ECF Classify

A small software pipeline for the discovery of potentially new ECF σ factors and the prediction of their functionality with regards to the new classification schema (Casas-Pastor et al.).

Prerequisite

Please install hmmer 3. Furthermore, you need to install the following python packages

# requirements.txt
numpy
biopython==1.78

python3 -m pip install -r requirements.txt

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.

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 / How to cite

Please cite:

Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 2021 Jan 4:gkaa1229. doi: 10.1093/nar/gkaa1229. Epub ahead of print. PMID: 33398323.

License

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