rs-spodgi

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.

How to build

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

How to run

./target/release/rs-spodgi -g test/t_small.gfa > t_small.ttl

docker

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