https://github.com/jervenbolleman/sapfhir-cli

A CLI tool to query GFA1 files with SPARQL
https://github.com/jervenbolleman/sapfhir-cli

Last synced: 19 days ago
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A CLI tool to query GFA1 files with SPARQL

• Host: GitHub
• URL: https://github.com/jervenbolleman/sapfhir-cli
• Owner: JervenBolleman
• License: gpl-3.0
• Created: 2020-12-08T20:30:55.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2024-03-27T20:38:34.000Z (9 months ago)
• Last Synced: 2024-05-18T07:42:15.413Z (8 months ago)
• Language: Java
• Size: 39.1 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# SapFhir-CLI

Join genomic variation graphs with public data or internal medical data e.g. FHIR.

by having a FAIR data access, using W3C sparql as a standard protocol.

This is a command line tool to quickly test the concept.

# Building

You need local checkouts of 

[handlegraph4j](https://github.com/JervenBolleman/handlegraph4j)

[handlegraph4jGFA](https://github.com/JervenBolleman/handlegraph4jGFA)

[handlegraph4jRDF](https://github.com/JervenBolleman/handlegraph4jRDF)

[handlegraph4j-simple](https://github.com/JervenBolleman/handlegraph4j-simple)

[sapfhir](https://github.com/JervenBolleman/sapfhir)

Build them with maven on java 11+

```

for i in handlegraph4j handlegraph4jGFA handlegraph4jRDF handlegraph4j-simple sapfhir

cd $i

    mvn install

cd ..

```

```

mvn package

```

# Run

```

java -jar target/sapfhir-cli-0.2-SNAPSHOT-jar-with-dependencies.jar \

    --gfa ~/git/odgi/test/t.gfa \

    -Xmx12g \

    "PREFIX vg: SELECT ?path WHERE {?path a vg:Path}"

```

# Status

This is a [RDF4j](https://rdf4j.org/) SAIL implementation that can take any handlegraph4j 

implementation and represent it as a [W3C sparql 1.1](https://www.w3.org/TR/sparql11-query/) endpoint. 

It is believed to be functionally complete.