bio-gfastqc 0.0.1

checksums.yaml

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data/.document

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+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"
+
+gem 'rubyzip'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "simplecov", ">= 0"
+  gem "jeweler"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+end

data/LICENSE.txt

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+Copyright (c) 2015 Raoul Jean Pierre Bonnal
+
+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-gfastqc
+
+[![Build Status](https://secure.travis-ci.org/helios/bioruby-gfastqc.png)](http://travis-ci.org/helios/bioruby-gfastqc)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-gfastqc
+```
+
+## Usage
+
+```ruby
+require 'bio-gfastqc'
+```
+
+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/helios/bioruby-gfastqc
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+
+Create a config YAML file 
+
+    config.yml
+
+it contents is for example:
+
+    samples:
+      Sample_A: /path_to_sampleA
+      Sample_B: /path_to_sampleB
+
+then run the script in the directory of the `config.yml` file and specify the sub directory for each sampel where is located the result of the FASTQC
+
+    ruby gfastqc.rb -a R1 -b R2
+
+in case you have the results of FastQC in a sub folder and you want to keep the definition of the sample independen from it, you can use the step option
+
+    ruby gfastqc.rb -a R1 -b R2 --step qc_pre_trimming
+
+Then open index.html in your browser
+
+
+
+## TODO
+
+* avoid user to specify -a and -b. By default discover zip files and ordering them define the first and second strand.
+* ~~package everything as a gem~~
+* provide better documentation for installing the gem on multiple system (GNU/Linux, OSX, Windows)
+
+
+## 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-gfastqc)
+
+## Copyright
+
+Copyright (c) 2015 Raoul Jean Pierre Bonnal. 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://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-gfastqc"
+  gem.homepage = "http://github.com/helios/bioruby-gfastqc"
+  gem.license = "MIT"
+  gem.summary = %Q{TODO: one-line summary of your gem}
+  gem.description = %Q{TODO: longer description of your gem}
+  gem.email = "ilpuccio.febo@gmail.com"
+  gem.authors = ["Raoul Jean Pierre Bonnal"]
+  # 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
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+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-gfastqc #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/gfastqc

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+#!/usr/bin/env ruby
+#
+# BioRuby bio-gfastqc Plugin BioGfastqc
+# Author:: Raoul Jean Pierre Bonnal
+# Copyright:: 2015
+require 'json'
+require 'base64'
+require 'yaml'
+require 'optparse'
+require 'ostruct'
+require 'zip'
+require 'erb'
+# Copyright 2015, Raoul Jean Pierre Bonnal <bonnal@ingm.org>
+# This scripts reads and input file in YAML format followint
+# the specification from pipengine for samples
+# generates a single comprehesive html page with a summary for
+# all the Quality Control data generated by FASTQC
+
+
+USAGE = "Describe bio-gfastqc"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+# print banner
+print "bio-gfastqc #{version} by Raoul Jean Pierre Bonnal 2015\n"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-gfastqc'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+
+class OptHandlingBox
+  def  self.parse(args)
+    options = OpenStruct.new
+    options.config = 'config.yml'
+    options.step = ''
+
+    opt_parser =  OptionParser.new do |opts|
+      opts.banner = 'Usage: qc_overview.rb '
+
+      opts.on('-c', '--config [config]',
+              'choose the config from get info about the samples') do |config|
+        options.config = config
+      end
+
+      opts.on('-s', '--step [STEP]',
+              'choose the step from which extract the fastqc data') do |step|
+        options.step = step
+      end
+
+      opts.on('-a', '--first [FIRST]',
+              'forward strand reads') do |first|
+        options.first = first
+      end
+
+      opts.on('-b', '--second [SECOND]',
+              'reverse strand reads') do |second|
+        options.second = second
+      end
+
+
+      opts.on_tail("-h", "--help", "Show this message") do
+        puts opts
+        exit
+      end
+    end #opt_parse
+
+    opt_parser.parse!(args)
+    options
+  end #parse
+end #class OptGtfSplit
+
+options = OptHandlingBox.parse(ARGV)
+
+if !File.exists?(options.config)
+  puts
+  puts "Warning: there is not config file #{options.config}"
+  exit
+end
+config = YAML.load_file(options.config)
+@data = {}
+@tables = {}
+@base_file_names = []
+@base_file_names << options.first #this must be mandatory
+@base_file_names << options.second if options.second # this can be optional
+
+
+config['samples'].each_pair do |name, path|
+  @data[name] = {}
+  @tables[name] = {}
+  @base_file_names.each do |base_file_name|
+    @data[name][base_file_name]={}
+    @tables[name][base_file_name]={}
+    file = File.join(path, options.step, "#{base_file_name}_fastqc.zip")
+    Zip::File.open(file) do |zip_file|
+      zip_file.glob('*/Images/*.png').each do |entry|
+        @data[name][base_file_name][File.basename(entry.name,".png")]=Base64.encode64(entry.get_input_stream.read)
+      end #each entry
+      zip_file.glob('*/fastqc_data.txt').each do |entry|
+        entry.get_input_stream.read.scan(/>>(.*?)>>END_MODULE/m).each do |match|
+          match_data = match.first.split("\n")
+          field_name, status = match_data[0].split("\t")
+          begin 
+            header = match_data[1].tr("#","").split("\t")
+            content = match_data[2..-1].map do |data_row|
+              data_row.split("\t")
+            end
+            # puts field_name
+            @tables[name][base_file_name][field_name.tr(" ","_")]={ "status" => status,
+              "header"=> header,
+              "content" => content
+            }
+          rescue
+            # $stderr.puts match_data.inspect #This is a generic warning to notify the user that this records has no data associated with.
+          end
+
+        end #match
+      end #fastq data.txt
+    end #zip
+  end #files
+end
+# File.open('test.json','w') do |file|
+#   file.write data.to_json
+# end
+
+@type_images = %w(kmer_profiles per_sequence_gc_content per_base_sequence_content duplication_levels sequence_length_distribution per_sequence_quality per_base_quality adapter_content per_base_n_content per_tile_quality)
+@type_tables = %w(Adapter_Content Basic_Statistics Kmer_Content Per_base_N_content Per_base_sequence_content Per_base_sequence_quality Per_sequence_quality_scores Sequence_Duplication_Levels Sequence_Length_Distribution)
+# dropped tables to avoid wast of space or not so informative:
+# Per_sequence_GC_content Overrepresented_sequences Per_tile_sequence_quality 
+# Overrepresented_sequences temporary removed it seems that when this fields pass the test there are no data associated with
+
+
+erb_file = 'index.html.erb'
+
+html_file = File.basename(erb_file, '.erb') #=>"page.html"
+
+erb_str = File.read(File.join(File.dirname(__FILE__),'../lib/bio-gfastqc',erb_file))
+
+renderer = ERB.new(erb_str)
+result = renderer.result()
+
+File.open(html_file, 'w') do |f|
+  f.write(result)
+end
+
+puts "Your comprehensive quality control file is ready in the current directory #{File.join(Dir.pwd,'index.html')}"
+
+

data/lib/bio-gfastqc.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-gfastqc/gfastqc.rb'
+

data/lib/bio-gfastqc/gfastqc.rb

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+
+module BioGfastqc
+end

data/lib/bio-gfastqc/index.html.erb

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+<!DOCTYPE html>
+<html>
+<head>
+  <title>Main FASTQC</title>
+  <script src="http://code.jquery.com/jquery-1.11.2.min.js"></script>
+  <script src="http://code.jquery.com/jquery-migrate-1.2.1.min.js"></script>
+
+  <!-- Latest compiled and minified CSS -->
+  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
+
+  <!-- Optional theme -->
+  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css">
+  <link rel="stylesheet" href="https://cdn.datatables.net/1.10.5/css/jquery.dataTables.min.css">
+  <!-- Latest compiled and minified JavaScript -->
+  <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>  
+  <script src="https://cdnjs.cloudflare.com/ajax/libs/holder/2.5.2/holder.min.js"></script> 
+  <script src="https://cdn.datatables.net/1.10.5/js/jquery.dataTables.min.js"></script>
+</head>
+<body>
+
+
+
+  <div id="main-container" class="container">
+    <div class="page-header">
+      <h1>G-FastQC</h1>
+      <h3><small>Aggregate FastQC results in single web page. You can explore Charts and Tables.</small></h3>
+    </div>
+
+    <div class="row">
+      <div class="col-xs-12">
+
+        <div role="tabpanel">
+          <ul class="nav nav-tabs" role="tablist" >
+              <li role="presentation"><a href="#charts" aria-controls="charts" role="tab" data-toggle="tab">Charts</a></li>
+              <li role="presentation"><a href="#tables" aria-controls="tables" role="tab" data-toggle="tab">Tables</a></li>
+          </ul>
+          <div class="tab-content">
+
+            <div role="tabpanel" class="tab-pane" id="charts">
+      <!-- Charts Start-->
+        <div role="tabpanel">
+          <ul class="nav nav-pills" role="tablist" >
+            <% @type_images.each do |type| %>
+              <li role="presentation"><a href="#<%= type %>" aria-controls="<%= type %>" role="tab" data-toggle="tab"><%= type %></a></li>
+            <% end %>
+          </ul>
+          <div class="tab-content">
+          <% @type_images.each do |type| %>
+            <div role="tabpanel" class="tab-pane" id="<%= type %>">
+              <div class="row">
+                <% @data.each_pair do |sample_name, pairs| %>
+                <div class="col-xs-6 col-md-6">
+                  <div class="caption">
+                  <h3><%= sample_name %></h3>
+                  <a href="#" class="thumbnail">
+                    <img data-src="holder.js/300x200" src="data:image/png;base64,<%= pairs[@base_file_names[0]][type] %>" alt="<%= sample_name + ' ' + @base_file_names[0] %>">
+                  </a>
+                  <a href="#" class="thumbnail">
+                    <img data-src="holder.js/300x200" src="data:image/png;base64,<%= pairs[@base_file_names[1]][type] %>" alt="<%= sample_name + ' ' + @base_file_names[1] %>">
+                  </a>
+                  </div>
+                </div>
+                <% end %>  
+              </div>             
+            </div>
+          <% end %>
+          </div>
+        </div>
+      <!-- Charts End-->
+            </div>
+
+            <div role="tabpanel" class="tab-pane" id="tables">
+      <!-- Tables Start-->
+        <div role="tabpanel">
+          <ul class="nav nav-pills" role="tablist" >
+            <% @type_tables.each do |type| %>
+              <li role="presentation"><a href="#<%= type %>_div_table" aria-controls="<%= type %>_div_table" role="tab" data-toggle="tab"><%= type %></a></li>
+            <% end %>
+          </ul>
+          <div class="tab-content">
+
+          <% @type_tables.each do |type| %>
+            <div role="tabpanel" class="tab-pane" id="<%= type %>_div_table">
+              <div class="row">
+                <% @tables.each_pair do |sample_name, reads| %>
+                  <% reads.each_pair do |reads_name, tables| %>
+                    <table id="<%= type %>_<%= sample_name %>_<%= reads_name %>_table" class="display" cellspacing="0" width="100%">
+                      <thead>
+                        <tr>
+                        <% tables[type]["header"].each do |col_name| %>
+                          <th><%= col_name %></th>
+                        <% end %>  
+                        </tr>
+                      </thead>
+                      <tbody>
+                      <% tables[type]["content"].each do |row| %>
+                        <tr>
+                        <% row.each do |col_value| %>
+                          <td><%= col_value %></td>
+                        <% end %>
+                        </tr>
+                      <% end %>
+                      </tbody>
+                    </table>
+                  <% end %>
+                <% end %>
+              </div>             
+            </div>
+          <% end %>
+          </div>
+        </div>
+      <!-- Charts End-->  
+            </div>
+
+
+          </div>
+        </div>
+
+
+
+
+      </div>
+    </div>
+  </div>
+</body>
+<script type="text/javascript">
+$(document).ready(function() {
+<% @type_tables.each do |type| %>
+  <% @tables.each_pair do |sample_name, reads| %>
+    <% reads.each_pair do |reads_name, tables| %>                    
+      $("#<%= type %>_<%= sample_name %>_<%= reads_name %>_table").DataTable();
+    <% end %>
+  <% end %>
+<% end %>
+} );
+</script>
+
+</html>

data/test/config.yml

@@ -0,0 +1,3 @@
+samples:
+  Sample_A: /path_to/Sample_A
+  Sample_B: /path_to/Sample_B

data/test/helper.rb

@@ -0,0 +1,34 @@
+require 'simplecov'
+
+module SimpleCov::Configuration
+  def clean_filters
+    @filters = []
+  end
+end
+
+SimpleCov.configure do
+  clean_filters
+  load_adapter 'test_frameworks'
+end
+
+ENV["COVERAGE"] && SimpleCov.start do
+  add_filter "/.rvm/"
+end
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-gfastqc'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-gfastqc.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioGfastqc < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,164 @@
+--- !ruby/object:Gem::Specification
+name: bio-gfastqc
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Raoul Jean Pierre Bonnal
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-03-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rubyzip
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !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: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+description: Bioinformatics. Aggregate FastQC (quality control for Next Generation
+  Sequencing -NGS-) results from many different samples in a single web page, with
+  charts and tables organized and simplified. The main goal is to speed up the communication
+  process with out colleagues (PIs, Biologists, BioInformaticians).
+email: ilpuccio.febo@gmail.com
+executables:
+- gfastqc
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/gfastqc
+- lib/bio-gfastqc.rb
+- lib/bio-gfastqc/gfastqc.rb
+- lib/bio-gfastqc/index.html.erb
+- test/config.yml
+- test/helper.rb
+- test/test_bio-gfastqc.rb
+homepage: http://github.com/helios/bioruby-gfastqc
+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: 2.4.3
+signing_key: 
+specification_version: 4
+summary: Bioinformatics. Aggregate FastQC (quality control for Next Generation Sequencing
+  -NGS-) results from many different samples in a single web page, with charts and
+  tables organized and simplified. The main goal is to speed up the communication
+  process with out colleagues (PIs, Biologists, BioInformaticians).
+test_files: []