rdf-vcf 0.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/AUTHORS +3 -0
- data/CREDITS +0 -0
- data/README +79 -0
- data/UNLICENSE +24 -0
- data/VERSION +1 -0
- data/bin/vcf2rdf +23 -0
- data/lib/rdf-vcf.rb +1 -0
- data/lib/rdf/vcf.rb +3 -0
- data/lib/rdf/vcf/jar/bzip2.jar +0 -0
- data/lib/rdf/vcf/jar/htsjdk-1.139.jar +0 -0
- data/lib/rdf/vcf/reader.rb +146 -0
- data/lib/rdf/vcf/record.rb +168 -0
- data/lib/rdf/vcf/version.rb +19 -0
- metadata +119 -0
checksums.yaml
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SHA1:
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metadata.gz: 0308e08c49b3ab4dafd99a2c4d7e1eb6f290f5d8
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data.tar.gz: 62ab5fbfbb17000b1e77ae49347cc08a43466fbd
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SHA512:
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metadata.gz: 6c91ef56c3884e0308a5ecf9c816a531eabb2d79fb18b0ec0e6d64a1fafd2dbfb2088d83d39ba368b04ab8bbd091cb2ec4a41459e807cc6977d5b2c8fad155dc
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data.tar.gz: 4b7ceefbdcf83a81f1aad75410c7062dd37acbecc3d6d2207faee57574908683024ed721db674b5fba882ab675f3acc8d1399564d48a7352f6b7b36b5b97920d
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data/CREDITS
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File without changes
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data/README
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RDF::VCF
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========
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This is an [RDF.rb](https://github.com/ruby-rdf/rdf) reader plugin for
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Variant Call Format (VCF) files, widely used in bioinformatics.
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This project grew out of [BioHackathon 2014](http://2014.biohackathon.org/)
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[work](https://github.com/dbcls/bh14/wiki/On-The-Fly-RDF-converter) by
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[Raoul J.P. Bonnal](https://github.com/helios) and [Francesco
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Strozzi](https://github.com/fstrozzi), and was further developed during
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[BioHackathon 2015](http://2015.biohackathon.org/).
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Note: at present, the project requires JRuby 9.0 (or newer) due to the
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Java-based VCF parser. We hope to eventually substitute the pure-Ruby
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[Bio-vcf](https://github.com/pjotrp/bioruby-vcf) instead.
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Features
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========
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* Implements an RDF.rb reader for VCF and BCF files, supporting also
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bgzipped files.
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* Includes a CLI tool called `vcf2rdf` to transform VCF files into RDF.
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Examples
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========
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Reading VCF Files
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-----------------
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The gem can be used like any other RDF.rb reader plugin:
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require 'rdf/vcf'
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RDF::VCF::Reader.open('Homo_sapiens.vcf.gz') do |reader|
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reader.each_statement do |statement|
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p statement
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end
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end
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Command-Line Interface (CLI)
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----------------------------
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The gem includes a CLI tool called `vcf2rdf` which transforms VCF files into
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RDF (currently, N-Triples):
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vcf2rdf your_vcf_file.vcf.gz
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Input files can be either plain text VCF or else compressed by `bgzip`, as
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above.
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Notes
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-----
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Please create the [`tabix`](http://www.htslib.org/doc/tabix.html) index by
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youself. In the future, this gem will create the index automatically.
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Dependencies
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============
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* [JRuby](http://jruby.org) (>= 9.0)
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* [RDF.rb](https://github.com/ruby-rdf/rdf) (>= 1.1)
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Mailing List
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============
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* http://lists.w3.org/Archives/Public/public-rdf-ruby/
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Authors
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=======
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* [Arto Bendiken](https://github.com/bendiken)
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* [Raoul J.P. Bonnal](https://github.com/helios)
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* [Francesco Strozzi](https://github.com/fstrozzi)
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License
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=======
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This is free and unencumbered public domain software. For more information,
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see <http://unlicense.org/> or the accompanying {file:UNLICENSE} file.
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This is free and unencumbered software released into the public domain.
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Anyone is free to copy, modify, publish, use, compile, sell, or
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distribute this software, either in source code form or as a compiled
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binary, for any purpose, commercial or non-commercial, and by any
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means.
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In jurisdictions that recognize copyright laws, the author or authors
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of this software dedicate any and all copyright interest in the
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software to the public domain. We make this dedication for the benefit
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of the public at large and to the detriment of our heirs and
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successors. We intend this dedication to be an overt act of
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relinquishment in perpetuity of all present and future rights to this
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software under copyright law.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
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OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
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ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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OTHER DEALINGS IN THE SOFTWARE.
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For more information, please refer to <http://unlicense.org/>
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data/VERSION
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0.1.2
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data/bin/vcf2rdf
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#!/usr/bin/env jruby
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$:.unshift(File.expand_path('../lib', __dir__))
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require 'rdf/vcf'
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if ARGV.empty? || ARGV.include?('--help') || ARGV.include?('-h')
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abort "usage: #{$0} file.vcf[.gz]..."
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end
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ARGV.each do |pathname|
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# TODO: support an --output=MIME option:
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writer = RDF::Writer.for(:nquads).new($stdout)
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RDF::VCF::Reader.open(pathname) do |reader|
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reader.each_statement do |statement|
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begin
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writer << statement
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rescue => error
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# @see https://github.com/ruby-rdf/rdf/issues/210
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warn error # skip statements that cannot be serialized
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end
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end
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end
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end
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data/lib/rdf-vcf.rb
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require 'rdf/vcf'
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require 'java' # requires JRuby
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require 'rdf/vcf/jar/htsjdk-1.139.jar'
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require 'rdf/vcf/jar/bzip2.jar'
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require 'digest/md5'
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require 'rdf/vcf/record'
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module RDF; module VCF
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##
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# VCF file reader.
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#
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# This is a user-friendly wrapper for the HTSJDK implementation.
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#
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# @see https://github.com/samtools/htsjdk
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# @see https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/vcf/VCFFileReader.html
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class Reader
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java_import 'htsjdk.variant.vcf.VCFFileReader'
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REF_BASE_URI = 'http://rdf.ebi.ac.uk/resource/ensembl/%s/chromosome:%s:%s'.freeze
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def ref_base_uri #
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@file_iri ||= RDF::URI(REF_BASE_URI % [reference_md5, file_date || "" , source || ""])
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end
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##
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# @param [#to_s] pathname
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def self.open(pathname, &block)
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reader = self.new(pathname)
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block.call(reader)
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ensure
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#reader.close
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end
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##
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# @param [#to_s] pathname
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def initialize(pathname)
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pathname = pathname.to_s
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@vcf_file = java.io.File.new(pathname)
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@tbi_file = java.io.File.new("#{pathname}.tbi") rescue nil
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@reader = VCFFileReader.new(@vcf_file, @tbi_file, false)
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end
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##
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# @return [Boolean]
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def closed?
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@reader.nil?
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end
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##
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# @return [void]
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def close
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@reader.close if @reader
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ensure
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@reader, @vcf_file, @tbi_file = nil, nil, nil
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end
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##
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# @yield [statement]
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# @yieldparam [RDF::Statement] statement
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# @yieldreturn [void]
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# @return [void]
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def each_statement(&block)
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self.each_record do |record|
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record.to_rdf.each(&block)
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end
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end
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##
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# @yield [record]
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# @yieldparam [Record] record
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# @yieldreturn [void]
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# @return [void]
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def each_record(&block)
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return unless @reader
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@reader.iterator.each do |variant_context| # VariantContext
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record = Record.new(variant_context, self)
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block.call(record)
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end
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end
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##
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# @param [String] chromosome
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# @param [Integer] start_pos
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# @param [Integer] end_pos
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# @yield [record]
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# @yieldparam [Record] record
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# @yieldreturn [void]
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# @return [void]
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def find_records(chromosome: nil, start_pos: nil, end_pos: nil, &block)
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return unless @reader
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start_pos ||= 0
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end_pos ||= java.lang.Integer::MAX_VALUE
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@reader.query(chromosome, start_pos, end_pos).each do |variant_context| # VariantContext
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record = Record.new(variant_context, self)
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block.call(record)
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end
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end
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##
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# @param [Integer] pos
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# @return [Boolean]
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def has_position?(pos)
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true # TODO
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end
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##
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# @return [String]
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def reference()
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@reference ||= @reader.getFileHeader().getMetaDataLine("reference").getKey rescue nil
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end
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def reference_md5
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::Digest::MD5.hexdigest(reference|| "")
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end
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##
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# @return [String]
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def file_date
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@file_date ||= @reader.getFileHeader().getMetaDataLine("fileDate").getKey rescue nil
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end
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##
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# @return [String]
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def source
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@source ||= @reader.getFileHeader().getMetaDataLine("source").getKey rescue nil
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end
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end # Reader
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end; end # RDF::VCF
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if $0 == __FILE__
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VCF::Reader.open('Homo_sapiens.vcf.gz') do |file|
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p file
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file.find_records(chromosome: "Y") do |record|
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#file.each_record do |record|
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p record
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#record.to_rdf.each do |statement|
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# p statement
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#end
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end
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end
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end
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require 'java' # requires JRuby
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require 'rdf/vcf/jar/htsjdk-1.139.jar'
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require 'rdf/vcf/jar/bzip2.jar'
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require 'digest/md5'
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require 'rdf'
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module RDF; module VCF
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##
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# VCF file record.
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#
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# This is a user-friendly wrapper for the HTSJDK implementation.
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#
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# @see https://github.com/samtools/htsjdk
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# @see https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/variantcontext/VariantContext.html
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class Record
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include RDF
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java_import 'htsjdk.variant.variantcontext.VariantContext'
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FALDO = RDF::Vocabulary.new("http://biohackathon.org/resource/faldo#")
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VAR_BASE_URI = 'http://rdf.ebi.ac.uk/terms/ensemblvariation/%s'.freeze
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##
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# @param [VariantContext] variant_context
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def initialize(variant_context, reader)
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@vcf = variant_context
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@reader = reader
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end
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##
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# @return [String]
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def id
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@id ||= case (id = @vcf.getID)
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when '.'
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label = "%s:%s:%s-%s" % ['', @vcf.getChr, @vcf.getStart, @vcf.getEnd] # TODO: species
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::Digest::MD5.hexdigest(label)
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else id
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end
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end
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##
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# @return [String]
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def uri
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@uri ||= VAR_BASE_URI % self.id
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end
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##
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# @return [String]
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def chromosome
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@vcf.getChr
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end
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def start
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@vcf.getStart
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end
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def stop
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@vcf.getEnd
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end
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##
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# @return [Hash{String => String}]
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def attributes
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@vcf.getAttributes
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end
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##
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# @return [String]
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def reference
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@reader.reference
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end
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##
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# @return [String]
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def file_date
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@reader.file_date
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78
|
+
end
|
79
|
+
|
80
|
+
##
|
81
|
+
# @return [String]
|
82
|
+
def source
|
83
|
+
@reader.source
|
84
|
+
end
|
85
|
+
|
86
|
+
##
|
87
|
+
# @return [URI]
|
88
|
+
def ref_base_uri
|
89
|
+
@reader.ref_base_uri
|
90
|
+
end
|
91
|
+
|
92
|
+
|
93
|
+
def get_alleles(&block)
|
94
|
+
@vcf.getAlleles.each do |allele|
|
95
|
+
block.call(allele)
|
96
|
+
end
|
97
|
+
end
|
98
|
+
|
99
|
+
def get_alternate_alleles(&block)
|
100
|
+
@vcf.getAlternateAlleles.each do |allele|
|
101
|
+
block.call(allele)
|
102
|
+
end
|
103
|
+
end
|
104
|
+
##
|
105
|
+
# @return [String]
|
106
|
+
def get_reference_allele
|
107
|
+
@vcf.getReference.getBaseString
|
108
|
+
end
|
109
|
+
|
110
|
+
##
|
111
|
+
# @return [String]
|
112
|
+
# def get_alternate_allele
|
113
|
+
# @vcf.getAlternateAlleles.first.getBaseString
|
114
|
+
# end
|
115
|
+
|
116
|
+
##
|
117
|
+
# @return [Double]
|
118
|
+
def get_phred_scaled_qual
|
119
|
+
@vcf.getPhredScaledQual
|
120
|
+
end
|
121
|
+
|
122
|
+
##
|
123
|
+
# @return [RDF::Graph]
|
124
|
+
def to_rdf
|
125
|
+
var_uri = RDF::URI(self.uri)
|
126
|
+
RDF::Graph.new do |graph|
|
127
|
+
graph << [var_uri, RDF::DC.identifier, self.id]
|
128
|
+
graph << [var_uri, RDF::RDFS.label, self.id]
|
129
|
+
graph << [self.ref_base_uri,DC.identifier,self.id]
|
130
|
+
faldoRegion = ref_base_uri+":#{self.start}-#{self.stop}:1"
|
131
|
+
graph << [var_uri,FALDO.location,faldoRegion]
|
132
|
+
graph << [faldoRegion,RDFS.label,"#{self.id}:#{self.start}-#{self.stop}:1"]
|
133
|
+
graph << [faldoRegion,RDF.type,FALDO.Region]
|
134
|
+
graph << [faldoRegion,FALDO.begin,self.ref_base_uri+":#{self.start}:1"]
|
135
|
+
graph << [faldoRegion,FALDO.end,self.ref_base_uri+":#{self.stop}:1"]
|
136
|
+
graph << [faldoRegion,FALDO.reference,self.ref_base_uri]
|
137
|
+
if self.start == self.stop
|
138
|
+
faldoExactPosition = self.ref_base_uri+":#{self.start}:1"
|
139
|
+
graph << [faldoExactPosition,RDF.type,"faldo:ExactPosition"]
|
140
|
+
graph << [faldoExactPosition,RDF.type,"faldo:ForwardStrandPosition"]
|
141
|
+
graph << [faldoExactPosition,FALDO.position,self.start]
|
142
|
+
graph << [faldoExactPosition,FALDO.reference,self.ref_base_uri]
|
143
|
+
end
|
144
|
+
|
145
|
+
# TODO check if there are multiple alleles and iterate over them
|
146
|
+
# TODO what happends if there is an insertion?
|
147
|
+
refAlleleURI = var_uri+"\##{get_reference_allele}"
|
148
|
+
graph << [var_uri,var_uri+":has_allele",refAlleleURI]
|
149
|
+
graph << [refAlleleURI,RDFS.label,"#{self.id} allele #{get_reference_allele}"]
|
150
|
+
graph << [refAlleleURI,RDF.type,var_uri+":reference_allele"]
|
151
|
+
self.get_alternate_alleles do |altAllele|
|
152
|
+
altAlleleURI = var_uri+"\##{altAllele.getBaseString}"
|
153
|
+
graph << [var_uri,var_uri+":has_allele",altAlleleURI]
|
154
|
+
graph << [altAlleleURI,RDFS.label,"#{self.id} allele #{altAllele.getBaseString}"]
|
155
|
+
graph << [altAlleleURI, RDF.type, var_uri+":ancestral_allele"]
|
156
|
+
|
157
|
+
end
|
158
|
+
graph << [var_uri,URI(VAR_BASE_URI % "/vcf/quality"), RDF::Literal(get_phred_scaled_qual)]
|
159
|
+
|
160
|
+
@vcf.attributes.each do |k, v|
|
161
|
+
graph << [var_uri, RDF::URI( VAR_BASE_URI % "vcf/attribute\##{k}"), v] if v
|
162
|
+
end
|
163
|
+
|
164
|
+
end #new graph
|
165
|
+
|
166
|
+
end #to_rdf
|
167
|
+
end # Record
|
168
|
+
end; end # RDF::VCF
|
@@ -0,0 +1,19 @@
|
|
1
|
+
module RDF; module VCF
|
2
|
+
module VERSION
|
3
|
+
FILE = File.expand_path('../../../VERSION', __dir__).freeze
|
4
|
+
STRING = File.read(FILE).chomp.freeze
|
5
|
+
MAJOR, MINOR, TINY, EXTRA = STRING.split('.').map(&:to_i).freeze
|
6
|
+
|
7
|
+
##
|
8
|
+
# @return [String]
|
9
|
+
def self.to_s() STRING end
|
10
|
+
|
11
|
+
##
|
12
|
+
# @return [String]
|
13
|
+
def self.to_str() STRING end
|
14
|
+
|
15
|
+
##
|
16
|
+
# @return [Array(Integer, Integer, Integer)]
|
17
|
+
def self.to_a() [MAJOR, MINOR, TINY].freeze end
|
18
|
+
end # VERSION
|
19
|
+
end; end # RDF::VCF
|
metadata
ADDED
@@ -0,0 +1,119 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: rdf-vcf
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.2
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Arto Bendiken
|
8
|
+
- Raoul J.P. Bonnal
|
9
|
+
- Francesco Strozzi
|
10
|
+
autorequire:
|
11
|
+
bindir: bin
|
12
|
+
cert_chain: []
|
13
|
+
date: 2015-09-18 00:00:00.000000000 Z
|
14
|
+
dependencies:
|
15
|
+
- !ruby/object:Gem::Dependency
|
16
|
+
requirement: !ruby/object:Gem::Requirement
|
17
|
+
requirements:
|
18
|
+
- - "~>"
|
19
|
+
- !ruby/object:Gem::Version
|
20
|
+
version: '1.1'
|
21
|
+
name: rdf
|
22
|
+
prerelease: false
|
23
|
+
type: :runtime
|
24
|
+
version_requirements: !ruby/object:Gem::Requirement
|
25
|
+
requirements:
|
26
|
+
- - "~>"
|
27
|
+
- !ruby/object:Gem::Version
|
28
|
+
version: '1.1'
|
29
|
+
- !ruby/object:Gem::Dependency
|
30
|
+
requirement: !ruby/object:Gem::Requirement
|
31
|
+
requirements:
|
32
|
+
- - "~>"
|
33
|
+
- !ruby/object:Gem::Version
|
34
|
+
version: '10'
|
35
|
+
name: rake
|
36
|
+
prerelease: false
|
37
|
+
type: :development
|
38
|
+
version_requirements: !ruby/object:Gem::Requirement
|
39
|
+
requirements:
|
40
|
+
- - "~>"
|
41
|
+
- !ruby/object:Gem::Version
|
42
|
+
version: '10'
|
43
|
+
- !ruby/object:Gem::Dependency
|
44
|
+
requirement: !ruby/object:Gem::Requirement
|
45
|
+
requirements:
|
46
|
+
- - "~>"
|
47
|
+
- !ruby/object:Gem::Version
|
48
|
+
version: '3'
|
49
|
+
name: rspec
|
50
|
+
prerelease: false
|
51
|
+
type: :development
|
52
|
+
version_requirements: !ruby/object:Gem::Requirement
|
53
|
+
requirements:
|
54
|
+
- - "~>"
|
55
|
+
- !ruby/object:Gem::Version
|
56
|
+
version: '3'
|
57
|
+
- !ruby/object:Gem::Dependency
|
58
|
+
requirement: !ruby/object:Gem::Requirement
|
59
|
+
requirements:
|
60
|
+
- - "~>"
|
61
|
+
- !ruby/object:Gem::Version
|
62
|
+
version: '0.8'
|
63
|
+
name: yard
|
64
|
+
prerelease: false
|
65
|
+
type: :development
|
66
|
+
version_requirements: !ruby/object:Gem::Requirement
|
67
|
+
requirements:
|
68
|
+
- - "~>"
|
69
|
+
- !ruby/object:Gem::Version
|
70
|
+
version: '0.8'
|
71
|
+
description: |2
|
72
|
+
This is an RDF.rb reader plugin for Variant Call Format (VCF) files,
|
73
|
+
widely used in bioinformatics.
|
74
|
+
email: public-rdf-ruby@w3.org
|
75
|
+
executables:
|
76
|
+
- vcf2rdf
|
77
|
+
extensions: []
|
78
|
+
extra_rdoc_files: []
|
79
|
+
files:
|
80
|
+
- AUTHORS
|
81
|
+
- CREDITS
|
82
|
+
- README
|
83
|
+
- UNLICENSE
|
84
|
+
- VERSION
|
85
|
+
- bin/vcf2rdf
|
86
|
+
- lib/rdf-vcf.rb
|
87
|
+
- lib/rdf/vcf.rb
|
88
|
+
- lib/rdf/vcf/jar/bzip2.jar
|
89
|
+
- lib/rdf/vcf/jar/htsjdk-1.139.jar
|
90
|
+
- lib/rdf/vcf/reader.rb
|
91
|
+
- lib/rdf/vcf/record.rb
|
92
|
+
- lib/rdf/vcf/version.rb
|
93
|
+
homepage: https://github.com/ruby-rdf/rdf-vcf
|
94
|
+
licenses:
|
95
|
+
- Public Domain
|
96
|
+
metadata: {}
|
97
|
+
post_install_message:
|
98
|
+
rdoc_options: []
|
99
|
+
require_paths:
|
100
|
+
- lib
|
101
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
102
|
+
requirements:
|
103
|
+
- - ">="
|
104
|
+
- !ruby/object:Gem::Version
|
105
|
+
version: '2.2'
|
106
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
107
|
+
requirements:
|
108
|
+
- - ">="
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: '2.2'
|
111
|
+
requirements:
|
112
|
+
- JRuby (>= 9.0)
|
113
|
+
rubyforge_project:
|
114
|
+
rubygems_version: 2.4.8
|
115
|
+
signing_key:
|
116
|
+
specification_version: 4
|
117
|
+
summary: RDF.rb reader for Variant Call Format (VCF) files.
|
118
|
+
test_files: []
|
119
|
+
has_rdoc: false
|