bio-affy 0.1.0.alpha.1

data/.document

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

data/.rspec

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+--color

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 "rspec", "~> 2.7.0"
+  gem "bundler", "~> 1.0.12"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "ffi", ">= 1.0.11"
+  gem "mkrf", ">= 0.2.3"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    diff-lcs (1.1.3)
+    ffi (1.0.11)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    mkrf (0.2.3)
+    rake (0.9.2.2)
+    rcov (0.9.11)
+    rspec (2.7.0)
+      rspec-core (~> 2.7.0)
+      rspec-expectations (~> 2.7.0)
+      rspec-mocks (~> 2.7.0)
+    rspec-core (2.7.1)
+    rspec-expectations (2.7.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.7.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.12)
+  ffi (>= 1.0.11)
+  jeweler (~> 1.6.4)
+  mkrf (>= 0.2.3)
+  rcov
+  rspec (~> 2.7.0)

data/LICENSE.txt

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+Copyright (c) 2011 Pjotr Prins
+
+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-affy
+
+WARNING: This software is currently being developed! It may not be usable.
+
+Affymetrix microarray file format parser (CEL/CDF) for Ruby.
+
+== Introduction
+
+This is a port of the Biolib-1.0 Affy parser for the Ruby FFI, which
+in turn, is an adaptation of Ben Bolstad's work for R. 
+
+To use this tool you do not need to know Ruby.
+
+== Install
+
+Requirements: to install this software you need an installation of R and Ruby 1.9, e.g on Debian
+
+  apt-get install r-base-core ruby1.9
+
+After installing ruby 1.9, you can use rubygems
+
+  gem install bio-affy
+
+Next run the tool with
+
+  bio-affy --help
+
+== Copyright
+
+Copyright (C) 2011 Pjotr Prins <pjotr.prins@thebird.nl> 
+
+See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'psych'
+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 'rake/clean'
+
+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-affy"
+  gem.homepage = "http://github.com/pjotrp/bioruby-affy"
+  gem.license = "MIT"
+  gem.summary = %Q{Parse Affymetrix CEL/CDF files}
+  gem.description = %Q{Affymetrix microarray file format parser
+  (CEL/CDF) for Ruby. FFI binding to Biolib port of R/Affyio by Benjamin Milo Bolstad}
+  gem.email = "pjotr.public01@thebird.nl"
+  gem.authors = ["Pjotr Prins"]
+  gem.extensions = "ext/src/mkrf_conf.rb"
+  gem.files += Dir['lib/**/*'] + Dir['ext/**/*']
+  gem.rubyforge_project = "nowarning"
+
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+CLEAN.include('ext/src/Rakefile')
+CLEAN.include('ext/src/*.log')
+CLEAN.include('ext/src/*.o')
+CLEAN.include('ext/src/*.so')
+CLEAN.include('lib/bio/*.so')
+
+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
+
+file "lib/libbio-affy.so" => Dir.glob("ext/src/*{.rb,.c}") do
+   Dir.chdir("ext/src") do
+     ruby "mkrf_conf.rb"
+     sh "rake"
+  end
+  cp "ext/src/libaffyext.so", "lib/bio/libaffyext.so"
+end
+
+desc "Default builds and tests bio-affy"
+task :default => [:build, :test]
+
+desc "Build extension"
+task :build => [ "lib/libbio-affy.so" ]
+
+task :test => [ :build, :spec ]
+
+# require 'rdoc/task'
+# Rake::RDocTask.new do |rdoc|
+#   version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+#   rdoc.rdoc_dir = 'rdoc'
+#   rdoc.title = "bio-affy #{version}"
+#   rdoc.rdoc_files.include('README*')
+#   rdoc.rdoc_files.include('lib/**/*.rb')
+# end

data/VERSION

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+0.1.0.alpha.1

data/bin/bio-affy

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+#!/usr/bin/env ruby
+#
+# BioRuby bio-affy Plugin
+# Version 0.0.0 
+# Author:: Pjotr Prins
+# Copyright:: 2011
+# License:: The Ruby License
+
+ROOT = File.dirname(__FILE__)
+$: << File.join([ROOT, "..","lib"])
+# ENV['LD_LIBRARY_PATH'] = File.join([ROOT, "..","lib"])
+
+USAGE = "bio-affy"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-affy'
+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-affy')
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end

data/bio-affy.gemspec

@@ -0,0 +1,128 @@
+# 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 = "bio-affy"
+  s.version = "0.1.0.alpha.1"
+
+  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Pjotr Prins"]
+  s.date = "2011-12-03"
+  s.description = "Affymetrix microarray file format parser\n  (CEL/CDF) for Ruby. FFI binding to Biolib port of R/Affyio by Benjamin Milo Bolstad"
+  s.email = "pjotr.public01@thebird.nl"
+  s.executables = ["bio-affy"]
+  s.extensions = ["ext/src/mkrf_conf.rb"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/bio-affy",
+    "bio-affy.gemspec",
+    "ext/DESCRIPTION",
+    "ext/HISTORY",
+    "ext/LICENSE",
+    "ext/NAMESPACE",
+    "ext/R/check.cdf.type.R",
+    "ext/R/read.cdffile.list.R",
+    "ext/R/read.celfile.R",
+    "ext/R/read.celfile.header.R",
+    "ext/R/read.probematrices.R",
+    "ext/README_BIOLIB",
+    "ext/aclocal.m4",
+    "ext/configure",
+    "ext/configure.in",
+    "ext/man/check.cdf.type.Rd",
+    "ext/man/read.cdffile.list.Rd",
+    "ext/man/read.celfile.Rd",
+    "ext/man/read.celfile.header.Rd",
+    "ext/man/read.celfile.probeintensity.matrices.Rd",
+    "ext/src/CMakeLists.txt",
+    "ext/src/Makevars.in",
+    "ext/src/Makevars.win",
+    "ext/src/Rakefile",
+    "ext/src/biolib_affyio.c",
+    "ext/src/biolib_affyio.h",
+    "ext/src/biolib_affyio.o",
+    "ext/src/fread_functions.c",
+    "ext/src/fread_functions.h",
+    "ext/src/fread_functions.o",
+    "ext/src/libaffyext.so",
+    "ext/src/mkrf.log",
+    "ext/src/mkrf_conf.rb",
+    "ext/src/read_abatch.c",
+    "ext/src/read_abatch.h",
+    "ext/src/read_abatch.o",
+    "ext/src/read_bpmap.c",
+    "ext/src/read_bpmap.o",
+    "ext/src/read_cdf.h",
+    "ext/src/read_cdf_xda.c",
+    "ext/src/read_cdf_xda.o",
+    "ext/src/read_cdffile2.c",
+    "ext/src/read_cdffile2.o",
+    "ext/src/read_celfile_generic.c",
+    "ext/src/read_celfile_generic.h",
+    "ext/src/read_celfile_generic.o",
+    "ext/src/read_clf.c",
+    "ext/src/read_clf.o",
+    "ext/src/read_generic.c",
+    "ext/src/read_generic.h",
+    "ext/src/read_generic.o",
+    "ext/src/read_pgf.c",
+    "ext/src/read_pgf.o",
+    "lib/bio-affy.rb",
+    "lib/bio/affy.rb",
+    "lib/bio/affyext.rb",
+    "lib/bio/libaffyext.so",
+    "spec/bio-affy_spec.rb",
+    "spec/spec_helper.rb",
+    "test/data/affy/GSM103328.CEL.gz",
+    "test/data/affy/GSM103329.CEL.gz",
+    "test/data/affy/GSM103330.CEL.gz",
+    "test/data/affy/MG_U74Av2.CDF.gz"
+  ]
+  s.homepage = "http://github.com/pjotrp/bioruby-affy"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = "nowarning"
+  s.rubygems_version = "1.8.10"
+  s.summary = "Parse Affymetrix CEL/CDF files"
+
+  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_development_dependency(%q<rspec>, ["~> 2.7.0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.12"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<ffi>, [">= 1.0.11"])
+      s.add_development_dependency(%q<mkrf>, [">= 0.2.3"])
+    else
+      s.add_dependency(%q<rspec>, ["~> 2.7.0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.12"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<ffi>, [">= 1.0.11"])
+      s.add_dependency(%q<mkrf>, [">= 0.2.3"])
+    end
+  else
+    s.add_dependency(%q<rspec>, ["~> 2.7.0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.12"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<ffi>, [">= 1.0.11"])
+    s.add_dependency(%q<mkrf>, [">= 0.2.3"])
+  end
+end
+

data/ext/DESCRIPTION

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+Package: affyio
+Version: 1.15.1
+Title: Tools for parsing Affymetrix data files
+Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
+Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
+Depends: R (>= 2.6.0), methods
+Description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
+License: LGPL (>= 2)
+biocViews: Microarray, DataImport, Infrastructure
+LazyLoad: yes
+Packaged: 2009-11-10 20:54:53 UTC; biocbuild

data/ext/HISTORY

@@ -0,0 +1,3 @@
+Nov 29, 2005 - Initial importation of existing C source code from the affy and makecdfenv packages.
+
+Dec 1, 2005 - comment cleaning in C source code. Add read.cdffile.list.R, check.cdf.type.R 

data/ext/LICENSE

@@ -0,0 +1,456 @@
+		  GNU LESSER GENERAL PUBLIC LICENSE
+		       Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+     51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL.  It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
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+specially designated software packages--typically libraries--of the
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