schicluster.cool.utilities

Contents

`schicluster.cool.utilities`#

Module Contents#

get_chrom_offsets(bins_df)[source]#

write_coo(path, matrix, chunk_size=5000000)[source]#: Write chromosome contacts as chunked pixel df (cooler input)

chrom_iterator(input_dir, chrom_order, chrom_offset, chrom_wildcard='{chrom}.hdf', csr=False)[source]#

aggregate_chromosomes(chrom_size_path, resolution, input_dir, output_path, chrom_wildcard='{chrom}.hdf', csr=False)[source]#

cell_chunk(cell_url, chrom_sizes, chunk=50000000)[source]#

aggregate_cells(output_path, cell_dir, chrom_size_path, resolution)[source]#