TreeClusters

Wanna do something with every cluster in a Newick tree? So do we!

Installation

Add this line to your application's Gemfile:

gem 'tree_clusters'

And then execute:

$ bundle

Or install it yourself as:

$ gem install tree_clusters

Command line scripts

key_cols

Use this to find key columns in an alignment. For more information, run

key_cols --help

API

Documentation

Checkout TreeClusters docs for the full api documentation.

Usage

Here is a small example.

# 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.

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 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.