bio-krona 0.0.1

data/.document

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

data/.rspec

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+--color

data/.travis.yml

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+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

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.8.0"
+  gem "yard", "~> 0.7"
+  gem "rdoc", "~> 3.12"
+  gem "cucumber", ">= 0"
+  gem "jeweler", "~> 1.8.3"
+  gem "bundler", ">= 1.0.21"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J. Woodcroft
+
+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.md

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+# bio-krona
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-krona.png)](http://travis-ci.org/wwood/bioruby-krona)
+
+This biogem is built around [Krona](http://krona.sourceforge.net/), a flashy way of representing hierarchical data.
+
+## Usage
+
+```bio-krona``` is a pretty simple gem, at this stage, and only implements two useful methods. 
+The first, the static method ```Bio::Krona#html``` is to call the krona software itself (specifically, ```ktImportText```) to generate
+the visualisation in HTML form.
+
+```ruby
+require 'bio-krona'
+
+html = Bio::Krona.html({
+      ['Sponge','Amphimedon']=>3,
+      ['Sponge','Calciums']=>4,
+    })
+
+```
+
+It takes as input a hash, where the keys are arrays representing the metadata, and the values are the weightings. In the example above, 
+the data has two levels of hierarchy - first Sponge, second Ampphimedon/Calciums.
+
+The second method ```collapse``` implements a pre-processing step that might be of use when the data is overly complex. 
+It collapses the data so that only a limited number of hierarchy levels are accounted for. 
+The weightings are preseverd by adding up the individual abundances.
+
+```ruby
+Bio::Krona.collapse({
+   ['Sponge','Amphimedon']=>3,
+   ['Sponge','Calciums']=>4,
+}, 1)
+#=> {['Sponge'] => 7}
+``` 
+
+## Installation
+
+```sh
+gem install bio-krona
+```
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-krona
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+```bio-krona``` is currently unpublished. However Krona itself is - see http://krona.sourceforge.net
+
+## Biogems.info
+
+This Biogem is published at [#bio-krona](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Ben J. Woodcroft. 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-krona"
+  gem.homepage = "http://github.com/wwood/bioruby-krona"
+  gem.license = "MIT"
+  gem.summary = %Q{This biogem is built around Krona, a flashy way of representing hierarchical data.}
+  gem.description = %Q{This biogem is built around Krona, a flashy way of representing hierarchical data.}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+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
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec
+
+require 'yard'
+YARD::Rake::YardocTask.new

data/VERSION

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+0.0.1

data/lib/bio-krona.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-krona/krona.rb'
+

data/lib/bio-krona/krona.rb

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+require 'bio'
+require 'tempfile'
+
+module Bio
+  class Krona
+    # Given a count_hash, return the html generated by krona
+    # * count_hash: hash of Array => Numeric, where the array is a list of descriptors (e.g. [Eukaryota, Metazoa, Chordata]), and the Numeric is a count for the number of observations of that description
+    # * options:
+    # ** :krona_path: path to the ktImportText script in the krona directory (default 'ktImportText' i.e. assuming it is already in the PATH)
+    def self.html(count_hash, options={})
+      raise unless count_hash.kind_of?(Hash)
+      options[:krona_path] ||= %(ktImportText)
+      
+      Tempfile.open('krona') do |tempfile|
+        count_hash.each do |array, count|
+          raise unless array.kind_of?(Array)
+          raise unless count.kind_of?(Numeric)
+  
+          tempfile.puts [
+            count,
+            array
+          ].flatten.join("\t")
+        end
+        tempfile.close
+        
+        Tempfile.open('krona_out') do |output|
+          output.close
+          
+          command = [
+            options[:krona_path],
+            '-o',
+            output.path,
+            tempfile.path,
+          ].flatten
+          Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
+            err = stderr.read
+            raise err unless err==''
+          end
+          
+          return File.open(output.path).read
+        end
+      end
+    end
+    
+    # Take a count_hash (hash of Array => Numeric), and collapse the array down to some maximum number of levels. In krona, the collapsed output would now have less (max_level) rings.
+    #
+    # Returns the collapsed count_hash
+    def self.collapse(count_hash, max_level)
+      raise unless max_level.kind_of?(Integer) and max_level > 0
+      new_count_hash = {}
+      count_hash.each do |array, count|
+        raise unless array.kind_of?(Array)
+        raise unless count.kind_of?(Numeric)
+          
+        new_count_hash[array[0...max_level]] ||= 0
+        new_count_hash[array[0...max_level]] += count
+      end
+      return new_count_hash
+    end
+  end
+end

data/spec/bio-krona_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioKrona" do
+  it "should give a html when you give it a simple hash" do
+    html = Bio::Krona.html({
+      ['Sponge','Amphimedon']=>3,
+      ['Sponge','Calciums']=>4,
+    })
+    expected = <<EOF
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+  <meta charset="utf-8"/>
+  <link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
+  <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \\"http://krona.sourceforge.net\\"."}</script>
+  <script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
+ </head>
+ <body>
+  <img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
+  <img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
+  <noscript>Javascript must be enabled to view this page.</noscript>
+  <div style="display:none">
+  <krona collapse="true" key="true">
+   <attributes magnitude="magnitude">
+    <list>members</list>
+    <attribute display="Total">magnitude</attribute>
+   </attributes>
+   <datasets>
+    <dataset>input</dataset>
+   </datasets>
+<node name="all">
+ <magnitude><val>7</val></magnitude>
+ <node name="Sponge">
+  <magnitude><val>7</val></magnitude>
+  <node name="Amphimedon">
+   <magnitude><val>3</val></magnitude>
+  </node>
+  <node name="Calciums">
+   <magnitude><val>4</val></magnitude>
+  </node>
+ </node>
+</node>
+  </krona>
+</div></body></html>
+EOF
+    make_comparable = lambda do |string|
+      string.split("\n").reject{|line| line.match(/<dataset>/)}
+    end
+    expected = make_comparable.call(expected)
+    html = make_comparable.call(html)
+    
+    html.should eq(expected)
+  end
+  
+  # it "should give back the html split up for re-use" do
+    # h = Bio::Krona.reusable_html_chunks({
+      # ['Sponge','Amphimedon']=>3,
+      # ['Sponge','Calciums']=>4,
+    # })
+  # end
+  
+  it "should collapse hashes right" do
+    big = {%w(a b c)=>2, %w(a b f)=>4, %w(g)=>5}
+    
+    expected = {%w(a)=>6, %w(g)=>5}
+    Bio::Krona.collapse(big, 1).should eq(expected)
+    
+    expected = {%w(a b)=>6, %w(g)=>5}
+    Bio::Krona.collapse(big, 2).should eq(expected)
+    
+    Bio::Krona.collapse(big, 3).should eq(big)
+    Bio::Krona.collapse(big, 4).should eq(big)
+  end
+end

data/spec/data/krona/input.txt

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+3	Sponge	Amphimedon
+4	Sponge	Calciums

data/spec/data/krona/input.txt.krona

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+  <meta charset="utf-8"/>
+  <link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
+  <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>
+  <script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
+ </head>
+ <body>
+  <img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
+  <img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
+  <noscript>Javascript must be enabled to view this page.</noscript>
+  <div style="display:none">
+  <krona collapse="true" key="true">
+   <attributes magnitude="magnitude">
+    <list>members</list>
+    <attribute display="Total">magnitude</attribute>
+   </attributes>
+   <datasets>
+    <dataset>input</dataset>
+   </datasets>
+<node name="all">
+ <magnitude><val>7</val></magnitude>
+ <node name="Sponge">
+  <magnitude><val>7</val></magnitude>
+  <node name="Amphimedon">
+   <magnitude><val>3</val></magnitude>
+  </node>
+  <node name="Calciums">
+   <magnitude><val>4</val></magnitude>
+  </node>
+ </node>
+</node>
+  </krona>
+</div></body></html>

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-krona'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-krona
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-08-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &75478020 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *75478020
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &75477510 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: *75477510
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: &75477060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: *75477060
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &75547720 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *75547720
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: &75546890 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *75546890
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &75546480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: *75546480
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &75545940 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: *75545940
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &75545420 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *75545420
+description: This biogem is built around Krona, a flashy way of representing hierarchical
+  data.
+email: donttrustben near gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .rspec
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-krona.rb
+- lib/bio-krona/krona.rb
+- spec/bio-krona_spec.rb
+- spec/data/krona/input.txt
+- spec/data/krona/input.txt.krona
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-krona
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 415100237
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: This biogem is built around Krona, a flashy way of representing hierarchical
+  data.
+test_files: []