DbVar::RDF

Usage

Input: dbVar GVF (Genome Variation Format)
- GRCh37 ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh37/gvf/GRCh37.variant_call.gvf.gz ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh37/gvf/GRCh37.variant_region.gvf.gz
- GRCh38 ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh38/gvf/GRCh38.variant_call.gvf.gz ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh38/gvf/GRCh38.variant_region.gvf.gz
Output: Turtle formatted RDF

With docker

$ docker build --tag dbvar-rdf .
$ zcat GRCh38.variant_call.gvf.gz | docker run --rm -i dbvar-rdf convert variant_call 2> dbVar.variant_call.GRCh38.log | gzip -c > dbVar.variant_call.GRCh38.ttl.gz
$ zcat GRCh38.variant_region.gvf.gz | docker run --rm -i dbvar-rdf convert variant_region 2> dbVar.variant_region.GRCh38.log | gzip -c > dbVar.variant_region.GRCh38.ttl.gz

In your code

require 'dbvar/rdf'

DbVar::RDF::Writer::Turtle.new do |writer| # to standard output
  DbVar::RDF::Reader::GVF.new.each do |data| # from standard input
    writer << data.to_rdf(DbVar::RDF::Models::VariantCall) # or DbVar::RDF::Models::VariantRegion
  end
end

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/med2rdf/dbvar-rdf. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.

License

The gem is available as open source under the terms of the MIT License.

Code of Conduct

Everyone interacting in the DbVar::RDF project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the code of conduct.