nucbox 0.1.1

Ultra fast chromosome 3D reconstraction.

NucBox

Ultra fast chromosome 3D reconstraction.

Install

Install from source:

$ git clone https://github.com/Nanguage/NucBox.git
$ cd NucBox
$ pip install -e .

Usage

Reconstruct genome using Nuc Dynamics algorithm:

$ python -m nucbox.simu.nucdyn --arch=cuda ./cell1.pairs.gz ./out1.csv --use-grid=True --scale=0.01

Visualize the reconstructed genome:

$ python -m nucbox.gui.browser ./out1.csv

Convert the particles csv file to pdb file(for visualization in pymol or vmd):

$ python -m nucbox.utils.io particles_to_pdb ./out1.csv ./out1.pdb --split-by-chrom=True