rbbt-dm 1.1.6 → 1.1.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7a4d1889c790a3df527cb658469c4507765fd55a
-  data.tar.gz: b3fba784b73403c4eb130e6f21e39a3040ae938f
+  metadata.gz: 2a64441aa1cd02aa113a218e75d8a45e8679404d
+  data.tar.gz: 3d8ec7e4202bdb5ec1f79baa95e534ad84270369
 SHA512:
-  metadata.gz: ed2f7a8490762d392caa8f1e2bd4d53891a80d1414748c199f67b53492ba3fbcd018c87be368c41941af00d10c284988337a78c22a964ce914e4ebd453cd9235
-  data.tar.gz: b433ca84f94cb88eb2510a0195498a9f7df24897b927d672d18170ffd6efb9ea7a234f155c1ced83499b7c59760eb6db93d0cacb977b4afa55db3031cab79a07
+  metadata.gz: 79dde04bbfa4955f595c6bc702c9c5791029ed0a52e5720cf8e453036cfa6279ac1aea49fd5eba399fc68e1a8fcdc2db7428beba21cf5fec68bb3f93653b5533
+  data.tar.gz: f43dc00fa73c817da58a807163feba66b3ce2275ff4b1c51f42ba458f3c8448047cc013da82c8be6aadd3cd57111dbe376a39166985497328867e34c0c0880ab

data/lib/rbbt/matrix/differential.rb

@@ -6,9 +6,28 @@ class Matrix
       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)
+    name = data_file =~ /:>/ ? File.basename(data_file) : data_file
+    Persist.persist(name, :tsv, :update => true, 
+                    :other => {:main => main_samples, :contrast => contrast_samples}, 
+                    :prefix => "Diff", :dir => Matrix.matrix_dir.differential, :no_load => true) do |file|
+
+      log2 = value_type.nil? or value_type == "count"
+      log2 = false
+      two_channel = false
+      FileUtils.mkdir_p File.dirname(file) unless file.nil? or File.exists? File.dirname(file)
+      cmd = "source('#{Rbbt.share.R["MA.R"].find}'); rbbt.dm.matrix.differential(#{ R.ruby2R data_file }, main = #{R.ruby2R(main_samples)}, contrast = #{R.ruby2R(contrast_samples)}, log2=#{ R.ruby2R log2 }, outfile = #{R.ruby2R path}, key.field = #{R.ruby2R format}, two.channel = #{R.ruby2R two_channel})"
+      R.run(cmd)
+      nil
     end
   end
 end
+
+
+#def self.analyze(datafile,  main, contrast = nil, log2 = false, outfile = nil, key_field = nil, two_channel = nil)
+#  FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
+#  GE.run_R("rbbt.GE.process(#{ R.ruby2R datafile }, main = #{R.ruby2R(main, :strings => true)}, contrast = #{R.ruby2R(contrast, :strings => true)}, log2=#{ R.ruby2R log2 }, outfile = #{R.ruby2R outfile}, key.field = #{R.ruby2R key_field}, two.channel = #{R.ruby2R two_channel})")
+#end
+#def self.barcode(datafile, outfile, factor = 2)
+#  FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
+#  GE.run_R("rbbt.GE.barcode(#{ R.ruby2R datafile }, #{ R.ruby2R outfile }, #{ R.ruby2R factor })")
+#end

data/lib/rbbt/matrix.rb

@@ -92,7 +92,10 @@ class Matrix
 
   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
+
+    name = data_file =~ /:>/ ? File.basename(data_file) : data_file
+
+    file = Persist.persist(data_file, :tsv, :prefix => "Gene", :dir => Matrix.matrix_dir.values, :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|

data/lib/rbbt/statistics/random_walk.rb

@@ -257,17 +257,18 @@ module RandomWalk
   end
 
   def self.persisted_permutations(size, total, missing = 0, times = 10_000)
-    repo_file = "/tmp/rw_repo5"
+    repo_file = "/tmp/rw_repo7"
     repo = Persist.open_tokyocabinet(repo_file, false, :float_array)
     key = Misc.digest([size, total, missing, times, scoring_method].inspect)
+    repo.read
     if repo[key]
       repo[key]
     else
       p = permutations(size, total, missing, times)
-      repo.write
-      repo[key] = p
-      repo.read
-      repo[key]
+      repo.write_and_close do
+        repo[key] = p
+      end
+      p
     end
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.6
+  version: 1.1.7
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-02 00:00:00.000000000 Z
+date: 2014-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util