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Contents
require 'rbbt'
require 'rbbt/tsv'
require 'rbbt/resource'
module TFacts
extend Resource
self.subdir = "share/databases/TF"
TFacts.claim TFacts.source["Catalogues.xls"], :url, "http://www.tfacts.org/TFactS-new/TFactS-v2/tfacts/data/Catalogues.xls"
TFacts.claim TFacts.targets, :proc do
require 'spreadsheet'
book = Spreadsheet.open TFacts.source["Catalogues.xls"].produce.find
sheet = book.worksheet 0
tsv = TSV.setup({}, :key_field => "Associated Gene Name", :fields => ["Transcription Factor Associated Gene Name"], :namespace => "Hsa", :type => :flat)
sheet.each do |row|
target, tf = row.values_at 0, 1
tsv[target] ||= []
tsv[target] << tf
end
tsv.to_s
end
TFacts.claim TFacts.targets_signed, :proc do
require 'spreadsheet'
book = Spreadsheet.open TFacts.source["Catalogues.xls"].produce.find
sheet = book.worksheet 0
tsv = TSV.setup({}, :key_field => "Associated Gene Name", :fields => ["Transcription Factor Associated Gene Name", "Sign"], :namespace => "Hsa", :type => :double)
sheet.each do |row|
target, tf, sign = row.values_at 0, 1, 2
tsv[target] ||= [[],[]]
tsv[target][0] << tf
tsv[target][1] << sign
end
tsv.to_s
end
TFacts.claim TFacts.regulators, :proc do
TFacts.targets.tsv.reorder("Transcription Factor Associated Gene Name").to_s
end
end
if defined? Entity and defined? Gene and Entity === Gene
module Gene
property :is_transcription_factor? => :array2single do
tfs = TFacts.targets.keys
self.name.collect{|gene| tfs.include? gene}
end
property :transcription_regulators => :array2single do
Gene.setup(TFacts.regulators.tsv(:persist => true).values_at(*self.name), "Associated Gene Name", self.organism)
end
property :transcription_targets => :array2single do
Gene.setup(TFacts.targets.tsv(:persist => true).values_at(*self.name), "Associated Gene Name", self.organism)
end
end
end
Version data entries
45 entries across 45 versions & 1 rubygems