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Multi-genome amino acid similarity pipeline
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README.md

AAI

License: MIT

Calculate Seanie's multi-genome (or genome bin, or metagenome sample) amino acid similarity.

Requirements

The following programs must be installed and on your PATH for aai to work.

For versions >= 0.4

For versions < 0.4

Installation

Install with RubyGems

Run

$ gem install aai

If bundling aai in another ruby program

Add this line to your application's Gemfile:

gem 'aai'

And then execute:

$ bundle

Usage

Example

After installing with gem install then the aai program should be available to you. Try and get the help page:

$ aai --help

Then run the program like this:

$ aai --infiles *.fa --outdir aai_output

Note: Each input file is treated as a file of ORFs (amino acid gene predictions) for a single genome.

Options

Options:
  -c, --cpus=<i>        Number of CPUs to use (default: 1)
  -i, --infiles=<s+>    Input files
  -o, --outdir=<s>      Output directory (default: .)
  -b, --basename=<s>    Base name for output file (default: aai_scores)
  -v, --version         Print version and exit
  -h, --help            Show this message

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]/aai. 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.

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