rbbt-marq 1.0.0 → 1.0.1

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data/R/CustomDS.R CHANGED
@@ -4,17 +4,26 @@ CustomDS.process <- function(prefix, cross_platform, conditions, description, tw
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  # Read data
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  genes = scan(file=paste(prefix,'codes',sep = "/"), what=character(),sep="\n",quiet=T);
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  m = matrix(scan(file=paste(prefix,'values',sep = "/"), sep="\t",quiet=T),length(genes),byrow=T);
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+ str(m);
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+ str(genes);
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  rownames(m) <- genes
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+
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  # Read conditions
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  conditions.list = vector();
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  names = vector();
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+ str(conditions)
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  for (file in conditions){
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- values = scan(paste(prefix,file,sep="/"),what=character(),sep="\n",quiet=T)
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+ str(paste(prefix,file,sep="/"));
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+ values = scan(paste(prefix,file,sep="/"),what=character(), sep = "\n")
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  names = c(names, file)
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+ str(values)
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  conditions.list = cbind(conditions.list, values)
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  }
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+ colnames(conditions.list) <- names;
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+ str(conditions.list)
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+
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@@ -39,7 +48,6 @@ CustomDS.process <- function(prefix, cross_platform, conditions, description, tw
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  if (cross_platform){
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  prefix = paste(prefix,'cross_platform', sep="_")
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  }
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- colnames(conditions.list) <- names;
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  values <- MA.process(m, conditions.list, two.channel);
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@@ -164,7 +164,7 @@ end
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  task 'annotate_Words' do
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  require 'MARQ/annotations'
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- require 'rbbt/util/misc'
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+ require 'rbbt/bow/bow'
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  annotations('Words'){|dataset|
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  terms = {}
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  description = Open.read(GEO.dataset_path(dataset) + '.description')
data/lib/MARQ/CustomDS.rb CHANGED
@@ -1,6 +1,7 @@
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  require 'rbbt/util/open'
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  require 'MARQ'
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  require 'MARQ/ID'
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+
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  module CustomDS
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  @@r = nil
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@@ -9,6 +10,7 @@ module CustomDS
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  end
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  def self.r
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+ require 'rsruby'
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  if @@r.nil?
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  RSRuby.instance.source(MARQ.rootdir + '/R/MA.R')
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  RSRuby.instance.source(MARQ.rootdir + '/R/CustomDS.R')
@@ -62,10 +64,7 @@ module CustomDS
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  Dir.glob(File.join(customdir, org) + '/*.orders').collect{|f| clean(File.basename(f.sub(/.orders/,'')))}.uniq
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  end
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- def self.process(name)
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- puts "Processing #{ name }"
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- org = organism(name)
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- prefix = File.join(customdir, org, name)
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+ def self.process_matrix(prefix, org)
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  conditions = Dir.glob(prefix + '/*').collect{|f| File.basename(f)} - %w(values codes info description cross_platform)
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  description = Open.read(File.join(prefix, 'description'))
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@@ -82,6 +81,14 @@ module CustomDS
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  end
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  end
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+ def self.process(name)
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+ puts "Processing #{ name }"
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+ org = organism(name)
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+ prefix = File.join(customdir, org, name)
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+
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+ CustomDS::process_matrix(prefix, org)
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+ end
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+
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  end
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@@ -89,6 +96,7 @@ if __FILE__ == $0
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  p CustomDS::datasets('sgd')
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  p CustomDS::path('HaploidData')
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  p CustomDS::path('HaploidData_cross_platform')
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+
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  exit
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  org = 'sgd'
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-marq
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  version: !ruby/object:Gem::Version
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- version: 1.0.0
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+ version: 1.0.1
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  platform: ruby
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  authors:
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  - Miguel Vazquez