ECF Classify

Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file lib/ecf_classify. To experiment with that code, run bin/console for an interactive prompt.

TODO: Delete this and the text above, and describe your gem

Installation

As a command line tool

You can install ecf_classify with the ruby package manager

gem install ecf_classify

As a Ruby module

Add this line to your application's Gemfile:

gem 'ecf_classify'

And then execute:

$ bundle

Or install it yourself as:

$ bundle install 
$ rake install 

Usage

General

ecf_classify commands:
  ecf_classify --version         # print the version
  ecf_classify groups [FILE]     # Classifies protein sequences into ECF groups
  ecf_classify help [COMMAND]    # Describe available commands or one specific command
  ecf_classify subgroups [FILE]  # Classifies protein sequences into ECF subgroups

Options:
  -h, [--help], [--no-help]

Groups

Usage:
  ecf_classify groups [FILE]

Options:
  -p, [--probabilities=PROBABILTIES]
  -h, [--help], [--no-help]

Classifies protein sequences into ECF groups

Subgroups

Usage:
  ecf_classify subgroups [FILE]

Options:
  -p, [--probabilities=PROBABILTIES]
  -h, [--help], [--no-help]

Classifies protein sequences into ECF subgroups

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.

--> This will not be done before submission 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/r-mllr/ecf_classify.

Publication

Please cite:

(unpublished) Casas-Pastor D., Müller R.R., Jaenicke S., Brinkrolf K., Mascher T., Goesmann A., Fritz G. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

License

The gem is available as open source under the terms of the GPL-3.