Python scripting library for generating designs readable by scadnano.
Project description
scadnano-python-package
The scadnano Python module is a library for describing synthetic DNA nanostructures (e.g., DNA origami).
If you find scadnano useful in a scientific project, please cite its associated paper:
Overview
This module is used to write Python scripts outputting .dna
files readable by scadnano, a web application useful for displaying and manually editing these structures. The purpose of this module is to help automate some of the task of creating DNA designs, as well as making large-scale changes to them that are easier to describe programmatically than to do by hand in scadnano.
Reporting issues
Please report issues in the web interface at the scadnano web interface GitHub repository, and report issues in the Python scripting library at the scadnano Python package GitHub repository.
Installation
The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow this link to install it.
Once Python is installed, there are two ways you can install the scadnano Python package:
-
pip
Use pip to install the package by executing the following at the command line:
pip install scadnano
If your Python installation does not already have pip installed, you may have to install it. Executing this Python script should work; see also https://docs.python.org/3/installing/index.html or https://www.liquidweb.com/kb/install-pip-windows/.
-
download
As a simple alternative, you can download and place the following file(s) (located in the scadnano/ subfolder) in your PYTHONPATH (e.g., in the same directory as the scripts you are running):
- required: scadnano.py
- optional: modifications.py; This contains some common DNA modifications such as biotin and Cy3.
- optional: origami_rectangle.py; This can help create origami rectangles, but it is not necessary to use scadnano.
Unfortunately, the scadnano package depends on the Python package xlwt, so xlwt must be installed. To install, type
pip install xlwt
at the command line. If this does not work, then you can comment out the lineimport xlwt
inscadnano.py
, but then you will not be able to call the methodDNADesign.write_idt_plate_excel_file()
to export an Excel file with DNA sequences.
Documentation
Online documentation of the package API is located here: https://scadnano-python-package.readthedocs.io
Tutorial
A tutorial shows how to create a "standard" 24-helix DNA origami rectangle using the scripting library.
Examples
Several example scripts are located in the examples/ subfolder. Their output is contained in the examples/output_designs/ subfolder.
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