bio-affy 0.1.0.alpha.1

data/lib/bio-affy.rb

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+require 'rubygems'
+require 'ffi'
+
+require 'bio/affyext'
+require 'bio/affy'

data/lib/bio/affy.rb

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+
+module Bio
+
+  module Affy
+  end
+
+end

data/lib/bio/affyext.rb

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+
+module Bio
+
+  module Affy
+
+    module Ext
+
+      extend FFI::Library
+      DIR = File.dirname(__FILE__)
+
+      ffi_lib File.join(DIR,'libaffyext.so')  # <-- fix for OSX
+      ffi_convention :stdcall
+
+      attach_function :has_affyext, [ :int ], :int
+      # attach_function :open_cdffile, [ :string ], :pointer
+      def open_cdffile s
+      end
+
+    end
+
+  end
+
+end

data/spec/bio-affy_spec.rb

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+ROOT = File.dirname(__FILE__)
+$: << File.join([ROOT, "..","lib"])
+# ENV['LD_LIBRARY_PATH'] = File.join([ROOT, "..","lib"])
+
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio-affy'
+
+DATADIR = ROOT + File.join('test','data','affy')
+CDF = DATADIR+"MG_U74Av2.CDF.gz"
+CEL1 = DATADIR+"GSM103328.CEL.gz"
+
+describe "BioAffy" do
+  it "should find the shared library" do
+    Bio::Affy::Ext.has_affyext(5).should == 60
+  end
+  it "should open a CDF file" do
+    @cdf = Bio::Affy::Ext.open_cdffile(CDF)
+  end
+  it "should open a CEL file"
+  it "should find the probe values"
+  it "should name the probes"
+end

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-affy'
+
+# 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-affy
+version: !ruby/object:Gem::Version
+  version: 0.1.0.alpha.1
+  prerelease: 6
+platform: ruby
+authors:
+- Pjotr Prins
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-12-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &18461260 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
+  type: :development
+  prerelease: false
+  version_requirements: *18461260
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &18460160 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.12
+  type: :development
+  prerelease: false
+  version_requirements: *18460160
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &18459540 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *18459540
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &18458800 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *18458800
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: &18458220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.11
+  type: :development
+  prerelease: false
+  version_requirements: *18458220
+- !ruby/object:Gem::Dependency
+  name: mkrf
+  requirement: &18457560 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.2.3
+  type: :development
+  prerelease: false
+  version_requirements: *18457560
+description: ! "Affymetrix microarray file format parser\n  (CEL/CDF) for Ruby. FFI
+  binding to Biolib port of R/Affyio by Benjamin Milo Bolstad"
+email: pjotr.public01@thebird.nl
+executables:
+- bio-affy
+extensions:
+- ext/src/mkrf_conf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+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
+homepage: http://github.com/pjotrp/bioruby-affy
+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: 4468183158933499689
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: nowarning
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Parse Affymetrix CEL/CDF files
+test_files: []