💥 spars: disk-based sparse matrix tools

spars is a memory-efficient tool for working with sparse matrices in the Matrix Market format on-disk.

Usage

Subset a matrix on-disk:

spars subset -i <matrix.mtx> --rows <row_index.txt> --cols <col_index.txt> -o <matrix_subset.mtx>

Compute matrix statistics (nonzero count, sum, mean, variance, standard deviation, min, max) for each row and column:

spars stats -i <matrix.mtx> -o <filename>

Installation

From cargo

cargo install spars

From GitHub

To compile, clone the git repo and run cargo install:

git clone [email protected]:stuart-lab/spars.git
cd spars; cargo install --path .

Precompiled binaries are also available in the release

Man Pages

The tool includes man pages (documentation) that can be generated and installed after installation:

# generate manpages
spars generate-manpages --outdir /tmp/spars-man

# install man pages (requires sudo)
# note that this path may be different on different systems
sudo cp /tmp/spars-man/*.1 /usr/local/share/man/man1/

# on linux, update the manual page cache by running mandb
sudo mandb

Once installed, you can view the documentation with:

man spars         # main command documentation
man spars-stats   # stats subcommand
man spars-subset  # subset subcommand

Alternatively, you can view the man pages directly without installation:

man /tmp/spars-man/spars.1