https://github.com/andreaguarracino/rs-spodgi

Line-by-line converter from GFA to RDF (turtle)
https://github.com/andreaguarracino/rs-spodgi

bioinformatics gfa variationgraphs

Last synced: about 1 month ago
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Line-by-line converter from GFA to RDF (turtle)

• Host: GitHub
• URL: https://github.com/andreaguarracino/rs-spodgi
• Owner: AndreaGuarracino
• License: mit
• Created: 2020-08-29T21:30:52.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-11-16T16:31:16.000Z (about 4 years ago)
• Last Synced: 2023-08-04T01:39:01.229Z (over 1 year ago)
• Topics: bioinformatics, gfa, variationgraphs
• Language: Rust
• Homepage:
• Size: 20.5 KB
• Stars: 3
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# rs-spodgi

A(n incomplete) counterpart of [spodgi](https://github.com/pangenome/spodgi) implemented in Rust.

The functionality implemented is a line-by-line converter from [GFA](https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md) to [RDF (turtle)](https://www.w3.org/TR/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 

FLAGS:

    -h, --help       Prints help information

    -V, --version    Prints version information

OPTIONS:

    -g, --gfa     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

```