@dugla/swc

@dugla/swc is CLI (command line tool) to support the SpaceWalk project. Use this tool to convert a legacy ensemble or point-cloud file to the file format supported by SpaceWalk.

Requirements

• Node >= v10.13.0
• NPM >= v6.9.0

Installation

npm install -g @dugla/swc

Usage

cd to the location of the file to be converted

If a point cloud file is being converted:

swc --pointcloud filename --output filename [--dir output-directory] --chromosome name --genome-assembly assembly

If an ensemble file is being converted:

swc --ensemble filename --output filename [--dir output-directory] --chromosome name --genome-assembly assembly

Options have the following aliases. Either may be used:

--pointcloud, -p
--ensemble, -e
--output, -o
--dir, -d
--chromosome, -c
--genome-assembly, -g

Example Point Cloud File

snippet ...

genome_start,genome_end,size_kb,x,y,z
7400000,8680000,1280,11233.5,6388.48,682.982
7400000,8680000,1280,10894.7,6438.6,735.657
7400000,8680000,1280,11195.4,6304.68,836.743
...

Example Ensemble File

snippet ...

The center positions (in nm) in each chromosome of the 30kb segments comprising region chr21:34.6Mb-37.1Mb in HCT116 cells after cell division in auxin treatment (EdU+ and Geminin-)
Chromosome index,Segment index,Z,X,Y
1,1,7289,76301,99573
1,2,6939,76531,99485
1,3,7361,76513,99361
...

The default output directory is the current directory. Include --dir output-directory to specify a different directory.

License

MIT

Author

• Douglass Turner [email protected]