.. Autogenerated by build.py

********
Main CLI
********

These are the workhorse programs of BPReveal.
Each one accepts a single argument, which is the name of a JSON file. For example,

.. highlight:: none

::

   trainSoloModel trainingConfig.json

The JSON files are actually a superset of JSON that supports limited evaluation
of expressions. Details can be found in :doc:`bnf` and
:py:mod:`interpreter<bpreveal.internal.interpreter>`.


..
    Copyright 2022-2025 Charles McAnany. This file is part of BPReveal. BPReveal is free software: You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version. BPReveal is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with BPReveal. If not, see <https://www.gnu.org/licenses/>.

.. toctree::
    :maxdepth: 2

    interpretFlat
    interpretPisa
    makePisaFigure
    makePredictions
    motifScan
    motifSeqletCutoffs
    prepareBed
    prepareTrainingData
    trainCombinedModel
    trainSoloModel
    trainTransformationModel