rbbt-marq 2.1.1 → 2.1.2

data/README.rdoc

@@ -8,6 +8,9 @@ interface to the system with several additional features.
 
 == Installation
 
+Quick install
+ rbbt_config prepare all; rbbt_config install organisms; rbbt_genecodis prepare all; rbbt_genecodis install data; marq_config prepare identifiers; marq_config prepare GEO; marq_config install GEO; marq_config prepare CustomDS; marq_config install CustomDS
+
 Install the gem and all the dependencies. This gem depends on several others,
 including Rbbt. Rbbt offers an API with the gene identifier translation used in
 MARQ. To install MARQ follow this recipie:

data/install_scripts/GEO/series/GSE1404.yaml

@@ -593,4 +593,4 @@
     mutant: YMR239C TET_mutant
   GSM22975: 
     mutant: YGR245C TET_mutant
-:platform: GPL1229
+:platform: GPL1229_GPL1237

data/install_scripts/GEO/series/GSE5938.yaml

@@ -184,4 +184,4 @@
   We construced combinations of genetic deletions to infer genetic interactions in genomic expression data.
   Keywords: combinatorial genetic perturbations
 :title: Expression data for filamentous-form yeast with genetic perturbations
-:platform: GPL90
+:platform: GPL2622_GPL90

data/install_scripts/rake_includes.rb

@@ -1,4 +1,5 @@
 require 'progress-monitor'
+require 'genecodis/main'
 
 $expr_threshold ||= (ENV['threshold'] || 0.05).to_f
 $folds          ||= (ENV['folds'] || 2.5).to_f
@@ -39,11 +40,21 @@ module CustomDS
   end
 end
 
+def try3times
+  tries = 0
+  begin
+    yield
+  rescue
+    tries += 1
+    retry if tries <= 3
+  end
+end
+
 desc "Analyze datasets"
 task 'data' do 
   platforms_to_save = []
 
-  platforms = process_list
+  platforms = try3times { process_list }
 
   Progress.monitor("Processing #{platforms.keys.length} platforms") if platforms.keys.length > 1
   platforms.each{|platform, datasets|
@@ -72,10 +83,10 @@ task 'data' do
         MARQ::Dataset.process(dataset, platform)
         MARQ::Dataset.process(MARQ::Name.cross_platform(dataset), platform) if MARQ::Platform.has_cross_platform?(platform)
       rescue
-        puts "Error processing dataset #{ dataset }"
+        puts "Error processing dataset #{ dataset } [#{ platform }]"
         puts $!.message
         puts "\n" * 3
-        #puts $!.backtrace.join("\n")
+        puts $!.backtrace.join("\n")
       end
     }
     
@@ -97,7 +108,7 @@ task 'data' do
 end
 
 def annotations(name, cross_platform = false, &block)
-  platforms = process_list
+  platforms = try3times { process_list }
 
   Progress.monitor("Processing #{platforms.keys.length} platforms for #{ name } annotations")
   platforms.each do |platform, datasets|
@@ -105,13 +116,11 @@ def annotations(name, cross_platform = false, &block)
     Progress.monitor("Processing #{datasets.length} datasets", :announcement => Proc.new{|d| "Dataset #{ d }" }) if datasets.length > 1
     datasets.each do |dataset|
       begin
+        next if ! MARQ::Dataset.exists?(dataset)
         next if File.exist?(File.join("annotations", name, dataset)) && ! $force
-        next if MARQ::Dataset.path(dataset).nil?
 
         FileUtils.mkdir_p File.join("annotations", name)
         filename = File.join("annotations", name, dataset)
-        dataset += MARQ::Name.cross_platform(dataset) if cross_platform && MARQ::Platform::has_cross_platform?(platform)
-        next if ! MARQ::Dataset.exists?(dataset)
         terms = block.call(dataset)
         Open.write(filename, terms.to_yaml)
       rescue
@@ -175,12 +184,12 @@ end
 
 def goterms(org, list, slim, threshold)
   return [] if list.empty?
-  results = Annotations::Genes::Genecodis::Local.analysis(org, list, slim)
+  results = Genecodis.analysis(org, 'biological_process', list, :algorithm => Genecodis::Algorithm::SINGLE)
   return [] if results.nil?
   results.
-    select{|info| info[:s].to_i  > 2 }.
-    select{|info| info[:hyp_c].to_f < threshold }.
-    collect{|info| info[:items]}.collect{|id| GO::id2name(id)}
+    select{|info| info["S"].to_i  > 2 }.
+    select{|info| info["Hyp_c"].to_f < threshold }.
+    collect{|info| info["Items"]}.collect{|id| GO::id2name(id)}
 end
 
 task 'annotate_GO' do
@@ -189,7 +198,7 @@ task 'annotate_GO' do
   options = { :cut_off => $expr_threshold, :fdr => $fdr, :folds => $folds, :do_folds => $do_folds, :nth_genes => $nth_genes}
   annotations('GO_up', true) do |dataset|
     org = MARQ::Dataset.organism(dataset)
-    genes = Annotations::Genes.get_genes(dataset, options)
+    genes = Annotations::Genes.get_genes(MARQ::Name.cross_platform(dataset), options)
 
     up = {}
     genes[:up] ||= []
@@ -201,7 +210,7 @@ task 'annotate_GO' do
 
   annotations('GO_down', true) do |dataset|
     org = MARQ::Dataset.organism(dataset)
-    genes = Annotations::Genes.get_genes(dataset, options)
+    genes = Annotations::Genes.get_genes(MARQ::Name.cross_platform(dataset), options)
 
     down = {}
     genes[:down] ||= []
@@ -213,7 +222,7 @@ task 'annotate_GO' do
 
   annotations('GOSlim_up', true) do |dataset|
     org = MARQ::Dataset.organism(dataset)
-    genes = Annotations::Genes.get_genes(dataset, options)
+    genes = Annotations::Genes.get_genes(MARQ::Name.cross_platform(dataset), options)
 
     up = {}
     genes[:up] ||= []
@@ -225,7 +234,7 @@ task 'annotate_GO' do
 
   annotations('GOSlim_down', true) do |dataset|
     org = MARQ::Dataset.organism(dataset)
-    genes = Annotations::Genes.get_genes(dataset, options)
+    genes = Annotations::Genes.get_genes(MARQ::Name.cross_platform(dataset), options)
 
     down = {}
     genes[:down] ||= []

data/lib/MARQ/GEO.rb

@@ -364,7 +364,6 @@ module GEO
 
       FileUtils.cp(platform_codes_file, prefix + '.codes')
       Open.write(prefix + '.swap', platform_positions.join("\n"))
-
     end
 
     def self.GSE(series, info)
@@ -388,17 +387,17 @@ module GEO
       adhoc_platform = platform.match(/_/) != nil
 
       raise PlatformNotProcessedError if ! adhoc_platform && ! MARQ::Platform.exists?(platform)
-      raise AdhocPlatformCollisionError if adhoc_platform && MARQ::Platform.exists?(platform)
-
-      cross_platform = MARQ::Name.is_cross_platform?(series)
+      raise AdhocPlatformCollisionError if adhoc_platform && MARQ::Platform.exists?(platform) && ! MARQ::Name.is_cross_platform?(series)
 
-      platform_path = GEO.platform_path(platform)
+      platform_path = GEO.platform_path(platform) || File.join(MARQ.datadir, 'GEO', platform)
 
       prefix = File.join(platform_path, 'GSE', series)
+      
+      FileUtils.mkdir_p File.join(platform_path, 'GSE') unless File.exists? File.join(platform_path, 'GSE')
 
       FileUtils.rm(prefix + '.skip') if File.exist?(prefix + '.skip')
 
-      if ! cross_platform
+      if ! MARQ::Name.is_cross_platform?(series)
         R.GSE(gsms, conditions, do_log, prefix, nil, fields, info[:title], info[:description])
 
         # Set up codes and cross_platform for adhoc platforms
@@ -407,15 +406,33 @@ module GEO
           organism     = GEO.platform_organism(platform.split(/_/)[0])
           translations = translate(organism, codes) 
           FileUtils.cp(prefix + '.codes', File.join(platform_path,'codes'))
-          Open.write(File.join(platform_path, 'translations'), translations.collect{|v| v || "NO MATCH"}.join("\n"))
-          Open.write(File.join(platform_path, 'cross_platform'), translations.compact.sort.uniq.join("\n"))
+          if translations.compact.length > codes.length.to_f / 10
+            Open.write(File.join(platform_path, 'translations'), translations.collect{|v| v || "NO MATCH"}.join("\n"))
+            Open.write(File.join(platform_path, 'cross_platform'), translations.compact.sort.uniq.join("\n"))
+          end
         else
-          fix_GSE_ids(File.join(platform_path, 'codes'),prefix);
+          fix_GSE_ids(File.join(platform_path, 'codes'), prefix);
         end
 
       else
-        R.GSE(gsms, conditions, do_log, prefix, File.join(platform_path, 'translations'), fields, info[:title], info[:description])
+        FileUtils.cp(File.join(platform,'translations'), prefix + '.translations')
+
+        swap_file = File.join(MARQ::Dataset.path(MARQ::Name.clean series) + '.swap')
+        if File.exist?(swap_file)
+          orders = Open.read(swap_file).collect{|l| l.chomp}
+          inverse_orders = Array.new(orders.length)
+          orders.each_with_index{|pos,i|
+            next if pos !~ /\d/
+              inverse_orders[pos.to_i] = i
+          }
+          rearange(inverse_orders, prefix + '.translations', "NO MATCH")
+        end
+
+        R.GSE(gsms, conditions, do_log, prefix, prefix +  '.translations', fields, info[:title], info[:description])
+
         fix_GSE_ids(File.join(platform_path, 'cross_platform'),prefix);
+
+        FileUtils.rm(prefix + '.translations') if File.exist?(prefix + '.translations')
       end
 
     end
@@ -611,7 +628,7 @@ module GEO
     when :GDS
       GEO::Process.GDS(dataset, platform)
     when :GSE
-      info = YAML::load(File.open("series/#{ dataset }.yaml"))
+      info = YAML::load(File.open("series/#{ MARQ::Name.clean dataset }.yaml"))
       FileUtils.rm("platforms/#{ info[:platform] }.skip") if File.exist?  "platforms/#{ info[:platform] }.skip"
       GEO::Process.GSE(dataset, info)
     end

data/lib/MARQ/MADB.rb

@@ -66,18 +66,24 @@ module MADB
 
   # {{{ Loading Positions
 
+  # Number of probes in the platform
   def self.platform_entries(platform)
     DBcache.num_rows(platform + '_codes')
   end
 
-  def self.load_positions(dataset, genes, platform_entries)
-    gene_positions = DBcache.load(dataset, genes)
-    data = {}
-    matched = gene_positions.keys 
+  # Return the positions of the genes in the signatures derived from the
+  # dataset. Returns a 3 value array: hash of arrays of positions (keys are
+  # signatures), array of the gene ids in the same order as the positions,
+  # and total number of probes in the platform.
+  #
+  def self.load_positions(dataset, genes, platform_entries) 
+    gene_positions = DBcache.load(dataset, genes) 
+
+    matched = gene_positions.keys.sort 
 
-    # Get experiments
+    # Get signature names
     experiments = DBcache.load(dataset + '_experiments').sort{|a,b| 
-      a[0].to_i <=> b[0].to_i
+a[0].to_i <=> b[0].to_i
     }.collect{|p| 
       MARQ::Name.clean(dataset) + ": " + p[1].first
     }
@@ -92,6 +98,7 @@ module MADB
       end 
     }
 
+    data = {} 
     # Get experiment positions and scale them
     experiment_x_gene = gene_positions.values_at(*matched).transpose
     experiments.each_with_index{|experiment, i|
@@ -103,6 +110,8 @@ module MADB
     [data, matched, platform_entries]
   end
  
+  # Load positions of genes in signatures from the given datasets. Returns a
+  # tree value array just like load_positions
   def self.dataset_positions(dataset, genes)
     return [{},[],0] if genes.empty?
 
@@ -113,6 +122,11 @@ module MADB
   end
 
 
+  # Loads the data from all signatures for datasets of the platform. The return
+  # value is the same as in dataset_positions and load_positins, except that
+  # the matched gene names need not be in the same order as the actual positions
+  # of the signatures, it just the super set of all genes matched on the
+  # signatures
   def self.platform_positions(platform, genes)
     return [{},[],0] if genes.empty?
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-marq
 version: !ruby/object:Gem::Version 
-  version: 2.1.1
+  version: 2.1.2
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-02-15 00:00:00 +01:00
+date: 2010-03-04 00:00:00 +01:00
 default_executable: marq_config
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -90,252 +90,6 @@ files:
 - bin/marq_config
 - install_scripts/CustomDS/Rakefile
 - install_scripts/GEO/Rakefile
-- install_scripts/GEO/platforms/GPL100.yaml
-- install_scripts/GEO/platforms/GPL1002.yaml
-- install_scripts/GEO/platforms/GPL1007.yaml
-- install_scripts/GEO/platforms/GPL101.yaml
-- install_scripts/GEO/platforms/GPL1010.yaml
-- install_scripts/GEO/platforms/GPL1073.yaml
-- install_scripts/GEO/platforms/GPL1074.yaml
-- install_scripts/GEO/platforms/GPL1090.yaml
-- install_scripts/GEO/platforms/GPL1104.yaml
-- install_scripts/GEO/platforms/GPL118.yaml
-- install_scripts/GEO/platforms/GPL1205.yaml
-- install_scripts/GEO/platforms/GPL1211.yaml
-- install_scripts/GEO/platforms/GPL1213.yaml
-- install_scripts/GEO/platforms/GPL1219.yaml
-- install_scripts/GEO/platforms/GPL1223.yaml
-- install_scripts/GEO/platforms/GPL1226.yaml
-- install_scripts/GEO/platforms/GPL1229.yaml
-- install_scripts/GEO/platforms/GPL1230.yaml
-- install_scripts/GEO/platforms/GPL1231.yaml
-- install_scripts/GEO/platforms/GPL1232.yaml
-- install_scripts/GEO/platforms/GPL1260.yaml
-- install_scripts/GEO/platforms/GPL1261.yaml
-- install_scripts/GEO/platforms/GPL127.yaml
-- install_scripts/GEO/platforms/GPL128.yaml
-- install_scripts/GEO/platforms/GPL1290.yaml
-- install_scripts/GEO/platforms/GPL1292.yaml
-- install_scripts/GEO/platforms/GPL1293.yaml
-- install_scripts/GEO/platforms/GPL1294.yaml
-- install_scripts/GEO/platforms/GPL1295.yaml
-- install_scripts/GEO/platforms/GPL13.yaml
-- install_scripts/GEO/platforms/GPL1310.yaml
-- install_scripts/GEO/platforms/GPL1313.yaml
-- install_scripts/GEO/platforms/GPL1323.yaml
-- install_scripts/GEO/platforms/GPL1331.yaml
-- install_scripts/GEO/platforms/GPL1352.yaml
-- install_scripts/GEO/platforms/GPL1355.yaml
-- install_scripts/GEO/platforms/GPL1382.yaml
-- install_scripts/GEO/platforms/GPL1387.yaml
-- install_scripts/GEO/platforms/GPL1397.yaml
-- install_scripts/GEO/platforms/GPL14.yaml
-- install_scripts/GEO/platforms/GPL1412.yaml
-- install_scripts/GEO/platforms/GPL1415.yaml
-- install_scripts/GEO/platforms/GPL1420.yaml
-- install_scripts/GEO/platforms/GPL144.yaml
-- install_scripts/GEO/platforms/GPL1449.yaml
-- install_scripts/GEO/platforms/GPL1458.yaml
-- install_scripts/GEO/platforms/GPL1523.yaml
-- install_scripts/GEO/platforms/GPL1524.yaml
-- install_scripts/GEO/platforms/GPL1528.yaml
-- install_scripts/GEO/platforms/GPL153.yaml
-- install_scripts/GEO/platforms/GPL1530.yaml
-- install_scripts/GEO/platforms/GPL1535.yaml
-- install_scripts/GEO/platforms/GPL155.yaml
-- install_scripts/GEO/platforms/GPL163.yaml
-- install_scripts/GEO/platforms/GPL168.yaml
-- install_scripts/GEO/platforms/GPL169.yaml
-- install_scripts/GEO/platforms/GPL1704.yaml
-- install_scripts/GEO/platforms/GPL1708.yaml
-- install_scripts/GEO/platforms/GPL1739.yaml
-- install_scripts/GEO/platforms/GPL1740.yaml
-- install_scripts/GEO/platforms/GPL1749.yaml
-- install_scripts/GEO/platforms/GPL177.yaml
-- install_scripts/GEO/platforms/GPL1790.yaml
-- install_scripts/GEO/platforms/GPL1792.yaml
-- install_scripts/GEO/platforms/GPL181.yaml
-- install_scripts/GEO/platforms/GPL1818.yaml
-- install_scripts/GEO/platforms/GPL1820.yaml
-- install_scripts/GEO/platforms/GPL1823.yaml
-- install_scripts/GEO/platforms/GPL1826.yaml
-- install_scripts/GEO/platforms/GPL183.yaml
-- install_scripts/GEO/platforms/GPL1831.yaml
-- install_scripts/GEO/platforms/GPL1833.yaml
-- install_scripts/GEO/platforms/GPL1872.yaml
-- install_scripts/GEO/platforms/GPL1911.yaml
-- install_scripts/GEO/platforms/GPL1914.yaml
-- install_scripts/GEO/platforms/GPL1928.yaml
-- install_scripts/GEO/platforms/GPL1942.yaml
-- install_scripts/GEO/platforms/GPL1945.yaml
-- install_scripts/GEO/platforms/GPL1964.yaml
-- install_scripts/GEO/platforms/GPL198.yaml
-- install_scripts/GEO/platforms/GPL1981.yaml
-- install_scripts/GEO/platforms/GPL200.yaml
-- install_scripts/GEO/platforms/GPL2006.yaml
-- install_scripts/GEO/platforms/GPL201.yaml
-- install_scripts/GEO/platforms/GPL2011.yaml
-- install_scripts/GEO/platforms/GPL2026.yaml
-- install_scripts/GEO/platforms/GPL205.yaml
-- install_scripts/GEO/platforms/GPL207.yaml
-- install_scripts/GEO/platforms/GPL2136.yaml
-- install_scripts/GEO/platforms/GPL220.yaml
-- install_scripts/GEO/platforms/GPL226.yaml
-- install_scripts/GEO/platforms/GPL24.yaml
-- install_scripts/GEO/platforms/GPL246.yaml
-- install_scripts/GEO/platforms/GPL247.yaml
-- install_scripts/GEO/platforms/GPL2507.yaml
-- install_scripts/GEO/platforms/GPL2529.yaml
-- install_scripts/GEO/platforms/GPL2531.yaml
-- install_scripts/GEO/platforms/GPL254.yaml
-- install_scripts/GEO/platforms/GPL2569.yaml
-- install_scripts/GEO/platforms/GPL257.yaml
-- install_scripts/GEO/platforms/GPL2598.yaml
-- install_scripts/GEO/platforms/GPL260.yaml
-- install_scripts/GEO/platforms/GPL2614.yaml
-- install_scripts/GEO/platforms/GPL2622.yaml
-- install_scripts/GEO/platforms/GPL2623.yaml
-- install_scripts/GEO/platforms/GPL2660.yaml
-- install_scripts/GEO/platforms/GPL2670.yaml
-- install_scripts/GEO/platforms/GPL2677.yaml
-- install_scripts/GEO/platforms/GPL2700.yaml
-- install_scripts/GEO/platforms/GPL2721.yaml
-- install_scripts/GEO/platforms/GPL2727.yaml
-- install_scripts/GEO/platforms/GPL273.yaml
-- install_scripts/GEO/platforms/GPL2763.yaml
-- install_scripts/GEO/platforms/GPL2824.yaml
-- install_scripts/GEO/platforms/GPL284.yaml
-- install_scripts/GEO/platforms/GPL287.yaml
-- install_scripts/GEO/platforms/GPL2872.yaml
-- install_scripts/GEO/platforms/GPL288.yaml
-- install_scripts/GEO/platforms/GPL2883.yaml
-- install_scripts/GEO/platforms/GPL289.yaml
-- install_scripts/GEO/platforms/GPL2895.yaml
-- install_scripts/GEO/platforms/GPL2897.yaml
-- install_scripts/GEO/platforms/GPL2902.yaml
-- install_scripts/GEO/platforms/GPL2987.yaml
-- install_scripts/GEO/platforms/GPL2995.yaml
-- install_scripts/GEO/platforms/GPL3039.yaml
-- install_scripts/GEO/platforms/GPL3050.yaml
-- install_scripts/GEO/platforms/GPL3084.yaml
-- install_scripts/GEO/platforms/GPL3113.yaml
-- install_scripts/GEO/platforms/GPL317.yaml
-- install_scripts/GEO/platforms/GPL319.yaml
-- install_scripts/GEO/platforms/GPL32.yaml
-- install_scripts/GEO/platforms/GPL3222.yaml
-- install_scripts/GEO/platforms/GPL3295.yaml
-- install_scripts/GEO/platforms/GPL3305.yaml
-- install_scripts/GEO/platforms/GPL3306.yaml
-- install_scripts/GEO/platforms/GPL3307.yaml
-- install_scripts/GEO/platforms/GPL333.yaml
-- install_scripts/GEO/platforms/GPL3341.yaml
-- install_scripts/GEO/platforms/GPL3349.yaml
-- install_scripts/GEO/platforms/GPL339.yaml
-- install_scripts/GEO/platforms/GPL340.yaml
-- install_scripts/GEO/platforms/GPL3408.yaml
-- install_scripts/GEO/platforms/GPL341.yaml
-- install_scripts/GEO/platforms/GPL3415.yaml
-- install_scripts/GEO/platforms/GPL3423.yaml
-- install_scripts/GEO/platforms/GPL3440.yaml
-- install_scripts/GEO/platforms/GPL3457.yaml
-- install_scripts/GEO/platforms/GPL3504.yaml
-- install_scripts/GEO/platforms/GPL3506.yaml
-- install_scripts/GEO/platforms/GPL355.yaml
-- install_scripts/GEO/platforms/GPL3558.yaml
-- install_scripts/GEO/platforms/GPL3607.yaml
-- install_scripts/GEO/platforms/GPL368.yaml
-- install_scripts/GEO/platforms/GPL3695.yaml
-- install_scripts/GEO/platforms/GPL371.yaml
-- install_scripts/GEO/platforms/GPL3834.yaml
-- install_scripts/GEO/platforms/GPL4006.yaml
-- install_scripts/GEO/platforms/GPL4055.yaml
-- install_scripts/GEO/platforms/GPL409.yaml
-- install_scripts/GEO/platforms/GPL4191.yaml
-- install_scripts/GEO/platforms/GPL4226.yaml
-- install_scripts/GEO/platforms/GPL4371.yaml
-- install_scripts/GEO/platforms/GPL4567.yaml
-- install_scripts/GEO/platforms/GPL4685.yaml
-- install_scripts/GEO/platforms/GPL483.yaml
-- install_scripts/GEO/platforms/GPL49.yaml
-- install_scripts/GEO/platforms/GPL50.yaml
-- install_scripts/GEO/platforms/GPL500.yaml
-- install_scripts/GEO/platforms/GPL507.yaml
-- install_scripts/GEO/platforms/GPL51.yaml
-- install_scripts/GEO/platforms/GPL513.yaml
-- install_scripts/GEO/platforms/GPL519.yaml
-- install_scripts/GEO/platforms/GPL52.yaml
-- install_scripts/GEO/platforms/GPL529.yaml
-- install_scripts/GEO/platforms/GPL53.yaml
-- install_scripts/GEO/platforms/GPL5356.yaml
-- install_scripts/GEO/platforms/GPL538.yaml
-- install_scripts/GEO/platforms/GPL54.yaml
-- install_scripts/GEO/platforms/GPL543.yaml
-- install_scripts/GEO/platforms/GPL544.yaml
-- install_scripts/GEO/platforms/GPL545.yaml
-- install_scripts/GEO/platforms/GPL546.yaml
-- install_scripts/GEO/platforms/GPL547.yaml
-- install_scripts/GEO/platforms/GPL549.yaml
-- install_scripts/GEO/platforms/GPL550.yaml
-- install_scripts/GEO/platforms/GPL56.yaml
-- install_scripts/GEO/platforms/GPL560.yaml
-- install_scripts/GEO/platforms/GPL564.yaml
-- install_scripts/GEO/platforms/GPL57.yaml
-- install_scripts/GEO/platforms/GPL570.yaml
-- install_scripts/GEO/platforms/GPL571.yaml
-- install_scripts/GEO/platforms/GPL576.yaml
-- install_scripts/GEO/platforms/GPL58.yaml
-- install_scripts/GEO/platforms/GPL5823.yaml
-- install_scripts/GEO/platforms/GPL59.yaml
-- install_scripts/GEO/platforms/GPL5915.yaml
-- install_scripts/GEO/platforms/GPL5947.yaml
-- install_scripts/GEO/platforms/GPL61.yaml
-- install_scripts/GEO/platforms/GPL64.yaml
-- install_scripts/GEO/platforms/GPL6419.yaml
-- install_scripts/GEO/platforms/GPL6424.yaml
-- install_scripts/GEO/platforms/GPL65.yaml
-- install_scripts/GEO/platforms/GPL6574.yaml
-- install_scripts/GEO/platforms/GPL6649.yaml
-- install_scripts/GEO/platforms/GPL67.yaml
-- install_scripts/GEO/platforms/GPL6720.yaml
-- install_scripts/GEO/platforms/GPL7054.yaml
-- install_scripts/GEO/platforms/GPL737.yaml
-- install_scripts/GEO/platforms/GPL738.yaml
-- install_scripts/GEO/platforms/GPL74.yaml
-- install_scripts/GEO/platforms/GPL75.yaml
-- install_scripts/GEO/platforms/GPL76.yaml
-- install_scripts/GEO/platforms/GPL764.yaml
-- install_scripts/GEO/platforms/GPL772.yaml
-- install_scripts/GEO/platforms/GPL782.yaml
-- install_scripts/GEO/platforms/GPL783.yaml
-- install_scripts/GEO/platforms/GPL784.yaml
-- install_scripts/GEO/platforms/GPL80.yaml
-- install_scripts/GEO/platforms/GPL81.yaml
-- install_scripts/GEO/platforms/GPL82.yaml
-- install_scripts/GEO/platforms/GPL83.yaml
-- install_scripts/GEO/platforms/GPL85.yaml
-- install_scripts/GEO/platforms/GPL86.yaml
-- install_scripts/GEO/platforms/GPL87.yaml
-- install_scripts/GEO/platforms/GPL870.yaml
-- install_scripts/GEO/platforms/GPL875.yaml
-- install_scripts/GEO/platforms/GPL884.yaml
-- install_scripts/GEO/platforms/GPL887.yaml
-- install_scripts/GEO/platforms/GPL89.yaml
-- install_scripts/GEO/platforms/GPL890.yaml
-- install_scripts/GEO/platforms/GPL891.yaml
-- install_scripts/GEO/platforms/GPL90.yaml
-- install_scripts/GEO/platforms/GPL91.yaml
-- install_scripts/GEO/platforms/GPL92.yaml
-- install_scripts/GEO/platforms/GPL920.yaml
-- install_scripts/GEO/platforms/GPL922.yaml
-- install_scripts/GEO/platforms/GPL924.yaml
-- install_scripts/GEO/platforms/GPL93.yaml
-- install_scripts/GEO/platforms/GPL96.yaml
-- install_scripts/GEO/platforms/GPL968.yaml
-- install_scripts/GEO/platforms/GPL97.yaml
-- install_scripts/GEO/platforms/GPL98.yaml
-- install_scripts/GEO/platforms/GPL981.yaml
-- install_scripts/GEO/platforms/GPL99.yaml
-- install_scripts/GEO/platforms/GPL999.yaml
 - install_scripts/GEO/series/GSE10018.yaml
 - install_scripts/GEO/series/GSE1002.yaml
 - install_scripts/GEO/series/GSE10066.yaml