rbbt-marq 1.0.9 → 1.1.0

data/lib/MARQ/ID.rb

@@ -1,4 +1,5 @@
 require 'MARQ'
+require 'rbbt/sources/organism'
 require 'DBcache'
 
 module ID

data/lib/MARQ/main.rb

@@ -22,9 +22,9 @@ module MARQ
   def self.platform_organism(platform)
     if platform_type(platform) == :GEO
       if platform.match(/^GPL/)
-        GEO::GPL_info(platform)[:organism]
+        GEO::SOFT::GPL(platform)[:organism]
       else
-        GEO::GPL_info(GEO::dataset_platform(platform))[:organism]
+        GEO::SOFT::GPL(GEO::dataset_platform(platform))[:organism]
       end
     else
       CustomDS::organism(platform)
@@ -50,6 +50,7 @@ module MARQ
       CustomDS::is_cross_platform?(platform)
     end
   end
+
   def self.complete_positions(positions, matched, genes)
 
     pos = Hash[*matched.zip(positions).flatten]
@@ -62,6 +63,83 @@ module MARQ
       end
     }
 
+  end
+
+  module Dataset
+
+    def self.exists?(dataset)
+      MARQ::dataset_path(dataset) != nil
+    end
+
+    def self.read_file(dataset, ext)
+      Open.read(MARQ::dataset_path(dataset) + '.' + ext)
+    end
+
+    def self.read_values(dataset, file)
+      result = {}
+
+      experiments = experiments(dataset)
+      experiments.each{|experiment| result[experiment] = [] }
+      read_file(dataset, file).split(/\n/).each do |line|
+        values = line.chomp.split(/\t/)
+        values.each_with_index{|value, i| result[experiments[i]] << (value == 'NA' ? nil : value.to_f) }
+      end
+
+      result
+    end
+
+    def self.read_values_t(dataset, file)
+      result = {}
+
+      experiments = experiments(dataset).select{|experiment| experiment !~ /\[ratio\]$/ }
+      return {} if experiments.empty?
+      experiments.each{|experiment| result[experiment] = [] }
+
+      read_file(dataset, file).split(/\n/).each do |line|
+        values = line.chomp.split(/\t/)
+        values.each_with_index{|value, i| result[experiments[i]] << (value == 'NA' ? nil : value.to_f) }
+      end
+
+      result
+    end
+
+
+    def self.platform_codes(platform)
+      if MARQ::is_cross_platform? platform
+        file = 'cross_platform'
+      else
+        file = 'codes'
+      end
+
+      Open.read(File.join(MARQ::platform_path(platform), file))
+    end
+
+    def self.experiments(dataset)
+      read_file(dataset, 'experiments').split(/\n/)
+    end
+
+    def self.codes(dataset)
+      read_file(dataset, 'codes').split(/\n/)
+    end
+
+    def self.orders(dataset)
+      read_values(dataset, 'orders')
+    end
+
+    def self.logratios(dataset)
+      read_values(dataset, 'logratios')
+    end
+    
+    def self.pvalues(dataset)
+      read_values_t(dataset, 'pvalues')
+    end
+
+    def self.t(dataset)
+      read_values_t(dataset, 't')
+    end
+
+
+
   end
 
   def self.platform_scores_up_down(platform, up, down)
@@ -189,6 +267,8 @@ module MARQ
 end
 
 if __FILE__ == $0
+  p MARQ::Dataset.orders('GDS2419')
+  exit
   #puts MARQ::organism_platforms('human')
   #puts MARQ.platform_organism("HaploidData")
   #puts MARQ::platform_scores_up_down("HaploidData",%w( YMR261c YDL140c YIL122w YPL093w YHR211w YDL142c YHR106w YOR103c YDR233c YLR181c),%w()).keys

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-marq
 version: !ruby/object:Gem::Version 
-  version: 1.0.9
+  version: 1.1.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-03 00:00:00 +01:00
+date: 2009-12-16 00:00:00 +01:00
 default_executable: marq_config
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -62,6 +62,16 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: png
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 description: Find microarray experiments with similar or opposite signature to a given query. A SOAP interface and a merb portal can be found in rbbt-marq-www.
 email: miguel.vazquez@fdi.ucm.es
 executables: 
@@ -74,6 +84,7 @@ extra_rdoc_files:
 files: 
 - R/CustomDS.R
 - R/GEO.R
+- R/GEOquery_patch.R
 - R/MA.R
 - R/MARQ.R
 - bin/marq_config