dbSNP::RDF

Usage

• Input: dbSNP VCF (Variant Call Format)

  • GRCh37 ftp://ftp.ncbi.nlm.nih.gov/snp/.redesign/latest_release/VCF/GCF_000001405.25.bgz
  • GRCh38 ftp://ftp.ncbi.nlm.nih.gov/snp/.redesign/latest_release/VCF/GCF_000001405.33.bgz

• Output: Turtle formatted RDF

With docker

$ docker build --tag dbsnp-rdf .
$ zcat GCF_000001405.33.vcf.bgz | docker run --rm -i dbsnp-rdf dbsnp-rdf convert 2> dbSNP.GRCh38.ttl.log | gzip -c > dbSNP.GRCh38.ttl.gz

On your system

See Prerequisites before running the code.

$ git clone https://github.com/med2rdf/dbsnp.git
$ cd dbsnp
$ bundle install
$ zcat GCF_000001405.33.vcf.bgz | bundle exec dbsnp-rdf convert 2> dbSNP.GRCh38.ttl.log | gzip -c > dbSNP.GRCh38.ttl.gz 

or in your ruby code

require 'dbsnp/rdf'

DbSNP::RDF::Writer::Turtle.new do |writer| # to standard output
  DbSNP::RDF::Reader::VCF.new.each do |data| # from standard input
    writer << data
  end
end

Prerequisites

• ruby 2.5.0+
• (Optional) raptor 2.0+

Note: In macOS, the raptor library installed with Homebrew is NOT applicable for now. Please build the library from source following the below instruction.

Install raptor (Optional)

apt

# apt-get update && apt-get install libraptor2

yum

# yum install raptor2

from source

$ wget http://download.librdf.org/source/raptor2-2.0.15.tar.gz
$ tar xvf raptor2-2.0.15.tar.gz
$ cd raptor2-2.0.15
$ ./configure --disable-debug --disable-dependency-tracking
$ make
(switch to super user if needed)
# make install

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/med2rdf/dbsnp-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 Dbsnp::Rdf project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the code of conduct.