rbbt-dm 1.1.3 → 1.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 0c0544425bc534c01138dec342824fe038f70904
-  data.tar.gz: 1baa83b3b56405ea352a6a7d6bc083330f1412b9
+  metadata.gz: 412564d1fb5e11cd74d9d5f5831d3169c3b41bfc
+  data.tar.gz: b8015384a48dd97d9aaacc87f409d4a003b6a25e
 SHA512:
-  metadata.gz: 76ca4bb51dc3a159e4b777b7e718d4d1ea87bd9fc8219bfa04ea5aebea1b8730e70f66caef8d7200a5419ca7f883f01452c78fc531c4ea184b2d1fa1f61b4d0e
-  data.tar.gz: 8416c3b16280feeab2b55e5ae01bf877e56299974a3c8460d679e09ac4a90c44ad2b2e7eb520f983b6a0963667e1b1c96147fbb636bd7e1185c9ac62b740fdb2
+  metadata.gz: 4c27963bc45ac247de676b90f64748a6c8e6108a27e5c493620156a758db8c0709c9666e3c9d016b273ec754c8063d6636e2887680ce7aef51db8f34ae69112c
+  data.tar.gz: 65da093976bce048ab5572f904e831628178eb01dba43888bdebb7c2f2e9150070905610cebe52a8c59ea1503505d57fe4c4a3d179f358e617a15dde6150f65f

data/lib/rbbt/matrix/barcode.rb

@@ -0,0 +1,14 @@
+require 'rbbt/util/R'
+
+class Matrix
+  def barcode(outfile, factor = 2)
+
+    FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
+    cmd =<<-EOF
+source('#{Rbbt.share.R['barcode.R'].find}')
+rbbt.GE.barcode(#{ R.ruby2R self.data_file }, #{ R.ruby2R outfile }, #{ R.ruby2R factor })
+    EOF
+
+    R.run(cmd, :stderr => true)
+  end
+end

data/lib/rbbt/matrix/differential.rb

@@ -0,0 +1,14 @@
+class Matrix
+  def differential(main, contrast, path = nil)
+    if Array === main and Array === contrast
+      main_samples, contrast_samples = main, contrast
+    else
+      main_samples, contrast_samples = comparison main, contrast
+    end
+
+    Persist.persist(data_file, :tsv, :other => {:main => main_samples, :contrast => contrast_samples}, :prefix => "GENE", :dir => Matrix.matrix_dir, :no_load => true, :path => path) do |file|
+      log2 = value_type == "count"
+      GE.analyze(data_file, main_samples, contrast_samples, log2, path, format)
+    end
+  end
+end

data/lib/rbbt/matrix.rb

@@ -0,0 +1,104 @@
+require 'rbbt-util'
+require 'rbbt/sources/organism'
+
+class Matrix
+
+  class << self
+    attr_accessor :matrix_dir
+    def matrix_dir
+      @matrix_dir ||= Rbbt.var.matrices
+    end
+  end
+
+  attr_accessor :data_file, :labels, :value_type, :format, :organism
+  def initialize(data_file, labels, value_type, format, organism=nil, identifiers=nil)
+    @data_file = data_file
+    @labels = labels
+    @value_type = value_type
+    @format = format
+    @organism = organism 
+    @organism ||=  begin
+                     TSV.parse_header(@data_file).namespace || "Hsa"
+                   end
+    @identifiers = identifiers || Organism.identifiers(organism)
+  end
+
+  def samples
+    @samples ||= TSV.parse_header(@data_file).fields
+  end
+
+  def subsets
+    @subsets ||= begin
+                   subsets = {}
+                   case @labels
+                   when TSV
+                     factors = @labels.fields
+                     @labels.through do |sample,values|
+                       factors.zip(values).each do |factor,value|
+                         subsets[factor] ||= {}
+                         subsets[factor][value] ||= []
+                         subsets[factor][value] << sample
+                       end
+                     end
+                   when Hash
+                     @labels.each do |factor,info|
+                       subsets[factors] ||= []
+                       info.each do |value, samples|
+                         subsets[factors][value] = case samples
+                                                   when Array 
+                                                     samples
+                                                   when String
+                                                     samples.split ','
+                                                   else
+                                                     raise "Format of samples not understood: #{Misc.finguerprint samples}"
+                                                   end
+
+                       end
+                     end
+                   end
+                   subsets
+                 end
+  end
+
+  def comparison(main, contrast, subsets = nil)
+
+    if main.index "="
+      main_factor, main_value = main.split "=" 
+      raise ParameterException, "Main selection not understood" if subsets[main_factor].nil? or subsets[main_factor][main_value].nil?
+      main_samples = subsets[main_factor][main_value].split ','
+    else
+      main_samples = main.split(/[|,\n]/)
+    end
+
+    if contrast
+      if contrast.index "="
+        contrast_factor, contrast_value = contrast.split "=" 
+        raise ParameterException, "Contrast selection not understood" if subsets[contrast_factor].nil? or subsets[contrast_factor][contrast_value].nil?
+        contrast_samples = subsets[contrast_factor][contrast_value].split ','
+      else
+        contrast_samples = contrast.split(/[|,\n]/)
+      end
+    else
+      if subsets and defined? main_factor
+        contrast_samples = subsets[main_factor].values.collect{|s| s.split ',' }.flatten.uniq - main_samples
+      else
+        contrast_samples = samples - main_samples
+      end
+    end
+
+    [main_samples, contrast_samples]
+  end
+
+
+  def to_gene(identifiers = nil)
+    require 'rbbt/tsv/change_id'
+    file = Persist.persist(data_file, :tsv, :prefix => "GENE", :dir => Matrix.matrix_dir, :no_load => true) do
+      identifiers = [Organism.identifiers(organism), @identifiers, identifiers].compact.uniq
+
+      data_file.tsv(:cast => :to_f).change_key("Ensembl Gene ID", :identifiers => identifiers) do |v|
+        Misc.mean(v.compact)
+      end
+    end
+    Matrix.new file, labels, value_type, format
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.3
+  version: 1.1.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-21 00:00:00.000000000 Z
+date: 2014-03-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -91,6 +91,9 @@ files:
 - lib/rbbt/expression_old/expression.rb
 - lib/rbbt/expression_old/matrix.rb
 - lib/rbbt/expression_old/signature.rb
+- lib/rbbt/matrix.rb
+- lib/rbbt/matrix/barcode.rb
+- lib/rbbt/matrix/differential.rb
 - lib/rbbt/network/paths.rb
 - lib/rbbt/plots/bar.rb
 - lib/rbbt/plots/heatmap.rb