descendant_leaves lchild
+
+      @right_leaves = descendant_leaves rchild
+
+      siblings = node.siblings
+      assert siblings.count == 1,
+             "Node #{node.name} has more than one sibling."
+      @sibling_leaves = descendant_leaves siblings.first
+
+      parent = node.parent
+      assert parent,
+             "Noge #{node.name} has no parent. Is it the root?"
+      @parent_leaves = descendant_leaves parent
+
+      @other_leaves =
+        Object::Set.new(tree.taxa) - Object::Set.new(all_leaves)
+    end
+
+    # Compares two Clades field by field.
+    #
+    # If all instance variables are == than the two clades are == as
+    # well.
+    def == clade
+      (
+        self.name == clade.name &&
+        self.all_leaves == clade.all_leaves &&
+        self.left_leaves == clade.left_leaves &&
+        self.right_leaves == clade.right_leaves &&
+        self.sibling_leaves == clade.sibling_leaves &&
+        self.parent_leaves == clade.parent_leaves &&
+        self.other_leaves == clade.other_leaves
+      )
+    end
+
+    # Alias for ==
+    def eql? clade
+      self == clade
+    end
+
+    private
+
+    def descendant_leaves node
+      if node.leaf?
+        [node.name]
+      else
+        node.
+          descendants.
+          flatten.
+          uniq.
+          select { |node| node.leaf? }.map(&:name)
+      end
+    end
+  end
+end

data/lib/tree_clusters/version.rb

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+module TreeClusters
+  VERSION = "0.1.0"
+end

data/test_files/test.rb

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+# Require the library
+require "tree_clusters"
+
+# Make the TreeClusters methods available under the namespace
+# TreeClusters
+TreeClusters.extend TreeClusters
+
+# Read in the Newick formatted tree
+tree = NewickTree.fromFile ARGV.first
+
+# Iterate through all the clades
+TreeClusters.all_clades(tree).each do |clade|
+  # Print out the clade name and the names of all leaves in that clade
+  printf "%s\t%s\n", clade.name, clade.all_leaves.join(", ")
+end

data/test_files/test.tre

@@ -0,0 +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;

data/tree_clusters.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "tree_clusters/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "tree_clusters"
+  spec.version       = TreeClusters::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+
+  spec.summary       = %q{Snazzy code for working with each cluster in a tree.}
+  spec.description   = spec.summary
+  spec.homepage      = "https://github.com/mooreryan/tree_clusters"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.required_ruby_version = ">= 2"
+
+  spec.add_development_dependency "bundler", "~> 1.15"
+  spec.add_development_dependency "coveralls", "~> 0.8.21"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "yard", "~> 0.9.9"
+
+  spec.add_runtime_dependency "abort_if", "~> 0.2.0"
+  spec.add_runtime_dependency "newick-ruby", "~> 1.0", ">= 1.0.4"
+end

metadata

@@ -0,0 +1,162 @@
+--- !ruby/object:Gem::Specification
+name: tree_clusters
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Ryan Moore
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-10-29 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.15'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.8.21
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+- !ruby/object:Gem::Dependency
+  name: abort_if
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: newick-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+description: Snazzy code for working with each cluster in a tree.
+email:
+- moorer@udel.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/tree_clusters.rb
+- lib/tree_clusters/version.rb
+- test_files/test.rb
+- test_files/test.tre
+- tree_clusters.gemspec
+homepage: https://github.com/mooreryan/tree_clusters
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '2'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.14
+signing_key: 
+specification_version: 4
+summary: Snazzy code for working with each cluster in a tree.
+test_files: []