A python port of the deepredeff R-package.
We were finding it difficult to get deepredeff to work in complex environments, and because dependencies were hard-coded it is increasingly difficult to update other software. All of these issues stem from the fact that Deepredeff internally creates abd yses a conda-environment to run a keras model in python. This is fine if you're using the package interactively, but it makes it a pain if you want to run in an existing conda environment. Soooo... why not just run it in python?
That's all we're doing.
THIS IS NOT OUR WORK!!! If you use this code, please cite the original deepredeff paper (https://doi.org/10.1186/s12859-021-04293-3).
This is primarily intended to be used as a command line tool.
deepredeff --outfile predictions.tsv --taxon fungi in.fasta
The default taxon is fungi. If --outfile is not provided we'll write the table to stdout.
If you want to pipe the fastas to the input, use - for the positional argument to indicate stdin.
e.g. cat in.fasta | deepredeff --taxon bacteria - > out.tsv
You can install this from the predector conda channel.
conda install -c predector deepredeff-py
If you'd like to use pip, you can run:
# use of Virtual environments (e.g. venv, conda) is strongly recommended.
# Never install python packages with pip as root user.
pip install git+https://github.com/darcyabjones/deepredeff-py.git