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        "description": "\nphenotrex\n=========\n\n\n.. image:: https://badge.fury.io/py/phenotrex.svg\n   :target: https://pypi.python.org/pypi/phenotrex\n   :alt: PyPI\n\n.. image:: https://codecov.io/gh/univieCUBE/phenotrex/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/univieCUBE/phenotrex\n   :alt: Codecov\n\n.. image:: https://img.shields.io/lgtm/grade/python/g/LokiLuciferase/phenotrex.svg?logo=lgtm&logoWidth=18\n   :target: https://lgtm.com/projects/g/LokiLuciferase/phenotrex/context:python\n   :alt: Code Quality\n\n.. image:: https://travis-ci.com/univieCUBE/phenotrex.svg?branch=master\n   :target: https://travis-ci.com/univieCUBE/phenotrex\n   :alt: Travis CI\n\n.. image:: https://ci.appveyor.com/api/projects/status/iursmhw1wocfgpua?svg=true\n   :target: https://ci.appveyor.com/project/VarIr/phenotrex\n   :alt: AppVeyor CI\n\n.. image:: https://readthedocs.org/projects/phenotrex/badge/?version=latest\n   :target: https://phenotrex.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n\n\nEnd-to-end Microbial Phenotypic Trait Prediction.\n\nInstallation\n------------\n\n.. code-block::\n\n    $ pip install phenotrex[fasta]\n\nUsage\n-----\n\nPhenotrex is a component of the `PhenDB`_ web server, which performs phenotypic trait prediction on\nuser-uploaded metagenomic bins. To try out phenotrex with PhenDB's pre-trained and curated set of\ntrait models, genomes may thus simply be `submitted to PhenDB`_.\n\nBasic Usage\n~~~~~~~~~~~\nTo use a trained phenotrex model ``MY_TRAIT.pkl`` for prediction of a phenotypic trait with a\ngiven genome ``genome.fna``:\n\n.. code-block::\n\n    $ phenotrex predict --classifier MY_TRAIT.pkl genome.fna > predictions.tsv\n\n\nThis yields a tabular file containing a prediction regarding the presence of the trait (YES or NO),\nas well as a confidence value the model ascribes to this prediction, ranging from 0.5 to 1.0.\n\nAdvanced Usage\n~~~~~~~~~~~~~~\nFor training, evaluation and explanation of phenotrex models on user data, please refer to the\nfull usage tutorial `here`_.\n\n.. _PhenDB: https://www.phendb.org/\n.. _submitted to PhenDB: https://phen.csb.univie.ac.at/phendb/\n.. _here: https://phenotrex.readthedocs.io/en/latest/usage.html\n\n\n=======\nHistory\n=======\n\n\n\n",
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