Metadata-Version: 2.1
Name: nucbox
Version: 0.1.1
Summary: Ultra fast chromosome 3D reconstraction.
Author-email: Weize Xu <vet.xwz@gmail.com>
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: taichi >=1.7.0
Requires-Dist: fire >=0.6.0
Requires-Dist: pandas >=2.0.3
Requires-Dist: vispy >=0.14.2
Requires-Dist: PyQt5 >=5.15.2
Requires-Dist: qdarkgraystyle >=1.0.2
Requires-Dist: h5py >=3.10.0
Requires-Dist: cooler >=0.9.3
Requires-Dist: scikit-learn >=1.3.2
Requires-Dist: matplotlib >=3.7.5

# NucBox

Ultra fast chromosome 3D reconstraction.

## Install

Install from source:

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

## Usage

Reconstruct genome using Nuc Dynamics algorithm:

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


Visualize the reconstructed genome:

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

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

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