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
1 maintainer
Metadata
1 maintainer
Release files for nucbox 0.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| nucbox-0.1.0.tar.gz | 20.3 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| nucbox-0.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 46.5 kB
Release files / nucbox-0.1.0.tar.gz
| Download URL | nucbox-0.1.0.tar.gz |
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| Size | 20.3 kB |
| Tags | Source |
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Release files / nucbox-0.1.0-py3-none-any.whl
| Download URL | nucbox-0.1.0-py3-none-any.whl |
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| Size | 26.1 kB |
| Tags | Python 3 |
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