rbbt-marq 1.0.8 → 1.0.9

data/R/GEO.R

@@ -169,8 +169,6 @@ GEO.GDS.data <- function(name, id.field = NULL, translation.file = NULL, cachedi
         m <- MA.translate(m, trans);
     }
 
-
-
     return (list(conditions = conditions, m = m, two.channel = two.channel, description = description))
 }
 

data/README.rdoc

@@ -15,10 +15,10 @@ MARQ. To install MARQ follow this recipie:
 * Install Rbbt
 
     rbbt_config configure
-    rbbt_config install identifiers
+    rbbt_config prepare identifiers
     rbbt_config organisms
     # Choose the organisms you are interested in, and take the keyword. Like sgd for yeast
-    rbbt_config update organisms -o sgd
+    rbbt_config install organisms -o sgd
 
 * Install R
   * Install bioconductor and GEOquery
@@ -34,8 +34,9 @@ MARQ. To install MARQ follow this recipie:
 
 * Install MARQ
     marq_config config
-    marq_config install identifiers
-    marq_config update GEO
+    marq_config prepare identifiers
+    marq_config prepare GEO
+    marq_config install GEO
 
 * MARQ depends on many gems. Some may be problematic to install, in particular
   rsruby. You may need to get the source and build it yourself instead 

data/bin/marq_config

@@ -69,12 +69,12 @@ $USAGE =<<EOT
   actions:
     * config:   Set paths for data, cache, and tmp directories
 
-    * install:
+    * prepare:
       * GEO: Install management files to process GEO datasets and series
       * CustomDS: Install management files to process data from other sources
       * identifiers: Load the identifier equivalences in the database
 
-    * update:
+    * install:
       * GEO: Process datasets and series from GEO
       * CustomDS: Process datasets from other sources
 
@@ -91,12 +91,12 @@ class Controller < SimpleConsole::Controller
   params :string => {:p => :platform, :s => :series,  :o => :organism}, :boolean => {:d => :update_db, :f => :force}, :integer => {:p => :port}
 
 
-  def install
+  def prepare
     $organism  = params[:organism] unless params[:organism].nil?
     @actions = params[:id] || %w(GEO)
   end
 
-  def update
+  def install
     $platform  = params[:platform] unless params[:platform].nil?
     $series    = params[:series]   unless params[:series].nil?
     $organism  = params[:organism] unless params[:organism].nil?
@@ -166,7 +166,7 @@ class View < SimpleConsole::View
     configure
   end
 
-  def install
+  def prepare
     require 'rbbt/sources/organism'
     require 'MARQ/ID'
     case
@@ -191,7 +191,7 @@ class View < SimpleConsole::View
     end
   end
 
-  def update
+  def install
 
     require 'rake'
     @actions = [@actions] if @actions === String

data/lib/MARQ/GEO.rb

@@ -350,23 +350,26 @@ module GEO
     end
   end
 
-  # Rearange the lines of a file with the given order
+  # Rearange the lines of a file with the given order. The order specifies, for
+  # each position in the original file, where it should en in the final file
   def self.rearange(order, file, missing = "NA")
-    orig_lines = File.open(file).collect
+    orig_lines = []
+    File.open(file).each_line{|l| orig_lines << l}
+
     return if orig_lines.empty?
     columns = orig_lines.first.split(/\t/).length
     
     lines = Array.new(order.length)
 
     orig_lines.each_with_index{|l,i|
-      next if l.nil? || order[i].nil?
+      next if order[i].nil?
       lines[order[i]] = l.chomp
     }
 
     lines = lines.collect{|l| l || [missing]*columns*"\t"}
 
     fout = File.open(file, 'w')
-    fout.write(lines.join("\n"))
+    fout.puts(lines.join("\n"))
     fout.close
   end
 
@@ -384,9 +387,9 @@ module GEO
     platform_positions = platform_order.values_at(*series_codes)
 
     # Fill with nil for missing positions
-    platform_positions[platform_codes.length] ||= nil
+    platform_positions[platform_codes.length - 1] ||= nil
 
-    %w(codes t logratios orders pvalues).each{|ext|
+    %w(t logratios orders pvalues).each{|ext|
       rearange(platform_positions, prefix + '.' + ext)
     }
 
@@ -435,6 +438,8 @@ module GEO
       # Are the codes of the series equivalent to the ones in the platform?
       if  File.open(File.join(platform_path(platform),'codes')).collect{|l| l.chomp} != File.open(prefix + '.codes').collect{|l| l.chomp}
         fix_GSE_ids(File.join(platform_path(platform), 'codes'),prefix);
+        FileUtils.cp(File.join(platform_path(platform), 'codes'),prefix + '.codes')
+
       end
     end
 
@@ -453,6 +458,7 @@ module GEO
       puts "-- Translated to cross_platform format"
       GEO.get_GSE(gsms, conditions, do_log, prefix + '_cross_platform', prefix + '.translations',fields, info[:title], info[:description])
       fix_GSE_ids(File.join(platform_path(platform), 'cross_platform'),prefix + '_cross_platform');
+      FileUtils.cp(File.join(platform_path(platform), 'cross_platform'),prefix + '_cross_platform.codes')
       FileUtils.rm(prefix + '.translations') if File.exist?(prefix + '.translations')
     end
      FileUtils.rm(prefix + '.swap') if File.exist?(prefix + '.swap')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-marq
 version: !ruby/object:Gem::Version 
-  version: 1.0.8
+  version: 1.0.9
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-11-13 00:00:00 +01:00
+date: 2009-12-03 00:00:00 +01:00
 default_executable: marq_config
 dependencies: 
 - !ruby/object:Gem::Dependency