bio-blastxmlparser 1.0.0 → 1.0.1

data/Gemfile

@@ -5,14 +5,14 @@ source "http://rubygems.org"
 
 # Runtime dependencies
 # gem "bio", ">= 1.3.1"
-gem "bio-logger", "> 0.8.0"
-gem "nokogiri", ">= 1.4.4"
+gem "bio-logger", ">= 1.0.0"
+gem "nokogiri", ">= 1.5.0"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rspec", "~> 2.3.0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
+  # gem "rspec", "~> 2.3.0"
+  gem "bundler", "~> 1.0.15"
+  gem "jeweler", "~> 1.6.4"
+  # gem "rcov", ">= 0"
 end

data/Gemfile.lock

@@ -1,34 +1,22 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    bio-logger (0.9.0)
+    bio-logger (1.0.0)
       log4r (>= 1.1.9)
-    diff-lcs (1.1.2)
     git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
       git (>= 1.2.5)
       rake
     log4r (1.1.9)
     nokogiri (1.5.0)
     rake (0.9.2)
-    rcov (0.9.9)
-    rspec (2.3.0)
-      rspec-core (~> 2.3.0)
-      rspec-expectations (~> 2.3.0)
-      rspec-mocks (~> 2.3.0)
-    rspec-core (2.3.1)
-    rspec-expectations (2.3.0)
-      diff-lcs (~> 1.1.2)
-    rspec-mocks (2.3.0)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bio-logger (> 0.8.0)
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
-  nokogiri (>= 1.4.4)
-  rcov
-  rspec (~> 2.3.0)
+  bio-logger (>= 1.0.0)
+  bundler (~> 1.0.15)
+  jeweler (~> 1.6.4)
+  nokogiri (>= 1.5.0)

data/README.rdoc

@@ -1,6 +1,9 @@
+blastxmlparser is listed at http://biogems.info/
+
 = bio-blastxmlparser
 
-blastxmlparser is a fast big-data BLAST XML file parser. Rather than
+blastxmlparser is a very fast big-data BLAST XML file parser, which can be
+used as command line utility, or as a Ruby library. Rather than
 loading everything in memory, XML is parsed by BLAST query
 (Iteration). Not only has this the advantage of low memory use, it
 also shows results early, and it may be faster when IO continues in
@@ -9,6 +12,13 @@ parallel (disk read-ahead).
 Next to the API, blastxmlparser comes as a command line utility, which
 can be used to filter results and requires no understanding of Ruby.
 
+= Quick start
+
+  gem install bio-blastxmlparser
+  blastxmlparser --help
+
+(see Installation, below, if it does not work)
+
 == Performance
 
 XML parsing is expensive. blastxmlparser uses the fast Nokogiri C, or Java, XML
@@ -45,12 +55,11 @@ Timings for parsing test/data/nt_example_blastn.m7 (file size 3.4Mb)
 
 == Install
 
-Quick install:
-
   gem install bio-blastxmlparser
 
 Important: the parser is written for Ruby >= 1.9. You can check with
 
+  ruby -v
   gem env
 
 Nokogiri XML parser is required. To install it,

data/Rakefile

@@ -15,8 +15,8 @@ Jeweler::Tasks.new do |gem|
   gem.name = "bio-blastxmlparser"
   gem.homepage = "http://github.com/pjotrp/blastxmlparser"
   gem.license = "MIT"
-  gem.summary = %Q{BLAST XML parser}
-  gem.description = %Q{Fast big data XML parser and library, written in Ruby}
+  gem.summary = %Q{Very fast BLAST XML parser and library for big data}
+  gem.description = %Q{Fast big data XML parser and library, libxml2 based 50x faster than BioRuby}
   gem.email = "pjotr.public01@thebird.nl"
   gem.authors = ["Pjotr Prins"]
   # Include your dependencies below. Runtime dependencies are required when using your gem,
@@ -26,16 +26,16 @@ Jeweler::Tasks.new do |gem|
 end
 Jeweler::RubygemsDotOrgTasks.new
 
-require 'rspec/core'
-require 'rspec/core/rake_task'
-RSpec::Core::RakeTask.new(:spec) do |spec|
-  spec.pattern = FileList['spec/**/*_spec.rb']
-end
+# require 'rspec/core'
+# require 'rspec/core/rake_task'
+# RSpec::Core::RakeTask.new(:spec) do |spec|
+#   spec.pattern = FileList['spec/**/*_spec.rb']
+# end
 
-RSpec::Core::RakeTask.new(:rcov) do |spec|
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.rcov = true
-end
+# RSpec::Core::RakeTask.new(:rcov) do |spec|
+#   spec.pattern = 'spec/**/*_spec.rb'
+#   spec.rcov = true
+# end
 
 task :default => :spec
 

data/VERSION

@@ -1 +1 @@
-1.0.0
+1.0.1

metadata

@@ -1,120 +1,69 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-blastxmlparser
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 1
-  - 0
-  - 0
-  version: 1.0.0
+version: !ruby/object:Gem::Version
+  version: 1.0.1
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-07-26 00:00:00 +02:00
-default_executable: blastxmlparser
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2011-07-31 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &83898200 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">"
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 8
-        - 0
-        version: 0.8.0
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
+  version_requirements: *83898200
+- !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &83897710 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 4
-        - 4
-        version: 1.4.4
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: rspec
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 2
-        - 3
-        - 0
-        version: 2.3.0
-  type: :development
-  prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
+  version_requirements: *83897710
+- !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &83897190 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
+      - !ruby/object:Gem::Version
+        version: 1.0.15
   type: :development
   prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
+  version_requirements: *83897190
+- !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &83895540 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 5
-        - 2
-        version: 1.5.2
+      - !ruby/object:Gem::Version
+        version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: rcov
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
-  type: :development
-  prerelease: false
-  version_requirements: *id006
-description: Fast big data XML parser and library, written in Ruby
+  version_requirements: *83895540
+description: Fast big data XML parser and library, libxml2 based 50x faster than BioRuby
 email: pjotr.public01@thebird.nl
-executables: 
+executables:
 - blastxmlparser
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - .rspec
 - Gemfile
@@ -124,7 +73,6 @@ files:
 - Rakefile
 - VERSION
 - bin/blastxmlparser
-- bio-blastxmlparser.gemspec
 - lib/bio-blastxmlparser.rb
 - lib/bio/db/blast/parser/nokogiri.rb
 - lib/bio/db/blast/xmliterator.rb
@@ -142,39 +90,32 @@ files:
 - test/data/nt_example.fasta
 - test/data/nt_example_blastn.m7
 - timings.sh
-has_rdoc: true
 homepage: http://github.com/pjotrp/blastxmlparser
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: -125380653
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -1032070769
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.8.6
 signing_key: 
 specification_version: 3
-summary: BLAST XML parser
-test_files: 
-- spec/bio-blastxmlparser_spec.rb
-- spec/spec_helper.rb
+summary: Very fast BLAST XML parser and library for big data
+test_files: []

data/bio-blastxmlparser.gemspec

@@ -1,88 +0,0 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
-# -*- encoding: utf-8 -*-
-
-Gem::Specification.new do |s|
-  s.name = %q{bio-blastxmlparser}
-  s.version = "1.0.0"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Pjotr Prins"]
-  s.date = %q{2011-07-26}
-  s.default_executable = %q{blastxmlparser}
-  s.description = %q{Fast big data XML parser and library, written in Ruby}
-  s.email = %q{pjotr.public01@thebird.nl}
-  s.executables = ["blastxmlparser"]
-  s.extra_rdoc_files = [
-    "LICENSE.txt",
-    "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-    ".rspec",
-    "Gemfile",
-    "Gemfile.lock",
-    "LICENSE.txt",
-    "README.rdoc",
-    "Rakefile",
-    "VERSION",
-    "bin/blastxmlparser",
-    "bio-blastxmlparser.gemspec",
-    "lib/bio-blastxmlparser.rb",
-    "lib/bio/db/blast/parser/nokogiri.rb",
-    "lib/bio/db/blast/xmliterator.rb",
-    "lib/bio/db/blast/xmlsplitter.rb",
-    "sample/bioruby.rb",
-    "sample/blastxmlparserdemo.rb",
-    "sample/libxml_sax.rb",
-    "sample/nokogiri_dom.rb",
-    "sample/nokogiri_sax.rb",
-    "sample/nokogiri_split_dom.rb",
-    "spec/bio-blastxmlparser_spec.rb",
-    "spec/spec_helper.rb",
-    "test/data/aa_example.fasta",
-    "test/data/aa_example_blastp.m7",
-    "test/data/nt_example.fasta",
-    "test/data/nt_example_blastn.m7",
-    "timings.sh"
-  ]
-  s.homepage = %q{http://github.com/pjotrp/blastxmlparser}
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.7}
-  s.summary = %q{BLAST XML parser}
-  s.test_files = [
-    "spec/bio-blastxmlparser_spec.rb",
-    "spec/spec_helper.rb"
-  ]
-
-  if s.respond_to? :specification_version then
-    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
-    s.specification_version = 3
-
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<bio-logger>, ["> 0.8.0"])
-      s.add_runtime_dependency(%q<nokogiri>, [">= 1.4.4"])
-      s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
-    else
-      s.add_dependency(%q<bio-logger>, ["> 0.8.0"])
-      s.add_dependency(%q<nokogiri>, [">= 1.4.4"])
-      s.add_dependency(%q<rspec>, ["~> 2.3.0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_dependency(%q<rcov>, [">= 0"])
-    end
-  else
-    s.add_dependency(%q<bio-logger>, ["> 0.8.0"])
-    s.add_dependency(%q<nokogiri>, [">= 1.4.4"])
-    s.add_dependency(%q<rspec>, ["~> 2.3.0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-    s.add_dependency(%q<rcov>, [">= 0"])
-  end
-end
-