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CadnanoModifier

A python3 script for modification of DNA Origami nano structure designed with caDNAno.

Dependencies

  • Python >= 3.7
    • click >= 7.0

Installation

git clone https://github.com/elija-feigl/cadnanoModifier
cd cadnano_modifier
python setup.py install

Usage

Implemented with click, the script provides three different commands:

  • modify: manipulate cadnano design files
  • merge: merge two cadnano design files
  • fix: fix faulty cadnano design files

all are called with:

  cadnanoModifier COMMAND

modify

manipulate cadnano design files for DNA Origami

cadnanoModifier modify [OPTIONS] CADNANO
  CADNANO is the name of the design file [.json]

Options:
  --shift-row INTEGER  shift helices by N rows. affected by selection
  --shift-col INTEGER  shift helices by N columns. affected by selection
  --shift-pos INTEGER  shift helices by N base positions. affected by
                       selection

  --fix-legacy         attempt to fix legacy design for version < 0.7
  --remove-skips       remove all skips. affected by selection
  --remove-loops       remove all loops. affected by selection
  --helix-subset TEXT  subset of helices selected by their number. format:
                       "[1,2,3]"

  --help               Show this message and exit.

merge

merge two cadnano design files for DNA Origami

cadnanoModifier merge [OPTIONS] CADNANO MERGE
  CADNANO is the name of the first design file [.json]
  MERGE is the name of the second design file [.json]

Options:
  --help  Show this message and exit.

fix

fix faulty cadnano design files for DNA Origami for: legacy cadnano (< 2.) and json_modifier06.py

cadnanoModifier fix [OPTIONS] CADNANO
  CADNANO is the name of the design file [.json]

Options:
  --help  Show this message and exit.