nuc2d

nuc2d is a Python library for parsing, annotating, laying out, and rendering nucleic acid secondary structures.

Installation

pip install nuc2d

Quick start

from nuc2d import draw_svg

dpp_string = "(((..+...)))"

svg = draw_svg(
    dpp_string=dpp_string,
)

svg.saveas("output.svg")

The dpp_string argument should be specified in dot-parens-plus notation.

If you are using Jupyter Notebook or JupyterLab, you can also display the generated SVG directly:

from IPython.display import SVG, display

display(SVG(svg.tostring()))

Sequence annotation

Nucleotide sequences can be provided through the sequences argument.

sequences = ["AUGCA", "UGCCAU"]

svg = draw_svg(
    dpp_string=dpp_string,
    sequences=sequences,
)

Base-pair probability visualization

Base-pair probabilities can be visualized by providing a symmetric base-pair probability matrix through the probs argument.

# Base-pair probability matrix from a structure prediction tool.
# probs[i][j] is the probability of nucleotides i and j forming a base pair.
# The diagonal probs[i][i] represents the probability that nucleotide i is unpaired.
probs = ...

svg = draw_svg(
    dpp_string=dpp_string,
    probs=probs,
)

Output

nuc2d renders structures as SVG, making the resulting figures suitable for further editing and use in presentations and publications.

License

This project is licensed under the MIT License.