bio-blastxmlparser 0.6.0
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.
- data/.document +5 -0
- data/.rspec +1 -0
- data/Gemfile +18 -0
- data/Gemfile.lock +34 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +211 -0
- data/Rakefile +50 -0
- data/VERSION +1 -0
- data/bin/blastxmlparser +165 -0
- data/bio-blastxmlparser.gemspec +88 -0
- data/lib/bio-blastxmlparser.rb +17 -0
- data/lib/bio/db/blast/parser/nokogiri.rb +203 -0
- data/lib/bio/db/blast/xmliterator.rb +19 -0
- data/lib/bio/db/blast/xmlsplitter.rb +43 -0
- data/sample/bioruby.rb +14 -0
- data/sample/blastxmlparserdemo.rb +17 -0
- data/sample/libxml_sax.rb +25 -0
- data/sample/nokogiri_dom.rb +17 -0
- data/sample/nokogiri_sax.rb +26 -0
- data/sample/nokogiri_split_dom.rb +34 -0
- data/spec/bio-blastxmlparser_spec.rb +104 -0
- data/spec/spec_helper.rb +12 -0
- data/test/data/aa_example.fasta +42 -0
- data/test/data/aa_example_blastp.m7 +5021 -0
- data/test/data/nt_example.fasta +88 -0
- data/test/data/nt_example_blastn.m7 +85538 -0
- data/timings.sh +28 -0
- metadata +180 -0
data/timings.sh
ADDED
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@@ -0,0 +1,28 @@
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#! /bin/sh
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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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# 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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metadata
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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
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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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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:
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- 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:
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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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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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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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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:
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- - ">="
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- !ruby/object:Gem::Version
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hash: 4630273
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segments:
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- 0
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version: "0"
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required_rubygems_version: !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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version: "0"
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requirements: []
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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
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