bio-blastxmlparser 0.6.0
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- 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
@@ -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
ADDED
@@ -0,0 +1,180 @@
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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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25
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- - ">"
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26
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- !ruby/object:Gem::Version
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segments:
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28
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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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35
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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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47
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type: :runtime
|
48
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prerelease: false
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49
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version_requirements: *id002
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50
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+
- !ruby/object:Gem::Dependency
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51
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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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65
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+
- !ruby/object:Gem::Dependency
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66
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name: bundler
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67
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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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92
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type: :development
|
93
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prerelease: false
|
94
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version_requirements: *id005
|
95
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+
- !ruby/object:Gem::Dependency
|
96
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name: rcov
|
97
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requirement: &id006 !ruby/object:Gem::Requirement
|
98
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none: false
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99
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requirements:
|
100
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- - ">="
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- !ruby/object:Gem::Version
|
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segments:
|
103
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- 0
|
104
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version: "0"
|
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type: :development
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prerelease: false
|
107
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version_requirements: *id006
|
108
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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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115
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- LICENSE.txt
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- README.rdoc
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files:
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118
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- .document
|
119
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- .rspec
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- Gemfile
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121
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- Gemfile.lock
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122
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- LICENSE.txt
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- README.rdoc
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- Rakefile
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125
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- VERSION
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126
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- bin/blastxmlparser
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127
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- bio-blastxmlparser.gemspec
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128
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- lib/bio-blastxmlparser.rb
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129
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- lib/bio/db/blast/parser/nokogiri.rb
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130
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- lib/bio/db/blast/xmliterator.rb
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131
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+
- lib/bio/db/blast/xmlsplitter.rb
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132
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- sample/bioruby.rb
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133
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- sample/blastxmlparserdemo.rb
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134
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- sample/libxml_sax.rb
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135
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+
- sample/nokogiri_dom.rb
|
136
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- sample/nokogiri_sax.rb
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137
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+
- sample/nokogiri_split_dom.rb
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138
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- spec/bio-blastxmlparser_spec.rb
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139
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- spec/spec_helper.rb
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140
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- test/data/aa_example.fasta
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141
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- test/data/aa_example_blastp.m7
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142
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+
- test/data/nt_example.fasta
|
143
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+
- test/data/nt_example_blastn.m7
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144
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- timings.sh
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145
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has_rdoc: true
|
146
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+
homepage: http://github.com/pjotrp/bioruby-blastxmlparser
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147
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licenses:
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148
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- MIT
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149
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post_install_message:
|
150
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rdoc_options: []
|
151
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+
|
152
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require_paths:
|
153
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- lib
|
154
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required_ruby_version: !ruby/object:Gem::Requirement
|
155
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none: false
|
156
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requirements:
|
157
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+
- - ">="
|
158
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- !ruby/object:Gem::Version
|
159
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hash: 4630273
|
160
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segments:
|
161
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- 0
|
162
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version: "0"
|
163
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required_rubygems_version: !ruby/object:Gem::Requirement
|
164
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none: false
|
165
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requirements:
|
166
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+
- - ">="
|
167
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+
- !ruby/object:Gem::Version
|
168
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segments:
|
169
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+
- 0
|
170
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version: "0"
|
171
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requirements: []
|
172
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+
|
173
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rubyforge_project:
|
174
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rubygems_version: 1.3.7
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175
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signing_key:
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176
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specification_version: 3
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summary: BLAST XML parser
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178
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test_files:
|
179
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- spec/bio-blastxmlparser_spec.rb
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180
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- spec/spec_helper.rb
|