bio-cd-hit-report 0.0.1

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

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"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "minitest"
+  gem "rdoc"
+  gem "bundler"
+  gem "jeweler"
+  gem "bio", "1.4.2"
+  gem "rdoc"
+end

data/LICENSE.txt

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+Copyright (c) 2012 georgeG
+
+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-cd-hit-report
+
+[![Build Status](https://secure.travis-ci.org/georgeG/bioruby-cd-hit-report.png)](http://travis-ci.org/georgeG/bioruby-cd-hit-report)
+
+A bioruby wrapper for parsing and reading CD-HIT cluster reports
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-cd-hit-report
+```
+
+## Usage
+
+```ruby
+  require 'bio-cd-hit-report'
+   
+   cluster_file = "cluster95.clstr"
+    report = Bio::CdHitReport.new(cluster_file)
+
+      puts report.max_members #print the max number of sequences in a cluster for the entire dataset
+      puts report.min_members #print the minimum number of sequences in a cluster for the entire dataset
+      puts report.total_clusters #print total number of clusters in the report
+
+      report.each_cluster do |c|
+        puts "#{c.name} - #{c.members}" #print cluster name/id with respective sequences in the cluster
+        puts c.size #print the total number of entries in the cluster
+      end
+```
+
+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/georgeG/bioruby-cd-hit-report
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## 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 [#bio-cd-hit-report](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 George Githinji. 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-cd-hit-report"
+  gem.homepage = "http://github.com/georgeG/bioruby-cd-hit-report"
+  gem.license = "MIT"
+  gem.summary = %Q{A bioruby wrapper for parsing and reading CD-HIT cluster reports}
+  gem.description = %Q{A bioruby wrapper for parsing and reading CD-HIT cluster reports}
+  gem.email = "georgkam@gmail.com"
+  gem.authors = ["George Githinji"]
+  # 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
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-cd-hit-report #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/bio-cd-hit-report

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+#!/usr/bin/env ruby
+#
+# BioRuby bio-cd-hit-report Plugin BioCdHitReport
+# Author:: georgeG
+# Copyright:: 2012
+
+ USAGE = "Describe bio-cd-hit-report"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-cd-hit-report'
+require 'optparse'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = {:example_switch=>false,:show_help=>false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
+
+  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
+    # TODO: your logic here, below an example
+    options[:example_parameter] = 'this is a parameter'
+  end
+  
+  o.separator ""
+  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
+    # TODO: your logic here, below an example
+    self[:example_switch] = true
+  end
+
+  # Uncomment the following when using the bio-logger 
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  # 
+  # o.on("-q", "--quiet", "Run quietly") do |q|
+  #   Bio::Log::CLI.trace('error')
+  # end
+  # 
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  # 
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  # Uncomment the following when using the bio-logger 
+  # Bio::Log::CLI.configure('bio-cd-hit-report')
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end

data/lib/bio-cd-hit-report.rb

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+require_relative "bio-cd-hit-report/cd-hit-report"
+
+#cluster_file = "#{ENV['HOME']}/DBL_tags/cluster/cd-hit/cluster95.clstr"
+
+#report = Bio::CdHitReport.new(cluster_file)
+#puts report.max_members #print the max number of sequences in a cluster for the entire dataset
+#puts report.min_members #print the minimum number of sequences in a cluster for the entire dataset
+#puts report.total_clusters #print total number of clusters in the report
+
+#report.each_cluster do |c|
+  #puts "#{c.name} - #{c.members}" #list cluster name/id with respective number of sequences in the cluster
+#end
+
+

data/lib/bio-cd-hit-report/cd-hit-report.rb

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+module Bio
+
+require_relative 'cluster.rb'
+
+  class CdHitReport
+
+    def initialize(file)
+      @file = file
+    end
+
+    def each_cluster(&block)
+      cluster_objs.each(&block)
+    end
+
+    def total_clusters
+      cluster_objs.size
+    end
+
+    def max_members
+      cluster_objs.map{|c|c.size}.max
+    end
+
+    def min_members
+      cluster_objs.map{|c| c.size}.min
+    end
+
+    private
+    def cluster_objs
+      raw_data.map do |line|
+        cluster = line.split("\n").delete_if{|x| x == ">Cluster "}
+        id = cluster.first
+        cluster.shift
+        Cluster.new(id,cluster)
+      end
+    end
+
+    def raw_data
+      File.open(@file).readlines
+    end
+
+  end #class
+end #module

data/lib/bio-cd-hit-report/cluster.rb

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+class Cluster < Struct.new(:name,:data)
+  $/ = ">Cluster "
+
+  def id
+    name
+  end
+
+  def size
+    entries.size
+  end
+
+  def members
+    entries.join(',')
+  end
+
+  private
+  def entries
+    data.map {|entry| entry.scan(/>(.+)\.{3}/)}.flatten
+  end
+end
+

data/test/helper.rb

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+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.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'bio-cd-hit-report'
+
+class MiniTest::Unit::TestCase
+end
+
+MiniTest::Unit.autorun

data/test/test_bio-cd-hit-report.rb

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+require 'helper'
+
+class TestBioCdHitReport < MiniTest::Unit::TestCase
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-cd-hit-report
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- George Githinji
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-09-14 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A bioruby wrapper for parsing and reading CD-HIT cluster reports
+email: georgkam@gmail.com
+executables:
+- bio-cd-hit-report
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/bio-cd-hit-report
+- lib/bio-cd-hit-report.rb
+- lib/bio-cd-hit-report/cd-hit-report.rb
+- lib/bio-cd-hit-report/cluster.rb
+- test/helper.rb
+- test/test_bio-cd-hit-report.rb
+homepage: http://github.com/georgeG/bioruby-cd-hit-report
+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: -2084256407332630455
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: A bioruby wrapper for parsing and reading CD-HIT cluster reports
+test_files: []