NucBox

Ultra fast chromosome 3D reconstraction.

Install

Install from source:

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

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

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution for nucbox 0.1.1
File	Size	Uploaded
nucbox-0.1.1.tar.gz	20.9 kB	Mar 30, 2024	Details

Table of built distributions (wheels) for nucbox 0.1.1
File	Interpreter	ABI	Platform	Reset
nucbox-0.1.1-py3-none-any.whl 26.7 kB Mar 30, 2024	Python 3	none	any	Details

Total release size: 47.6 kB

Download URL	nucbox-0.1.1.tar.gz
Size	20.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`3b814d534513555ed5df7c306e9b1d800e1c3e7eab4b94a63a863854e46ab180`
BLAKE2b-256 checksum How to use checksums	`285e763f9aaac1d97d452ab091b8e1e11d6cbcffb95dabd5f9a6cdc416401a43`
Upload date	Mar 30, 2024
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/5.0.0 CPython/3.12.2`

Download URL	nucbox-0.1.1-py3-none-any.whl
Size	26.7 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`495c8878ba56dfc15f7b763de3693d33508a34f453af01d0875ff8c90e0a0534`
BLAKE2b-256 checksum How to use checksums	`a74b172756e5f499355acc4c07436c719ad815524bb78cf54bac6bfad7f79cae`
Upload date	Mar 30, 2024
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/5.0.0 CPython/3.12.2`