RDF::VCF

This is an RDF.rb reader plugin for Variant Call Format (VCF) files, widely used in bioinformatics.

This project grew out of BioHackathon 2014 work by Raoul J.P. Bonnal and Francesco Strozzi, and was further developed during BioHackathon 2015.

Note: at present, the project requires JRuby 9.0 (or newer) due to the Java-based VCF parser. We hope to eventually substitute Bio-vcf instead.

Features

  • Implements an RDF.rb reader for VCF and BCF files, supporting also bgzipped files.
  • Includes a CLI tool called vcf2rdf to transform VCF files into RDF.

Examples

Reading VCF Files

The gem can be used like any other RDF.rb reader plugin:

require 'rdf/vcf'

RDF::VCF::Reader.open('Homo_sapiens.vcf.gz') do |reader|
  reader.each_statement do |statement|
    p statement
  end
end

Command-Line Interface (CLI)

The gem includes a CLI tool called vcf2rdf which transforms VCF files into RDF (currently, N-Triples):

vcf2rdf your_vcf_file.vcf.gz

files can be in plain text or bgzip compressed data

Notes

Please create the tabix index by youself, in future this gem will create the index automatically.

Dependencies

Mailing List

Authors

License

This is free and unencumbered public domain software. For more information, see http://unlicense.org/ or the accompanying UNLICENSE file.