keller-mark/higlass-zarr-converters

Command line scripts to convert files to formats supported by a Zarr data fetcher plugin for HiGlass

higlass-zarr-converters

Setup

conda env create -f environment.yml
conda activate higlass-zarr-converters

Converters

chromsizes-tsv to zarr

python src/chromsizes_tsv_to_zarr.py --help
python src/chromsizes_tsv_to_zarr.py \
    -i data/chromsizes/hg38.tsv \
    -o data/chromsizes/hg38.zarr

chromsizes-csv to zarr

python src/chromsizes_csv_to_zarr.py --help
python src/chromsizes_csv_to_zarr.py \
    -i data/chromsizes/hg38.csv \
    -o data/chromsizes/hg38.zarr

chromsizes-negspy to zarr

Browse available assemblies here.

python src/chromsizes_negspy_to_zarr.py --help
python src/chromsizes_negspy_to_zarr.py \
    -a hg38 \
    -o data/chromsizes/hg38.zarr