bio-blastxmlparser 0.6.0

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Files changed (28) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/Gemfile +18 -0
  4. data/Gemfile.lock +34 -0
  5. data/LICENSE.txt +20 -0
  6. data/README.rdoc +211 -0
  7. data/Rakefile +50 -0
  8. data/VERSION +1 -0
  9. data/bin/blastxmlparser +165 -0
  10. data/bio-blastxmlparser.gemspec +88 -0
  11. data/lib/bio-blastxmlparser.rb +17 -0
  12. data/lib/bio/db/blast/parser/nokogiri.rb +203 -0
  13. data/lib/bio/db/blast/xmliterator.rb +19 -0
  14. data/lib/bio/db/blast/xmlsplitter.rb +43 -0
  15. data/sample/bioruby.rb +14 -0
  16. data/sample/blastxmlparserdemo.rb +17 -0
  17. data/sample/libxml_sax.rb +25 -0
  18. data/sample/nokogiri_dom.rb +17 -0
  19. data/sample/nokogiri_sax.rb +26 -0
  20. data/sample/nokogiri_split_dom.rb +34 -0
  21. data/spec/bio-blastxmlparser_spec.rb +104 -0
  22. data/spec/spec_helper.rb +12 -0
  23. data/test/data/aa_example.fasta +42 -0
  24. data/test/data/aa_example_blastp.m7 +5021 -0
  25. data/test/data/nt_example.fasta +88 -0
  26. data/test/data/nt_example_blastn.m7 +85538 -0
  27. data/timings.sh +28 -0
  28. metadata +180 -0
data/timings.sh ADDED
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+ #! /bin/sh
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+
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+ echo Parsing test/data/nt_example_blastn.m7
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+ ls -l test/data/nt_example_blastn.m7
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+
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+ # first fill cache
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+ echo ====
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+ echo Null
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+ cat test/data/nt_example_blastn.m7 > /dev/null
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+ time cat test/data/nt_example_blastn.m7 > /dev/null
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+ echo ====
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+ echo Nokogiri SAX
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+ time ./sample/nokogiri_sax.rb > /dev/null
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+ echo ====
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+ echo LibXML SAX
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+ time ./sample/libxml_sax.rb > /dev/null
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+ echo ====
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+ echo Nokogiri DOM
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+ time sample/nokogiri_dom.rb > /dev/null
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+ echo ====
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+ echo Nokogiri split DOM
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+ time sample/nokogiri_split_dom.rb > /dev/null
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+ echo ====
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+ echo BioRuby ReXML DOM parser
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+ time sample/bioruby.rb > /dev/null
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+
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+
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+
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-blastxmlparser
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+ version: !ruby/object:Gem::Version
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+ prerelease: false
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+ segments:
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+ - 0
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+ - 6
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+ - 0
9
+ version: 0.6.0
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+ platform: ruby
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+ authors:
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+ - Pjotr Prins
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2011-02-14 00:00:00 +01:00
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+ default_executable: blastxmlparser
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bio-logger
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+ requirement: &id001 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">"
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 0
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+ - 8
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+ - 0
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+ version: 0.8.0
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *id001
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+ - !ruby/object:Gem::Dependency
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+ name: nokogiri
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+ requirement: &id002 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
43
+ - 1
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+ - 4
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+ - 4
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+ version: 1.4.4
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *id002
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
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+ requirement: &id003 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 2
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+ - 3
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+ - 0
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+ version: 2.3.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: *id003
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: &id004 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 1
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+ - 0
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+ - 0
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+ version: 1.0.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: *id004
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: &id005 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 1
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+ - 5
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+ - 2
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+ version: 1.5.2
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+ type: :development
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+ prerelease: false
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+ version_requirements: *id005
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+ - !ruby/object:Gem::Dependency
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+ name: rcov
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+ requirement: &id006 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
100
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
103
+ - 0
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+ version: "0"
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+ type: :development
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+ prerelease: false
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+ version_requirements: *id006
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+ description: Fast big data XML parser and library, written in Ruby
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+ email: pjotr.public01@thebird.nl
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+ executables:
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+ - blastxmlparser
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+ extensions: []
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+
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+ extra_rdoc_files:
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+ - LICENSE.txt
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+ - README.rdoc
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+ files:
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+ - .document
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+ - .rspec
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+ - Gemfile
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+ - Gemfile.lock
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+ - LICENSE.txt
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+ - README.rdoc
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+ - Rakefile
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+ - VERSION
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+ - bin/blastxmlparser
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+ - bio-blastxmlparser.gemspec
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+ - lib/bio-blastxmlparser.rb
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+ - lib/bio/db/blast/parser/nokogiri.rb
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+ - lib/bio/db/blast/xmliterator.rb
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+ - lib/bio/db/blast/xmlsplitter.rb
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+ - sample/bioruby.rb
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+ - sample/blastxmlparserdemo.rb
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+ - sample/libxml_sax.rb
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+ - sample/nokogiri_dom.rb
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+ - sample/nokogiri_sax.rb
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+ - sample/nokogiri_split_dom.rb
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+ - spec/bio-blastxmlparser_spec.rb
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+ - spec/spec_helper.rb
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+ - test/data/aa_example.fasta
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+ - test/data/aa_example_blastp.m7
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+ - test/data/nt_example.fasta
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+ - test/data/nt_example_blastn.m7
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+ - timings.sh
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+ has_rdoc: true
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+ homepage: http://github.com/pjotrp/bioruby-blastxmlparser
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+ licenses:
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+ - MIT
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+ post_install_message:
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+ rdoc_options: []
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+
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
157
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 4630273
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+ segments:
161
+ - 0
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+ version: "0"
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
165
+ requirements:
166
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 0
170
+ version: "0"
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+ requirements: []
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+
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+ rubyforge_project:
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+ rubygems_version: 1.3.7
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+ signing_key:
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+ specification_version: 3
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+ summary: BLAST XML parser
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+ test_files:
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+ - spec/bio-blastxmlparser_spec.rb
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+ - spec/spec_helper.rb