Metadata-Version: 2.1
Name: phenotrex
Version: 0.6.0
Summary: Microbial Phenotype Prediction
Home-page: https://github.com/univieCUBE/phenotrex
Author: Lukas Lüftinger
Author-email: lukas.lueftinger@outlook.com
License: MIT license
Keywords: phenotrex
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/x-rst
Requires-Dist: scikit-learn (<=0.23.2,>=0.22)
Requires-Dist: numpy (>=1.15)
Requires-Dist: matplotlib (>=3.1.3)
Requires-Dist: xgboost (<=1.3,>=1.0.1)
Requires-Dist: shap (<0.36,>=0.34)
Requires-Dist: click (>=7.0)
Requires-Dist: biopython (<=1.77,>=1.74)
Requires-Dist: tqdm (>=4.26.0)
Requires-Dist: pandas (>=1.0)
Provides-Extra: fasta
Requires-Dist: deepnog (==1.2.2) ; extra == 'fasta'
Requires-Dist: ete3 ; extra == 'fasta'


phenotrex
=========


.. image:: https://badge.fury.io/py/phenotrex.svg
   :target: https://pypi.python.org/pypi/phenotrex
   :alt: PyPI

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   :target: https://codecov.io/gh/univieCUBE/phenotrex
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   :alt: Code Quality

.. image:: https://travis-ci.com/univieCUBE/phenotrex.svg?branch=master
   :target: https://travis-ci.com/univieCUBE/phenotrex
   :alt: Travis CI

.. image:: https://ci.appveyor.com/api/projects/status/iursmhw1wocfgpua?svg=true
   :target: https://ci.appveyor.com/project/VarIr/phenotrex
   :alt: AppVeyor CI

.. image:: https://readthedocs.org/projects/phenotrex/badge/?version=latest
   :target: https://phenotrex.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status


End-to-end Microbial Phenotypic Trait Prediction.

Installation
------------

.. code-block::

    $ 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``:

.. code-block::

    $ 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`_.

.. _PhenDB: https://www.phendb.org/
.. _submitted to PhenDB: https://phen.csb.univie.ac.at/phendb/
.. _here: https://phenotrex.readthedocs.io/en/latest/usage.html


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