bio-blastxmlparser 1.0.1 → 1.1.0

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -12,7 +12,10 @@ gem "nokogiri", ">= 1.5.0"
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   # gem "rspec", "~> 2.3.0"
-  gem "bundler", "~> 1.0.15"
-  gem "jeweler", "~> 1.6.4"
+  gem "rake", ">= 0.9.2.2"
+  gem "bundler"
+  gem "jeweler", "~> 1.8.4"
+  gem "rspec", ">= 2.3.0"
+  gem "rdoc", ">= 2.4.2"
   # gem "rcov", ">= 0"
 end

data/Gemfile.lock

@@ -3,20 +3,36 @@ GEM
   specs:
     bio-logger (1.0.0)
       log4r (>= 1.1.9)
+    diff-lcs (1.1.3)
     git (1.2.5)
-    jeweler (1.6.4)
+    jeweler (1.8.4)
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
+      rdoc
+    json (1.6.5)
     log4r (1.1.9)
     nokogiri (1.5.0)
-    rake (0.9.2)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.8.0)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
   bio-logger (>= 1.0.0)
-  bundler (~> 1.0.15)
-  jeweler (~> 1.6.4)
+  bundler
+  jeweler (~> 1.8.4)
   nokogiri (>= 1.5.0)
+  rake (>= 0.9.2.2)
+  rdoc (>= 2.4.2)
+  rspec (>= 2.3.0)

data/README.rdoc

@@ -1,4 +1,4 @@
-blastxmlparser is listed at http://biogems.info/
+blastxmlparser is listed at http://biogems.info
 
 = bio-blastxmlparser
 

data/Rakefile

@@ -26,18 +26,26 @@ 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
 
-task :default => :spec
+task :default => [ :test, :spec ]
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  # test.pattern = 'test/**/test_*.rb'  # breaks in 1.9.3
+  test.test_files = Dir.glob("test/**/test_*.rb")
+  test.verbose = true
+end
 
 require 'rdoc/task'
 RDoc::Task.new do |rdoc|

data/VERSION

@@ -1 +1 @@
-1.0.1
+1.1.0

data/bio-blastxmlparser.gemspec

@@ -0,0 +1,86 @@
+# 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 = "bio-blastxmlparser"
+  s.version = "1.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Pjotr Prins"]
+  s.date = "2012-08-08"
+  s.description = "Fast big data XML parser and library, libxml2 based 50x faster than BioRuby"
+  s.email = "pjotr.public01@thebird.nl"
+  s.executables = ["blastxmlparser"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    ".travis.yml",
+    "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 = "http://github.com/pjotrp/blastxmlparser"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Very fast BLAST XML parser and library for big data"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bio-logger>, [">= 1.0.0"])
+      s.add_runtime_dependency(%q<nokogiri>, [">= 1.5.0"])
+      s.add_development_dependency(%q<rake>, [">= 0.9.2.2"])
+      s.add_development_dependency(%q<bundler>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
+      s.add_development_dependency(%q<rspec>, [">= 2.3.0"])
+      s.add_development_dependency(%q<rdoc>, [">= 2.4.2"])
+    else
+      s.add_dependency(%q<bio-logger>, [">= 1.0.0"])
+      s.add_dependency(%q<nokogiri>, [">= 1.5.0"])
+      s.add_dependency(%q<rake>, [">= 0.9.2.2"])
+      s.add_dependency(%q<bundler>, [">= 0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+      s.add_dependency(%q<rspec>, [">= 2.3.0"])
+      s.add_dependency(%q<rdoc>, [">= 2.4.2"])
+    end
+  else
+    s.add_dependency(%q<bio-logger>, [">= 1.0.0"])
+    s.add_dependency(%q<nokogiri>, [">= 1.5.0"])
+    s.add_dependency(%q<rake>, [">= 0.9.2.2"])
+    s.add_dependency(%q<bundler>, [">= 0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.4"])
+    s.add_dependency(%q<rspec>, [">= 2.3.0"])
+    s.add_dependency(%q<rdoc>, [">= 2.4.2"])
+  end
+end
+

data/lib/bio/db/blast/parser/nokogiri.rb

@@ -8,9 +8,9 @@ module Bio
     module XPath
       def field name
         res = if @prefix
-          @xml.xpath(@prefix+name+'/text()')
+          @xml.xpath(@prefix+name+'/text()').to_s
         else
-          @xml.xpath(name+'/text()')
+          @xml.xpath(name+'/text()').to_s
         end
         if res == nil
           logger = Bio::Log::LoggerPlus['bio-blastxmlparser']
@@ -68,6 +68,7 @@ module Bio
                         'Hsp_hit-frame'   => :hit_frame,
                         'Hsp_identity'    => :identity,
                         'Hsp_positive'    => :positive,
+                        'Hsp_gaps'        => :gaps,
                         'Hsp_align-len'   => :align_len
       MapXPath.define_f 'Hsp_bit-score'   => :bit_score,
                         'Hsp_evalue'      => :evalue

data/spec/bio-blastxmlparser_spec.rb

@@ -1,9 +1,9 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
 TESTFILE = "./test/data/nt_example_blastn.m7"
+include Bio::Blast
 
 describe "Bio::Blast::NokogiriBlastXml" do
-  include Bio::Blast
   before(:all) do
     n = NokogiriBlastXml.new(File.new(TESTFILE)).to_enum
     @iter1 = n.next
@@ -43,6 +43,7 @@ describe "Bio::Blast::NokogiriBlastXml" do
     hsp.identity.should == 73
     hsp.positive.should == 73
     hsp.align_len.should == 73
+    hsp.gaps.should == 0
     hsp.qseq.should == "AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG"
     hsp.hseq.should == "AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG"
     hsp.midline.should == "|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||"

data/test/data/nt_example_blastn.m7

@@ -46,6 +46,7 @@
               <Hsp_identity>73</Hsp_identity>
               <Hsp_positive>73</Hsp_positive>
               <Hsp_align-len>73</Hsp_align-len>
+              <Hsp_gaps>0</Hsp_gaps>
               <Hsp_qseq>AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG</Hsp_qseq>
               <Hsp_hseq>AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG</Hsp_hseq>
               <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-blastxmlparser
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-07-31 00:00:00.000000000Z
+date: 2012-08-08 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &83898200 !ruby/object:Gem::Requirement
+  requirement: &14068420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *83898200
+  version_requirements: *14068420
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &83897710 !ruby/object:Gem::Requirement
+  requirement: &14067240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,29 +32,62 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *83897710
+  version_requirements: *14067240
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &14066000 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.2.2
+  type: :development
+  prerelease: false
+  version_requirements: *14066000
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &83897190 !ruby/object:Gem::Requirement
+  requirement: &14064760 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.0.15
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *83897190
+  version_requirements: *14064760
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &83895540 !ruby/object:Gem::Requirement
+  requirement: &14063640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.6.4
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: *14063640
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &14062500 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.3.0
+  type: :development
+  prerelease: false
+  version_requirements: *14062500
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &14055400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.4.2
   type: :development
   prerelease: false
-  version_requirements: *83895540
+  version_requirements: *14055400
 description: Fast big data XML parser and library, libxml2 based 50x faster than BioRuby
 email: pjotr.public01@thebird.nl
 executables:
@@ -66,6 +99,7 @@ extra_rdoc_files:
 files:
 - .document
 - .rspec
+- .travis.yml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -73,6 +107,7 @@ 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
@@ -105,7 +140,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1032070769
+      hash: -1696395694674995706
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -114,7 +149,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Very fast BLAST XML parser and library for big data