bio-affy 0.1.0.alpha.1

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Files changed (72) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/Gemfile +15 -0
  4. data/Gemfile.lock +32 -0
  5. data/LICENSE.txt +20 -0
  6. data/README.rdoc +33 -0
  7. data/Rakefile +77 -0
  8. data/VERSION +1 -0
  9. data/bin/bio-affy +80 -0
  10. data/bio-affy.gemspec +128 -0
  11. data/ext/DESCRIPTION +11 -0
  12. data/ext/HISTORY +3 -0
  13. data/ext/LICENSE +456 -0
  14. data/ext/NAMESPACE +2 -0
  15. data/ext/R/check.cdf.type.R +18 -0
  16. data/ext/R/read.cdffile.list.R +23 -0
  17. data/ext/R/read.celfile.R +11 -0
  18. data/ext/R/read.celfile.header.R +37 -0
  19. data/ext/R/read.probematrices.R +29 -0
  20. data/ext/README_BIOLIB +36 -0
  21. data/ext/aclocal.m4 +32 -0
  22. data/ext/configure +4898 -0
  23. data/ext/configure.in +51 -0
  24. data/ext/man/check.cdf.type.Rd +22 -0
  25. data/ext/man/read.cdffile.list.Rd +20 -0
  26. data/ext/man/read.celfile.Rd +23 -0
  27. data/ext/man/read.celfile.header.Rd +22 -0
  28. data/ext/man/read.celfile.probeintensity.matrices.Rd +31 -0
  29. data/ext/src/CMakeLists.txt +39 -0
  30. data/ext/src/Makevars.in +3 -0
  31. data/ext/src/Makevars.win +2 -0
  32. data/ext/src/Rakefile +43 -0
  33. data/ext/src/biolib_affyio.c +416 -0
  34. data/ext/src/biolib_affyio.h +132 -0
  35. data/ext/src/biolib_affyio.o +0 -0
  36. data/ext/src/fread_functions.c +871 -0
  37. data/ext/src/fread_functions.h +60 -0
  38. data/ext/src/fread_functions.o +0 -0
  39. data/ext/src/libaffyext.so +0 -0
  40. data/ext/src/mkrf.log +11 -0
  41. data/ext/src/mkrf_conf.rb +6 -0
  42. data/ext/src/read_abatch.c +5484 -0
  43. data/ext/src/read_abatch.h +63 -0
  44. data/ext/src/read_abatch.o +0 -0
  45. data/ext/src/read_bpmap.c +888 -0
  46. data/ext/src/read_bpmap.o +0 -0
  47. data/ext/src/read_cdf.h +347 -0
  48. data/ext/src/read_cdf_xda.c +1342 -0
  49. data/ext/src/read_cdf_xda.o +0 -0
  50. data/ext/src/read_cdffile2.c +1576 -0
  51. data/ext/src/read_cdffile2.o +0 -0
  52. data/ext/src/read_celfile_generic.c +2061 -0
  53. data/ext/src/read_celfile_generic.h +33 -0
  54. data/ext/src/read_celfile_generic.o +0 -0
  55. data/ext/src/read_clf.c +870 -0
  56. data/ext/src/read_clf.o +0 -0
  57. data/ext/src/read_generic.c +1446 -0
  58. data/ext/src/read_generic.h +144 -0
  59. data/ext/src/read_generic.o +0 -0
  60. data/ext/src/read_pgf.c +1337 -0
  61. data/ext/src/read_pgf.o +0 -0
  62. data/lib/bio-affy.rb +5 -0
  63. data/lib/bio/affy.rb +7 -0
  64. data/lib/bio/affyext.rb +23 -0
  65. data/lib/bio/libaffyext.so +0 -0
  66. data/spec/bio-affy_spec.rb +22 -0
  67. data/spec/spec_helper.rb +13 -0
  68. data/test/data/affy/GSM103328.CEL.gz +0 -0
  69. data/test/data/affy/GSM103329.CEL.gz +0 -0
  70. data/test/data/affy/GSM103330.CEL.gz +0 -0
  71. data/test/data/affy/MG_U74Av2.CDF.gz +0 -0
  72. metadata +190 -0
@@ -0,0 +1,5 @@
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+ lib/**/*.rb
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+ bin/*
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+ -
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+ features/**/*.feature
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+ LICENSE.txt
data/.rspec ADDED
@@ -0,0 +1 @@
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+ --color
data/Gemfile ADDED
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+ source "http://rubygems.org"
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+ # Add dependencies required to use your gem here.
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+ # Example:
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+ # gem "activesupport", ">= 2.3.5"
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+
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+ # Add dependencies to develop your gem here.
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+ # Include everything needed to run rake, tests, features, etc.
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+ group :development do
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+ gem "rspec", "~> 2.7.0"
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+ gem "bundler", "~> 1.0.12"
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+ gem "jeweler", "~> 1.6.4"
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+ gem "rcov", ">= 0"
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+ gem "ffi", ">= 1.0.11"
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+ gem "mkrf", ">= 0.2.3"
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+ end
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+ GEM
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+ remote: http://rubygems.org/
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+ specs:
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+ diff-lcs (1.1.3)
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+ ffi (1.0.11)
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+ git (1.2.5)
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+ jeweler (1.6.4)
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+ bundler (~> 1.0)
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+ git (>= 1.2.5)
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+ rake
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+ mkrf (0.2.3)
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+ rake (0.9.2.2)
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+ rcov (0.9.11)
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+ rspec (2.7.0)
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+ rspec-core (~> 2.7.0)
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+ rspec-expectations (~> 2.7.0)
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+ rspec-mocks (~> 2.7.0)
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+ rspec-core (2.7.1)
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+ rspec-expectations (2.7.0)
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+ diff-lcs (~> 1.1.2)
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+ rspec-mocks (2.7.0)
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+
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+ PLATFORMS
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+ ruby
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+
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+ DEPENDENCIES
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+ bundler (~> 1.0.12)
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+ ffi (>= 1.0.11)
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+ jeweler (~> 1.6.4)
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+ mkrf (>= 0.2.3)
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+ rcov
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+ rspec (~> 2.7.0)
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+ Copyright (c) 2011 Pjotr Prins
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ = bio-affy
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+
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+ WARNING: This software is currently being developed! It may not be usable.
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+
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+ Affymetrix microarray file format parser (CEL/CDF) for Ruby.
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+
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+ == Introduction
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+
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+ This is a port of the Biolib-1.0 Affy parser for the Ruby FFI, which
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+ in turn, is an adaptation of Ben Bolstad's work for R.
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+
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+ To use this tool you do not need to know Ruby.
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+
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+ == Install
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+
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+ Requirements: to install this software you need an installation of R and Ruby 1.9, e.g on Debian
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+
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+ apt-get install r-base-core ruby1.9
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+
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+ After installing ruby 1.9, you can use rubygems
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+
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+ gem install bio-affy
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+
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+ Next run the tool with
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+
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+ bio-affy --help
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+
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+ == Copyright
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+
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+ Copyright (C) 2011 Pjotr Prins <pjotr.prins@thebird.nl>
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+
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+ See LICENSE.txt for further details.
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+
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+ # encoding: utf-8
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+
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+ require 'psych'
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+ require 'rubygems'
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+ require 'bundler'
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+
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'rake'
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+ require 'rake/clean'
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+
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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+ gem.name = "bio-affy"
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+ gem.homepage = "http://github.com/pjotrp/bioruby-affy"
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+ gem.license = "MIT"
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+ gem.summary = %Q{Parse Affymetrix CEL/CDF files}
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+ gem.description = %Q{Affymetrix microarray file format parser
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+ (CEL/CDF) for Ruby. FFI binding to Biolib port of R/Affyio by Benjamin Milo Bolstad}
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+ gem.email = "pjotr.public01@thebird.nl"
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+ gem.authors = ["Pjotr Prins"]
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+ gem.extensions = "ext/src/mkrf_conf.rb"
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+ gem.files += Dir['lib/**/*'] + Dir['ext/**/*']
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+ gem.rubyforge_project = "nowarning"
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+
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+ # dependencies defined in Gemfile
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+ end
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+ Jeweler::RubygemsDotOrgTasks.new
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+
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+ CLEAN.include('ext/src/Rakefile')
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+ CLEAN.include('ext/src/*.log')
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+ CLEAN.include('ext/src/*.o')
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+ CLEAN.include('ext/src/*.so')
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+ CLEAN.include('lib/bio/*.so')
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+
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+ require 'rspec/core'
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+ require 'rspec/core/rake_task'
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+ RSpec::Core::RakeTask.new(:spec) do |spec|
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+ spec.pattern = FileList['spec/**/*_spec.rb']
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+ end
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+
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+ RSpec::Core::RakeTask.new(:rcov) do |spec|
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+ spec.pattern = 'spec/**/*_spec.rb'
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+ spec.rcov = true
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+ end
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+
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+ file "lib/libbio-affy.so" => Dir.glob("ext/src/*{.rb,.c}") do
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+ Dir.chdir("ext/src") do
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+ ruby "mkrf_conf.rb"
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+ sh "rake"
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+ end
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+ cp "ext/src/libaffyext.so", "lib/bio/libaffyext.so"
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+ end
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+
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+ desc "Default builds and tests bio-affy"
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+ task :default => [:build, :test]
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+
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+ desc "Build extension"
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+ task :build => [ "lib/libbio-affy.so" ]
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+
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+ task :test => [ :build, :spec ]
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+
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+ # require 'rdoc/task'
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+ # Rake::RDocTask.new do |rdoc|
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+ # version = File.exist?('VERSION') ? File.read('VERSION') : ""
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+
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+ # rdoc.rdoc_dir = 'rdoc'
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+ # rdoc.title = "bio-affy #{version}"
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+ # rdoc.rdoc_files.include('README*')
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+ # rdoc.rdoc_files.include('lib/**/*.rb')
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+ # end
data/VERSION ADDED
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+ 0.1.0.alpha.1
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+ #!/usr/bin/env ruby
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+ #
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+ # BioRuby bio-affy Plugin
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+ # Version 0.0.0
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+ # Author:: Pjotr Prins
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+ # Copyright:: 2011
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+ # License:: The Ruby License
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+
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+ ROOT = File.dirname(__FILE__)
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+ $: << File.join([ROOT, "..","lib"])
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+ # ENV['LD_LIBRARY_PATH'] = File.join([ROOT, "..","lib"])
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+
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+ USAGE = "bio-affy"
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+
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+ if ARGV.size == 0
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+ print USAGE
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+ end
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+
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+ require 'bio-affy'
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+ require 'optparse'
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+
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+ # Uncomment when using the bio-logger
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+ # require 'bio-logger'
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+ # Bio::Log::CLI.logger('stderr')
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+ # Bio::Log::CLI.trace('info')
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+
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+ options = {:example_switch=>false,:show_help=>false}
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+ opts = OptionParser.new do |o|
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+ o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
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+
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+ o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
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+ # TODO: your logic here, below an example
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+ options[:example_parameter] = 'this is a parameter'
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+ end
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+
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+ o.separator ""
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+ o.on("--switch-example", 'TODO: put a description for the SWITCH') do
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+ # TODO: your logic here, below an example
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+ self[:example_switch] = true
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+ end
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+
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+ # Uncomment the following when using the bio-logger
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+ # o.separator ""
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+ # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
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+ # Bio::Log::CLI.logger(name)
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+ # end
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+ #
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+ # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
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+ # Bio::Log::CLI.trace(s)
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+ # end
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+ #
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+ # o.on("-q", "--quiet", "Run quietly") do |q|
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+ # Bio::Log::CLI.trace('error')
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+ # end
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+ #
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+ # o.on("-v", "--verbose", "Run verbosely") do |v|
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+ # Bio::Log::CLI.trace('info')
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+ # end
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+ #
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+ # o.on("--debug", "Show debug messages") do |v|
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+ # Bio::Log::CLI.trace('debug')
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+ # end
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+
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+ o.separator ""
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+ o.on_tail('-h', '--help', 'display this help and exit') do
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+ options[:show_help] = true
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+ end
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+ end
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+
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+ begin
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+ opts.parse!(ARGV)
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+
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+ # Uncomment the following when using the bio-logger
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+ # Bio::Log::CLI.configure('bio-affy')
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+
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+ # TODO: your code here
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+ # use options for your logic
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+ rescue OptionParser::InvalidOption => e
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+ options[:invalid_argument] = e.message
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+ end
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+ # Generated by jeweler
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+ # DO NOT EDIT THIS FILE DIRECTLY
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+ # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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+ # -*- encoding: utf-8 -*-
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+
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+ Gem::Specification.new do |s|
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+ s.name = "bio-affy"
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+ s.version = "0.1.0.alpha.1"
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+
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+ s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
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+ s.authors = ["Pjotr Prins"]
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+ s.date = "2011-12-03"
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+ s.description = "Affymetrix microarray file format parser\n (CEL/CDF) for Ruby. FFI binding to Biolib port of R/Affyio by Benjamin Milo Bolstad"
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+ s.email = "pjotr.public01@thebird.nl"
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+ s.executables = ["bio-affy"]
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+ s.extensions = ["ext/src/mkrf_conf.rb"]
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+ s.extra_rdoc_files = [
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+ "LICENSE.txt",
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+ "README.rdoc"
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+ ]
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+ s.files = [
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+ ".document",
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+ ".rspec",
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+ "Gemfile",
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+ "Gemfile.lock",
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+ "LICENSE.txt",
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+ "README.rdoc",
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+ "Rakefile",
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+ "VERSION",
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+ "bin/bio-affy",
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+ "bio-affy.gemspec",
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+ "ext/DESCRIPTION",
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+ "ext/HISTORY",
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+ "ext/LICENSE",
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+ "ext/NAMESPACE",
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+ "ext/R/check.cdf.type.R",
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+ "ext/R/read.cdffile.list.R",
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+ "ext/R/read.celfile.R",
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+ "ext/R/read.celfile.header.R",
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+ "ext/R/read.probematrices.R",
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+ "ext/README_BIOLIB",
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+ "ext/aclocal.m4",
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+ "ext/configure",
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+ "ext/configure.in",
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+ "ext/man/check.cdf.type.Rd",
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+ "ext/man/read.cdffile.list.Rd",
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+ "ext/man/read.celfile.Rd",
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+ "ext/man/read.celfile.header.Rd",
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+ "ext/man/read.celfile.probeintensity.matrices.Rd",
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+ "ext/src/CMakeLists.txt",
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+ "ext/src/Makevars.in",
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+ "ext/src/Makevars.win",
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+ "ext/src/Rakefile",
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+ "ext/src/biolib_affyio.c",
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+ "ext/src/biolib_affyio.h",
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+ "ext/src/biolib_affyio.o",
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+ "ext/src/fread_functions.c",
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+ "ext/src/fread_functions.h",
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+ "ext/src/fread_functions.o",
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+ "ext/src/libaffyext.so",
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+ "ext/src/mkrf.log",
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+ "ext/src/mkrf_conf.rb",
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+ "ext/src/read_abatch.c",
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+ "ext/src/read_abatch.h",
65
+ "ext/src/read_abatch.o",
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+ "ext/src/read_bpmap.c",
67
+ "ext/src/read_bpmap.o",
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+ "ext/src/read_cdf.h",
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+ "ext/src/read_cdf_xda.c",
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+ "ext/src/read_cdf_xda.o",
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+ "ext/src/read_cdffile2.c",
72
+ "ext/src/read_cdffile2.o",
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+ "ext/src/read_celfile_generic.c",
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+ "ext/src/read_celfile_generic.h",
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+ "ext/src/read_celfile_generic.o",
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+ "ext/src/read_clf.c",
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+ "ext/src/read_clf.o",
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+ "ext/src/read_generic.c",
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+ "ext/src/read_generic.h",
80
+ "ext/src/read_generic.o",
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+ "ext/src/read_pgf.c",
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+ "ext/src/read_pgf.o",
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+ "lib/bio-affy.rb",
84
+ "lib/bio/affy.rb",
85
+ "lib/bio/affyext.rb",
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+ "lib/bio/libaffyext.so",
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+ "spec/bio-affy_spec.rb",
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+ "spec/spec_helper.rb",
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+ "test/data/affy/GSM103328.CEL.gz",
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+ "test/data/affy/GSM103329.CEL.gz",
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+ "test/data/affy/GSM103330.CEL.gz",
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+ "test/data/affy/MG_U74Av2.CDF.gz"
93
+ ]
94
+ s.homepage = "http://github.com/pjotrp/bioruby-affy"
95
+ s.licenses = ["MIT"]
96
+ s.require_paths = ["lib"]
97
+ s.rubyforge_project = "nowarning"
98
+ s.rubygems_version = "1.8.10"
99
+ s.summary = "Parse Affymetrix CEL/CDF files"
100
+
101
+ if s.respond_to? :specification_version then
102
+ s.specification_version = 3
103
+
104
+ if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
105
+ s.add_development_dependency(%q<rspec>, ["~> 2.7.0"])
106
+ s.add_development_dependency(%q<bundler>, ["~> 1.0.12"])
107
+ s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
108
+ s.add_development_dependency(%q<rcov>, [">= 0"])
109
+ s.add_development_dependency(%q<ffi>, [">= 1.0.11"])
110
+ s.add_development_dependency(%q<mkrf>, [">= 0.2.3"])
111
+ else
112
+ s.add_dependency(%q<rspec>, ["~> 2.7.0"])
113
+ s.add_dependency(%q<bundler>, ["~> 1.0.12"])
114
+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
115
+ s.add_dependency(%q<rcov>, [">= 0"])
116
+ s.add_dependency(%q<ffi>, [">= 1.0.11"])
117
+ s.add_dependency(%q<mkrf>, [">= 0.2.3"])
118
+ end
119
+ else
120
+ s.add_dependency(%q<rspec>, ["~> 2.7.0"])
121
+ s.add_dependency(%q<bundler>, ["~> 1.0.12"])
122
+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
123
+ s.add_dependency(%q<rcov>, [">= 0"])
124
+ s.add_dependency(%q<ffi>, [">= 1.0.11"])
125
+ s.add_dependency(%q<mkrf>, [">= 0.2.3"])
126
+ end
127
+ end
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+
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+ Package: affyio
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+ Version: 1.15.1
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+ Title: Tools for parsing Affymetrix data files
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+ Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
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+ Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
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+ Depends: R (>= 2.6.0), methods
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+ Description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
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+ License: LGPL (>= 2)
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+ biocViews: Microarray, DataImport, Infrastructure
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+ LazyLoad: yes
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+ Packaged: 2009-11-10 20:54:53 UTC; biocbuild
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+ Nov 29, 2005 - Initial importation of existing C source code from the affy and makecdfenv packages.
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+
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+ Dec 1, 2005 - comment cleaning in C source code. Add read.cdffile.list.R, check.cdf.type.R
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+ GNU LESSER GENERAL PUBLIC LICENSE
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+ Version 2.1, February 1999
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+
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+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
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+ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
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+ Everyone is permitted to copy and distribute verbatim copies
7
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