bio-corgi 0.5.4

Classifier for ORganelle Genomes Inter alia

Installation

The software can be installed using pip

pip install bio-corgi

Warning

Do not try just pip install corgi because that is a different package.

To install the latest version from the repository, you can use this command:

pip install git+https://github.com/rbturnbull/corgi.git

Note

Soon corgi will be able to be installed using conda.

Usage

To make predictions, run the corgi command line tool:

corgi --input <input seq file> --output-csv <output csv file>

The input can be a FASTA file, a GenBank file, or a FASTQ file. This can be GZipped or uncompressed. It can also be a URL.

This will output all the predictions in a CSV file.

For more information about the other options, see the help with:

corgi --help

For help on training a model with corgi, run:

corgi-tools --help

Credits

• Robert Turnbull

• Vinícius Salazar

• Edoardo Tescari

• Heroen Verbruggen

With contributions from:

• Yuhao Tong

• Kamalpreet Singh

• Rafsan Al Mamun

• Diego Aranda Villarreal

Citation details to come.

• Created using torchapp (https://github.com/rbturnbull/torchapp)