BPReveal
4.3.0
  • Overview
  • Main CLI
    • interpretFlat
    • interpretPisa
    • makePisaFigure
    • makePredictions
    • motifScan
    • motifSeqletCutoffs
    • prepareBed
    • prepareTrainingData
    • trainCombinedModel
    • trainSoloModel
    • trainTransformationModel
  • Utility CLI
  • API
  • Tools Utility CLI
  • Tools Main CLI
  • Tools API
  • Internal
  • Development
BPReveal
  • Main CLI
  • View page source

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,

trainSoloModel trainingConfig.json

The JSON files are actually a superset of JSON that supports limited evaluation of expressions. Details can be found in BNF Grammars and interpreter.

  • interpretFlat
    • BNF
    • Parameter Notes
    • Output Specification
    • Additional Information
    • History
    • API
    • main()
    • Schema
  • interpretPisa
    • BNF
    • Parameter Notes
    • Output Specification
    • HISTORY
    • API
    • main()
    • Schema
  • makePisaFigure
    • BNF
    • Parameter notes
    • main()
    • Schema
  • makePredictions
    • BNF
    • Parameter Notes
    • Output Specification
    • API
    • getReader()
    • getWriter()
    • main()
    • Schema
  • motifScan
    • Configuration Json
    • Quantile json
    • Output Specification
    • API
    • main()
    • Schema
  • motifSeqletCutoffs
    • BNF
    • Parameter Notes
    • Output Specification
    • API
    • main()
    • Schema
  • prepareBed
    • BNF
    • Parameter Notes
    • Additional information
    • History
    • API
    • loadRegionsByChrom()
    • loadRegionsByBed()
    • loadRegionsByRegex()
    • loadRegions()
    • removeOverlaps()
    • filterByMaxCounts()
    • filterByMinCounts()
    • validateRegions()
    • rewriteOldBigwigsFormat()
    • prepareBeds()
    • Schema
  • prepareTrainingData
    • BNF
    • Parameter Notes
    • Output specification
    • Additional information
    • History
    • API
    • revcompSeq()
    • getSequences()
    • getHead()
    • writeH5()
    • Schema
  • trainCombinedModel
    • BNF
    • Parameter Notes
    • HISTORY
    • API
    • main()
    • Schema
  • trainSoloModel
    • BNF
    • Parameter Notes
    • Additional information
    • API
    • main()
    • Schema
  • trainTransformationModel
    • BNF
    • Parameter Notes
    • History
    • API
    • main()
    • Schema
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© Copyright 2024, Charles McAnany. License: GPLv2+: GNU GPL version 2 or later <https://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law..

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