bio-express_beta_diversity 0.0.1

checksums.yaml

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+SHA1:
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+  data.tar.gz: d9ca06baedd0dc7d991449d89c1925d57527f920
+SHA512:
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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-logger', '~>1.0'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.8"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", "~> 1.3"
+  gem "bio", "~> 1.4"
+end

data/LICENSE.txt

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+Copyright (c) 2013 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-express_beta_diversity
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-express_beta_diversity.png)](http://travis-ci.org/wwood/bioruby-express_beta_diversity)
+
+Ruby interface to [express beta diversity](https://github.com/dparks1134/ExpressBetaDiversity) things. Currently, functionality is limited to parsing the output distance matrices. 
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-express_beta_diversity
+```
+
+## Usage
+
+```ruby
+require 'bio-express_beta_diversity'
+
+dists = Bio::EBD::DistanceMatrix.parse_from_file 'Bray-Curtis.cluster.diss'
+dists.sample_names #=> ["sample1", "sample2", ... ]
+dists.distance('sample1','sample2') #=> 0.251761
+dists.distance('sample2','sample1') #=> 0.251761
+
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-express_beta_diversity
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-express_beta_diversity)
+
+## Copyright
+
+Copyright (c) 2013 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-express_beta_diversity"
+  gem.homepage = "http://github.com/wwood/bioruby-express_beta_diversity"
+  gem.license = "MIT"
+  gem.summary = %Q{Interface for express beta diversity}
+  gem.description = %Q{Interface for express beta diversity file formats}
+  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
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-express_beta_diversity #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-express_beta_diversity.rb

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+
+require 'bio-logger'
+Bio::Log::LoggerPlus.new('bio-velvet')
+module Bio::Velvet
+  module Logging
+    def log
+      Bio::Log::LoggerPlus['bio-velvet']
+    end
+  end
+end
+
+
+require 'bio-express_beta_diversity/distance_matrix.rb'
+

data/lib/bio-express_beta_diversity/distance_matrix.rb

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+require 'pp'
+require 'csv'
+
+module Bio
+  class EBD
+    # Distance matrix output from express beta diversity (Donovan Parks et al).
+    # Similar to phylip distance format, but not quite the same.
+    class DistanceMatrix
+      attr_accessor :distance_matrix
+      attr_accessor :sample_names
+
+      def initialize
+        @distance_matrix = []
+        @sample_names = []
+      end
+
+      def self.parse_from_file(filename)
+        ebd = Bio::EBD::DistanceMatrix.new
+
+        line = 1
+        expected_number_of_samples = nil
+        CSV.foreach(filename, :col_sep => "\t") do |row|
+          if line == 1
+            # First line is the number of samples
+            raise "Parse exception at this row: #{row.inspect}, expected" unless row.length == 1
+            expected_number_of_samples = row[0].to_i
+          else
+            # all other lines are the sample names and then the lower
+            # triangular distance matrix
+            sample_index = line-2
+            raise "Parse exception at this row: #{row.inspect}" unless row.length == sample_index+1
+            ebd.sample_names.push row[0]
+
+            distances = row[1...row.length].collect{|d| d.to_f}
+            ebd.distance_matrix[sample_index] = distances
+          end
+          line += 1
+        end
+
+        return ebd
+      end
+
+      def number_of_samples
+        @sample_names.length
+      end
+
+      # Return the floating point distance between a pair of samples
+      def distance(sample1, sample2)
+        index1 = @sample_names.find_index{|n| n==sample1}
+        index2 = @sample_names.find_index{|n| n==sample2}
+        raise "error extracting the EBD distance between #{sample1.inspect} and #{sample2.inspect}" unless index1 and index2 and index2 != index1
+        if index1 > index2
+          return @distance_matrix[index1][index2]
+        else
+          return @distance_matrix[index2][index1]
+        end
+      end
+    end
+  end
+end

data/spec/bio-express_beta_diversity_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioExpressBetaDiversity" do
+  it "should parse a distance matrix" do
+    eg = File.expand_path(File.dirname(__FILE__) + '/data/eg.diss')
+    d = Bio::EBD::DistanceMatrix.parse_from_file(eg)
+
+    #3
+    #4459
+    #4446    0.255099
+    #4451    0.258384        0.364525
+    d.number_of_samples.should == 3
+    d.distance_matrix.length.should == 3
+    d.distance_matrix[0].should == []
+    d.distance_matrix[1].should == [0.255099]
+    d.distance_matrix[2].should == [0.258384, 0.364525]
+    d.sample_names.should == %w(4459 4446 4451)
+    d.distance('4446','4451').should == 0.364525
+    d.distance('4451','4446').should == 0.364525
+  end
+end

data/spec/data/eg.diss

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+3
+4459
+4446	0.255099
+4451	0.258384	0.364525

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-express_beta_diversity'
+
+# 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-express_beta_diversity
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-01-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+description: Interface for express beta diversity file formats
+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-express_beta_diversity.rb
+- lib/bio-express_beta_diversity/distance_matrix.rb
+- spec/bio-express_beta_diversity_spec.rb
+- spec/data/eg.diss
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-express_beta_diversity
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0.rc.1
+signing_key: 
+specification_version: 4
+summary: Interface for express beta diversity
+test_files: []