bio-affy 0.5.0 → 0.5.1

data/README.rdoc

@@ -1,15 +1,29 @@
 = bio-affy
 
-WARNING: This software is currently being developed! It may not be usable.
-
 Affymetrix microarray file format parser (CEL/CDF) for Ruby.
 
+Are you tired waiting for R/Bioconductor to download and install? Are
+you weary of R's slowness and memory consumption? Do you want Ruby's
+convenience? Try creating a biogem, and use bio-affy's foreign
+function interface (FFI) strategy for linking against R's C libraries.
+
+For an example of the API see https://github.com/pjotrp/bioruby-affy/blob/master/spec/bio-affy_spec.rb
+
 == 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. 
+This is a port of the Biolib-1.0 Affy parser, which in turn is an
+adaptation of Ben Bolstad's Affyio library for R/Bioconductor.
+
+You can query CDF files for feature names of probesets, the number of probesets and 
+probe types, and the indices of probes on the array. 
+
+You can query CEL files for raw expression values of PM probes and MM probes.
+
+This implementation allows processing one or more microarrays at a
+time. It is not necessary to load all microarrays in RAM.
 
-To use this tool you do not need to know Ruby.
+To use the command line tool you do not need to know Ruby (note, the command line
+interface is not ready).
 
 == Install
 
@@ -28,18 +42,18 @@ Next run the tool with
 This module was written with 
 
   ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux]
-  Using rake (0.9.2.2) 
-  Using bundler (1.0.21) 
-  Using diff-lcs (1.1.3) 
-  Using ffi (1.0.11) 
-  Using git (1.2.5) 
-  Using jeweler (1.6.4) 
-  Using mkrf (0.2.3) 
-  Using rcov (0.9.11) 
-  Using rspec-core (2.7.1) 
-  Using rspec-expectations (2.7.0) 
-  Using rspec-mocks (2.7.0) 
-  Using rspec (2.7.0) 
+    Using rake (0.9.2.2) 
+    Using bundler (1.0.21) 
+    Using diff-lcs (1.1.3) 
+    Using ffi (1.0.11) 
+    Using git (1.2.5) 
+    Using jeweler (1.6.4) 
+    Using mkrf (0.2.3) 
+    Using rcov (0.9.11) 
+    Using rspec-core (2.7.1) 
+    Using rspec-expectations (2.7.0) 
+    Using rspec-mocks (2.7.0) 
+    Using rspec (2.7.0) 
 
 == Copyright
 

data/Rakefile

@@ -27,7 +27,7 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Pjotr Prins"]
   gem.extensions = "ext/src/mkrf_conf.rb"
   gem.files += Dir['lib/**/*'] + Dir['ext/**/*']
-  gem.files.reject! { | n | n =~ /\.(o|so|gz|CDF|R|Rd|log)$/ }
+  gem.files.reject! { | n | n =~ /\.(o|so|gz|CDF|cdf|CEL|cel|R|Rd|log)$/ }
   gem.rubyforge_project = "nowarning"
 
   # dependencies defined in Gemfile

data/VERSION

@@ -1 +1 @@
-0.5.0
+0.5.1

data/bio-affy.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-affy"
-  s.version = "0.5.0"
+  s.version = "0.5.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = "2011-12-05"
+  s.date = "2011-12-09"
   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"]

data/lib/bio/affy.rb

@@ -2,6 +2,19 @@
 module Bio
 
   module Affy
+
+    module Find 
+      def Find.probeset_by_feature_name cdf, name
+        num_probesets = Bio::Affy::Ext.cdf_num_probesets(cdf)
+        (0..num_probesets-1).each do | i |
+          probeset_ptr = Bio::Affy::Ext.cdf_probeset_info(cdf,i)
+          probeset = Bio::Affy::CDFProbeSet.new(probeset_ptr)
+          return i if probeset.name == name
+        end
+        nil
+      end
+    end
+
   end
 
 end

data/lib/bio/affyext.rb

@@ -3,6 +3,17 @@ module Bio
 
   module Affy
 
+    class CDFProbeInfo < FFI::Struct
+      layout :x, :uint,
+             :y, :uint
+      def x
+        self[:x]
+      end
+      def y
+        self[:y]
+      end
+    end
+
     class CDFProbeSet < FFI::Struct
       layout :isQC,    :int,
              :pm_num,  :int,
@@ -10,6 +21,10 @@ module Bio
              :pm,      :pointer,
              :mm,      :pointer,
              :name,    [:uint8, 64] 
+
+      def name 
+        self[:name].to_ptr.read_string 
+      end
     end
 
     module Ext
@@ -29,6 +44,10 @@ module Bio
       attach_function :cel_num_intensities, [ :pointer ], :uint64
       attach_function :cdf_num_probesets, [ :pointer ], :uint64
       attach_function :cdf_probeset_info, [ :pointer, :int ], :pointer
+      attach_function :cel_pm, [:pointer, :pointer, :int, :int ], :double
+      attach_function :cdf_pmprobe_info, [:pointer, :int, :int], :pointer
+      # more bindings are available, check out the functions defined in ./ext/src
+      # and the biolib test_affyio.rb file
     end
 
   end

data/spec/bio-affy_spec.rb

@@ -6,39 +6,132 @@ require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 require 'bio-affy'
 
 DATADIR = File.join([ROOT,'test','data','affy'])
-CDF = File.join(DATADIR,"MG_U74Av2.CDF")
+CDF = File.join(DATADIR,"MG_U74Av2.CDF")    # GPL81
 CDF2 = File.join(DATADIR,"ATH1-121501.CDF")
 CEL1 = File.join(DATADIR,"GSM103328.CEL.gz")
 
-describe "BioAffy" do
+describe "Bio::Affy::Ext1" do
+ 
   it "should find the shared library" do
     Bio::Affy::Ext.has_affyext(5).should == 60
   end
-  it "should open a CDF file" do
+end
+
+describe "Bio::Affy::Ext" do
+  before :all do 
+    # first start the R environment
     Bio::Affy::Ext.BioLib_R_Init()
-    cdf = Bio::Affy::Ext.open_cdffile(CDF)
-    cdf.null?.should == false
-    num_probesets = Bio::Affy::Ext.cdf_num_probesets(cdf)
+    # load the CDF once
+    @cdf = Bio::Affy::Ext.open_cdffile(CDF)
+    # load a CEL file once
+    @cel = Bio::Affy::Ext.open_celfile(CEL1)
+  end
+  it "should open a CDF file" do
+    @cdf.null?.should == false
+  end
+  it "should count the probesets" do
+    # Open the Mouse CDF file - in Bioconductor this would be
+    #
+    #   source("http://bioconductor.org/biocLite.R")
+    #   biocLite("affy")
+    #   library(affy)
+    #   library(makecdfenv)
+    #   make.cdf.package('test.cdf',species='test')
+    #   exit and R CMD INSTALL testcdf/
+    #   m <- ReadAffy(cdfname='test')
+    #
+    # because CDF files are not read directly. bio-affy, however can:
+    num_probesets = Bio::Affy::Ext.cdf_num_probesets(@cdf)
     num_probesets.should == 12501
   end
   it "should open a CEL file" do
-    cel1 = Bio::Affy::Ext.open_celfile(CEL1)
-    num = Bio::Affy::Ext.cel_num_intensities(cel1)
+    # Open the Mouse CEL files - in Bioconductor this would be
+    #
+    #   source("http://bioconductor.org/biocLite.R")
+    #   biocLite("affy")
+    #   library(affy)
+    #   m <- ReadAffy()
+    #   dim(m)
+    #     Cols Rows 
+    #     640  640  == 409600
+
+    num = Bio::Affy::Ext.cel_num_intensities(@cel)
     num.should == 409600 
   end
-  it "should find the probe value for 1511" do
-    cel = Bio::Affy::Ext.open_celfile(CEL1)
-    probe_value = Bio::Affy::Ext.cel_intensity(cel,1510)
+  it "should find the CDF cel intensity value" do
+    # In Bioconductor, after m <- ReadAffy()
+    #
+    probe_value = Bio::Affy::Ext.cel_intensity(@cel,1510)
     probe_value.should == 10850.8
   end
-  it "should name the probes for 1511" do
-    cdf = Bio::Affy::Ext.open_cdffile(CDF)
-    # memptr = MemoryPointer.new :pointer
-    probeset_ptr = Bio::Affy::Ext.cdf_probeset_info(cdf,1510)
+  it "should get the probeset indexes from the CDF" do
+    cdf_cols = 640 # (cdf.cols)
+    # R/Bioconductor:
+    #
+    # > as.vector(geneNames(m))[11657]
+    # [1] "98910_at"
+    # 
+    # cat(indexProbes(m, which="pm", genenames="98910_at")[[1]],sep=",")
+    # 344297,177348,21247,246762,200777,166097,382469,397538,66238,344987,11503,253234,206965,103391,54927,333474
+    #
+    # or
+    #
+    # pmindex(m,"98910_at")
+    #
+
+    pm0 = [ 344297,177348,21247,246762,200777,166097,382469,397538,66238,344987,11503,253234,206965,103391,54927,333474 ]
+    pm0.each_with_index do | index, i |
+      # call with probeset, probenum
+      probe_ptr = Bio::Affy::Ext.cdf_pmprobe_info(@cdf,1510,i)
+      probe = Bio::Affy::CDFProbeInfo.new(probe_ptr)
+      # p [probe.x, probe.y]
+      # p [ index, probe.x, probe.y, probe.x + probe.y*@cdf.cols + 1]
+      (probe.x + probe.y*cdf_cols + 1).should == index
+    end
+
+    
+  end
+
+  it "should get the probeset information" do
+    # In Bioconductor, after m <- ReadAffy()
+    #
+    # > length(featureNames(m))
+    # [1] 12488  (12501 in bio-affy - we add the 13 controls)
+    #
+    # Note also the feature numbering is different in the Bioconductor set:
+    # > as.vector(geneNames(m))[0:5]
+    # [1] "100001_at" "100002_at" "100003_at" "100004_at" "100005_at"
+    # > as.vector(geneNames(m))[1509:1512]
+    # [1] "101947_at" "101948_at" "101949_at" "101950_at"
+    # > as.vector(geneNames(m))[11657]
+    # [1] "98910_at"  <- this is what we test at index 1510.
+    probeset_ptr = Bio::Affy::Ext.cdf_probeset_info(@cdf,1510)
     probeset = Bio::Affy::CDFProbeSet.new(probeset_ptr)
     probeset[:isQC].should == 0
     probeset[:pm_num].should == 16
     probeset[:mm_num].should == 16
+    # 98910_at	144	P	0.009985 (normalized on GEO)
     probeset[:name].to_ptr.read_string.should == "98910_at"
+    # now use the convenience methods
+    probeset.name.should == "98910_at"
+  end
+  it "should fetch the PM (perfect match) values" do
+    # Test PM values; as in R's pm(m)[1,1:8]
+    #  mypmindex <- pmindex(m,"98910_at")
+    #  cat(intensity(m)[mypmindex$`98910_at`],sep=",")
+    # Bioconductor 1.9 - even with test.cdf ought to be
+
+    pms = [ 120,768,1046,1220.3,345.3,171.3,138,171.3,189,343.3,605.3,1064.5,4429.3,854.3,2675,886.3]
+    pms.each_with_index do | e, i |
+      # p Biolib::Affyio.cel_pm(@microarrays[1],@cdf,1510,i)
+      Bio::Affy::Ext.cel_pm(@cel,@cdf,1510,i).should == e
+    end
+  end
+  # convenience methods
+  it "should find the probeset for 98910_at" do
+    probeset_index = Bio::Affy::Find.probeset_by_feature_name(@cdf,"98910_at")
+    probeset_index.should == 1510
   end
 end
+
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-affy
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-05 00:00:00.000000000 Z
+date: 2011-12-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &21542960 !ruby/object:Gem::Requirement
+  requirement: &9651640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 2.7.0
   type: :development
   prerelease: false
-  version_requirements: *21542960
+  version_requirements: *9651640
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &21541680 !ruby/object:Gem::Requirement
+  requirement: &9650560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.0.12
   type: :development
   prerelease: false
-  version_requirements: *21541680
+  version_requirements: *9650560
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &21557520 !ruby/object:Gem::Requirement
+  requirement: &9649960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *21557520
+  version_requirements: *9649960
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &21557000 !ruby/object:Gem::Requirement
+  requirement: &9649400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *21557000
+  version_requirements: *9649400
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &21556440 !ruby/object:Gem::Requirement
+  requirement: &9648680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.11
   type: :development
   prerelease: false
-  version_requirements: *21556440
+  version_requirements: *9648680
 - !ruby/object:Gem::Dependency
   name: mkrf
-  requirement: &21555820 !ruby/object:Gem::Requirement
+  requirement: &9647920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: 0.2.3
   type: :development
   prerelease: false
-  version_requirements: *21555820
+  version_requirements: *9647920
 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
@@ -151,7 +151,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -420869817303685437
+      hash: 1450233903929841244
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: