phenotrex

End-to-end Microbial Phenotypic Trait Prediction.

Installation

$ pip install phenotrex[fasta]

Usage

Phenotrex is a component of the PhenDB web server, which performs phenotypic trait prediction on user-uploaded metagenomic bins. To try out phenotrex with PhenDB’s pre-trained and curated set of trait models, genomes may thus simply be submitted to PhenDB.

Basic Usage

To use a trained phenotrex model MY_TRAIT.pkl for prediction of a phenotypic trait with a given genome genome.fna:

$ phenotrex predict --classifier MY_TRAIT.pkl genome.fna > predictions.tsv

This yields a tabular file containing a prediction regarding the presence of the trait (YES or NO), as well as a confidence value the model ascribes to this prediction, ranging from 0.5 to 1.0.

Advanced Usage

For training, evaluation and explanation of phenotrex models on user data, please refer to the full usage tutorial here.