bio-lazyblastxml 0.2.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "libxml-ruby", ">=2.0.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.0"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.1.5000)
+    git (1.2.5)
+    jeweler (1.6.0)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    libxml-ruby (2.0.5)
+    rake (0.8.7)
+    rcov (0.9.9)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.1)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.0)
+  libxml-ruby (>= 2.0.5)
+  rcov
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2011 robsyme
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bio-lazyblastxml
+
+Description goes here.
+
+== Contributing to bio-lazyblastxml
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 robsyme. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-lazyblastxml"
+  gem.homepage = "http://github.com/robsyme/bioruby-lazyblastxml"
+  gem.license = "MIT"
+  gem.summary = %Q{A plugin that allows you to parse large blast XML output files lazily, reading only what you need. }
+  gem.description = %Q{This is very scrappy at the moment, and will need to be seriously cleaned up. It does what I need it to do for now. I'll fix it up in the coming weeks. Promise :)}
+  gem.email = "rob.syme@gmail.com"
+  gem.authors = ["robsyme"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-lazyblastxml #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.2.0

data/bio-lazyblastxml.gemspec

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+# 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-lazyblastxml}
+  s.version = "0.2.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["robsyme"]
+  s.date = %q{2011-05-30}
+  s.description = %q{This is very scrappy at the moment, and will need to be seriously cleaned up. It does what I need it to do for now. I'll fix it up in the coming weeks. Promise :)}
+  s.email = %q{rob.syme@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-lazyblastxml.gemspec",
+    "lib/bio-lazyblastxml.rb",
+    "lib/bio/appl/blast/lazyblastxml.rb",
+    "test/data/test.blastout.xml",
+    "test/helper.rb",
+    "test/test_bio-lazyblastxml.rb"
+  ]
+  s.homepage = %q{http://github.com/robsyme/bioruby-lazyblastxml}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.5.0}
+  s.summary = %q{A plugin that allows you to parse large blast XML output files lazily, reading only what you need.}
+
+  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<libxml-ruby>, [">= 2.0.5"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.0"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+    else
+      s.add_dependency(%q<libxml-ruby>, [">= 2.0.5"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.0"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+    end
+  else
+    s.add_dependency(%q<libxml-ruby>, [">= 2.0.5"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.0"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+  end
+end
+

data/lib/bio-lazyblastxml.rb

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+require 'bio/appl/blast/lazyblastxml'

data/lib/bio/appl/blast/lazyblastxml.rb

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+require "libxml"
+
+class Enumerator
+  def lazy_select(&block)
+    Enumerator.new do |yielder|
+      self.each do |val|
+        yielder.yield(val) if block.call(val)
+      end
+    end
+  end
+
+  def lazy_reject(&block)
+    Enumerator.new do |yielder|
+      self.each do |val|
+        yielder.yield(val) unless block.call(val)
+      end
+    end
+  end
+
+  def lazy_map(&block)
+    Enumerator.new do |yielder|
+      self.each do |value|
+        yielder.yield(block.call(value))
+      end
+    end
+  end
+end
+
+module Bio
+  class LazyBlast
+    module LazyNodeSelector
+      def find_nodes_named(*names)
+        @nodes.lazy_select{|reader| names.include?(reader.name)}
+      end
+
+      def next_node_named(*names)
+        find_nodes_named(*names).next
+      end
+
+      def next_value_named(*names)
+        next_node_named(*names).read_inner_xml
+      end
+    end
+  end
+end
+
+module Bio
+  class LazyBlast
+    class Report
+      include Enumerable
+      include Bio::LazyBlast::LazyNodeSelector
+
+      class Iteration
+        include Enumerable
+        include Bio::LazyBlast::LazyNodeSelector
+        attr_reader   :statistics
+        attr_accessor :num
+        attr_accessor :message
+        attr_accessor :query_id
+        attr_accessor :query_def
+        attr_accessor :query_len
+
+        def setup_hits(xml_reader)
+          @reader = xml_reader
+          hits_finished = false
+          @nodes = Enumerator.new do |yielder|
+            while @reader.read and !(@reader.name == "Iteration_hits" and @reader.node_type == LibXML::XML::Reader::TYPE_END_ELEMENT) and !(@reader.value == "No hits found")
+              yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT
+            end
+          end
+        end
+
+        def each
+          find_nodes_named("Hit").each do |reader|
+            hit = Hit.new
+            hit.num = next_value_named("Hit_num").to_i
+            hit.hit_id = next_value_named("Hit_id")
+            hit.definition = next_value_named("Hit_def")
+            hit.accession = next_value_named("Hit_accession")
+            hit.len = next_value_named("Hit_len")
+            hit.setup_hsps(@reader)
+
+            yield hit
+          end
+        end
+
+        alias :each_hit :each
+        
+        class Hit
+          include Enumerable
+          include Bio::LazyBlast::LazyNodeSelector
+          attr_accessor :num
+          attr_accessor :hit_id
+          attr_accessor :len
+          attr_accessor :definition
+          attr_accessor :accession
+
+          def setup_hsps(xml_reader)
+            @reader = xml_reader
+            @nodes = Enumerator.new do |yielder|
+              while @reader.read and !(@reader.name == "Hit_hsps" and @reader.node_type == LibXML::XML::Reader::TYPE_END_ELEMENT)
+                yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT
+              end
+            end
+          end
+
+          def each
+            find_nodes_named("Hsp").each do |reader|
+              hsp = Hsp.new
+              hsp.num = next_value_named("Hsp_num").to_i
+              hsp.bit_score = next_value_named("Hsp_bit-score").to_f
+              hsp.evalue = next_value_named("Hsp_evalue").to_f
+              hsp.query_from = next_value_named("Hsp_query-from").to_i
+              hsp.query_to = next_value_named("Hsp_query-to").to_i
+              hsp.hit_from = next_value_named("Hsp_hit-from").to_i
+              hsp.hit_to = next_value_named("Hsp_hit-to").to_i
+              hsp.query_frame = next_value_named("Hsp_query-frame").to_i
+              hsp.hit_frame = next_value_named("Hsp_hit-frame").to_i
+              hsp.identity = next_value_named("Hsp_positive").to_i
+              hsp.align_len = next_value_named("Hsp_align-len").to_i
+              hsp.qseq = next_value_named("Hsp_qseq").to_i
+              hsp.hseq = next_value_named("Hsp_hseq").to_i
+              hsp.midline = next_value_named("Hsp_midline").to_i
+              yield hsp
+            end
+          end
+
+          alias :each_hsp :each
+          
+          class Hsp
+            attr_accessor :num
+            attr_accessor :bit_score
+            attr_accessor :evalue
+            attr_accessor :query_from
+            attr_accessor :query_to
+            attr_accessor :hit_from
+            attr_accessor :hit_to
+            attr_accessor :query_frame
+            attr_accessor :hit_frame
+            attr_accessor :identity
+            attr_accessor :positive
+            attr_accessor :gaps
+            attr_accessor :align_len
+            attr_accessor :density
+            attr_accessor :qseq
+            attr_accessor :hseq
+            attr_accessor :midline
+            attr_accessor :percent_identity
+            attr_accessor :mismatch_count
+          end
+
+        end
+
+      end
+      
+      attr_reader :reader
+
+      def initialize(filename)
+        @reader = LibXML::XML::Reader.file(filename)
+        @nodes = Enumerator.new do |yielder|
+          while @reader.read 
+            yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT
+          end
+        end
+      end
+
+      def each
+        find_nodes_named("Iteration").each do |reader|
+          iteration = Iteration.new
+          iteration.num = next_value_named("Iteration_iter-num").to_i
+          iteration.query_id = next_value_named("Iteration_query-ID")
+          iteration.query_def = next_value_named("Iteration_query-def")
+          iteration.query_len = next_value_named("Iteration_query-len").to_i
+          iteration.setup_hits(@reader)
+
+          yield iteration
+        end
+      end
+
+      alias :each_iteration :each
+      
+    end
+  end
+end

data/test/data/test.blastout.xml

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+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastp</BlastOutput_program>
+  <BlastOutput_version>blastp 2.2.21 [Jun-14-2009]</BlastOutput_version>
+  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>db.fasta</BlastOutput_db>
+  <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
+  <BlastOutput_query-def>test</BlastOutput_query-def>
+  <BlastOutput_query-len>16</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>10</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>1</Iteration_iter-num>
+      <Iteration_query-ID>lcl|1_0</Iteration_query-ID>
+      <Iteration_query-def>test</Iteration_query-def>
+      <Iteration_query-len>16</Iteration_query-len>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>50</Statistics_db-num>
+          <Statistics_db-len>7350</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+      <Iteration_message>No hits found</Iteration_message>
+    </Iteration>
+    <Iteration>
+      <Iteration_iter-num>2</Iteration_iter-num>
+      <Iteration_query-ID>lcl|2_0</Iteration_query-ID>
+      <Iteration_query-def>SNOT_00028.1|EAT91523.1</Iteration_query-def>
+      <Iteration_query-len>321</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gnl|BL_ORD_ID|4</Hit_id>
+          <Hit_def>SNOT_00028.1|EAT91523.1</Hit_def>
+          <Hit_accession>4</Hit_accession>
+          <Hit_len>321</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>677.937</Hsp_bit-score>
+              <Hsp_score>1748</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>321</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>321</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>321</Hsp_identity>
+              <Hsp_positive>321</Hsp_positive>
+              <Hsp_align-len>321</Hsp_align-len>
+              <Hsp_qseq>MPHAKRRAISPTLAPYERIRPEETLNGTPKLKRHILIIGAVPFIAHHFQRDLASSFRFQITEKNYDVGDTWLENTYPGCTCGVPSDIYQYSFAPSKDWSTLFDSSGEIQNYLSRMVKRFSLHTHIEFDMVVEKCIWDEKRRKWLVNTRCEGIVAQGREADVVTIAAGIFNHYQNPEIPALETFKGIMMHTADWNHIVDLAGKKIGIIGAGASSFESYYNTLFPVFYRDSSTQHRKRQEMAAWMSGRIKDEDMRQKLVPKYELGCRRISPRESFLDAIQQDNVECVFEPIVSCKPKGLQTQAGAKQLDVIVAATGFNTSFRP</Hsp_qseq>
+              <Hsp_hseq>MPHAKRRAISPTLAPYERIRPEETLNGTPKLKRHILIIGAVPFIAHHFQRDLASSFRFQITEKNYDVGDTWLENTYPGCTCGVPSDIYQYSFAPSKDWSTLFDSSGEIQNYLSRMVKRFSLHTHIEFDMVVEKCIWDEKRRKWLVNTRCEGIVAQGREADVVTIAAGIFNHYQNPEIPALETFKGIMMHTADWNHIVDLAGKKIGIIGAGASSFESYYNTLFPVFYRDSSTQHRKRQEMAAWMSGRIKDEDMRQKLVPKYELGCRRISPRESFLDAIQQDNVECVFEPIVSCKPKGLQTQAGAKQLDVIVAATGFNTSFRP</Hsp_hseq>
+              <Hsp_midline>MPHAKRRAISPTLAPYERIRPEETLNGTPKLKRHILIIGAVPFIAHHFQRDLASSFRFQITEKNYDVGDTWLENTYPGCTCGVPSDIYQYSFAPSKDWSTLFDSSGEIQNYLSRMVKRFSLHTHIEFDMVVEKCIWDEKRRKWLVNTRCEGIVAQGREADVVTIAAGIFNHYQNPEIPALETFKGIMMHTADWNHIVDLAGKKIGIIGAGASSFESYYNTLFPVFYRDSSTQHRKRQEMAAWMSGRIKDEDMRQKLVPKYELGCRRISPRESFLDAIQQDNVECVFEPIVSCKPKGLQTQAGAKQLDVIVAATGFNTSFRP</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>2</Hit_num>
+          <Hit_id>gnl|BL_ORD_ID|0</Hit_id>
+          <Hit_def>SNOT_00009.1|EAT91504.1</Hit_def>
+          <Hit_accession>0</Hit_accession>
+          <Hit_len>74</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>18.4754</Hsp_bit-score>
+              <Hsp_score>36</Hsp_score>
+              <Hsp_evalue>4.05209</Hsp_evalue>
+              <Hsp_query-from>136</Hsp_query-from>
+              <Hsp_query-to>150</Hsp_query-to>
+              <Hsp_hit-from>41</Hsp_hit-from>
+              <Hsp_hit-to>55</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>5</Hsp_identity>
+              <Hsp_positive>7</Hsp_positive>
+              <Hsp_align-len>15</Hsp_align-len>
+              <Hsp_qseq>WDEKRRKWLVNTRCE</Hsp_qseq>
+              <Hsp_hseq>WDDAAGSWEFTTACQ</Hsp_hseq>
+              <Hsp_midline>WD+    W   T C+</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>3</Hit_num>
+          <Hit_id>gnl|BL_ORD_ID|48</Hit_id>
+          <Hit_def>SNOT_00532.1|EAT92027.1</Hit_def>
+          <Hit_accession>48</Hit_accession>
+          <Hit_len>110</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>18.0902</Hsp_bit-score>
+              <Hsp_score>35</Hsp_score>
+              <Hsp_evalue>5.33653</Hsp_evalue>
+              <Hsp_query-from>232</Hsp_query-from>
+              <Hsp_query-to>244</Hsp_query-to>
+              <Hsp_hit-from>24</Hsp_hit-from>
+              <Hsp_hit-to>36</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>5</Hsp_identity>
+              <Hsp_positive>9</Hsp_positive>
+              <Hsp_align-len>13</Hsp_align-len>
+              <Hsp_qseq>QHRKRQEMAAWMS</Hsp_qseq>
+              <Hsp_hseq>RHRREQDQDRWMT</Hsp_hseq>
+              <Hsp_midline>+HR+ Q+   WM+</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>4</Hit_num>
+          <Hit_id>gnl|BL_ORD_ID|35</Hit_id>
+          <Hit_def>SNOT_00418.1|EAT91913.1</Hit_def>
+          <Hit_accession>35</Hit_accession>
+          <Hit_len>228</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>17.705</Hsp_bit-score>
+              <Hsp_score>34</Hsp_score>
+              <Hsp_evalue>6.35851</Hsp_evalue>
+              <Hsp_query-from>200</Hsp_query-from>
+              <Hsp_query-to>211</Hsp_query-to>
+              <Hsp_hit-from>200</Hsp_hit-from>
+              <Hsp_hit-to>211</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>7</Hsp_identity>
+              <Hsp_positive>9</Hsp_positive>
+              <Hsp_align-len>12</Hsp_align-len>
+              <Hsp_qseq>AGKKIGIIGAGA</Hsp_qseq>
+              <Hsp_hseq>ARDEIGLFGAGA</Hsp_hseq>
+              <Hsp_midline>A  +IG+ GAGA</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>50</Statistics_db-num>
+          <Statistics_db-len>7350</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+  </BlastOutput_iterations>
+</BlastOutput>

data/test/helper.rb

@@ -0,0 +1,19 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'minitest/unit'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-lazyblastxml'
+
+class MiniTest::Unit::TestCase
+end
+
+MiniTest::Unit.autorun

data/test/test_bio-lazyblastxml.rb

@@ -0,0 +1,67 @@
+require "pp"
+require 'helper'
+
+class TestReport < MiniTest::Unit::TestCase
+  def setup
+    @blast_filename = 'test/data/test.blastout.xml'
+    @report = Bio::LazyBlast::Report.new(@blast_filename)
+  end
+
+  def test_report_creation
+    assert_kind_of Bio::LazyBlast::Report, @report, "Creating a new Report should return a report object"
+  end
+
+  def test_report_enumeration
+    assert_equal 2, @report.count, "Calling #count on the report object should return the number of iterations"
+  end
+
+  def test_report_iteration
+    assert @report.all?{|iteration| iteration.is_a? Bio::LazyBlast::Report::Iteration}, "All of the objects yielded by the report object should be a type of Bio::LazyBlast::Report::Iteration"
+  end
+
+  def test_report_instance_values
+    first_iteration = @report.first
+    assert_equal 1, first_iteration.num
+    assert_equal 'test', first_iteration.query_def
+    assert_equal 'lcl|1_0', first_iteration.query_id
+    assert_equal 16, first_iteration.query_len
+  end
+
+end
+
+class TestIteration < MiniTest::Unit::TestCase
+  def setup
+    @blast_filename = 'test/data/test.blastout.xml'
+    @report = Bio::LazyBlast::Report.new(@blast_filename)
+  end
+
+  def test_iteration_creation
+    assert_kind_of Bio::LazyBlast::Report::Iteration, @iter_1
+  end
+
+  def test_example_usage
+    outstring = ''
+    @report.each_iteration do |iteration|
+      outstring << "Query: %s\n" % iteration.query_def
+      iteration.each_hit do |hit|
+        outstring << "     | hit:  %s\n" % hit.definition
+        hit.each_hsp do |hsp|
+          outstring << "          | hsp: %s\n" % hsp.evalue
+        end
+      end
+    end
+    final_string = <<-teststring
+Query: test
+Query: SNOT_00028.1|EAT91523.1
+     | hit:  SNOT_00028.1|EAT91523.1
+          | hsp: 0.0
+     | hit:  SNOT_00009.1|EAT91504.1
+          | hsp: 4.05209
+     | hit:  SNOT_00532.1|EAT92027.1
+          | hsp: 5.33653
+     | hit:  SNOT_00418.1|EAT91913.1
+          | hsp: 6.35851
+teststring
+    assert_equal final_string, outstring
+  end
+end

metadata

@@ -0,0 +1,137 @@
+--- !ruby/object:Gem::Specification 
+name: bio-lazyblastxml
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.2.0
+platform: ruby
+authors: 
+- robsyme
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-05-30 00:00:00 +08:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: libxml-ruby
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.6.0
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+description: This is very scrappy at the moment, and will need to be seriously cleaned up. It does what I need it to do for now. I'll fix it up in the coming weeks. Promise :)
+email: rob.syme@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-lazyblastxml.gemspec
+- lib/bio-lazyblastxml.rb
+- lib/bio/appl/blast/lazyblastxml.rb
+- test/data/test.blastout.xml
+- test/helper.rb
+- test/test_bio-lazyblastxml.rb
+has_rdoc: true
+homepage: http://github.com/robsyme/bioruby-lazyblastxml
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3109622305771744063
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.5.0
+signing_key: 
+specification_version: 3
+summary: A plugin that allows you to parse large blast XML output files lazily, reading only what you need.
+test_files: []
+