A(n incomplete) counterpart of spodgi implemented in Rust.
The functionality implemented is a line-by-line converter from GFA to RDF (turtle), which avoids loading the entire input graph in memory.
git clone --recursive https://github.com/AndreaGuarracino/rs-spodgi
cd rs-spodgi
cargo build --release
./target/release/rs-spodgi -h
gfa2rdf 0.1.0
Andrea Guarracino
GFA to RDF converter
USAGE:
rs-spodgi --gfa <FILE>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-g, --gfa <FILE> GFA input file to convert
./target/release/rs-spodgi -g test/t_small.gfa > t_small.ttl
You can build a docker image locally using the Dockerfile:
git clone --recursive https://github.com/AndreaGuarracino/rs-spodgi
cd rs-spodgi
docker build . --file Dockerfile --tag rs_spodgi_img
and run it with
docker run --rm -it -v ${PWD}/test/:/test rs_spodgi_img rs-spodgi --gfa test/t.gfa