Sha256: c24c298a49d79dc62331a7034eb97087aa29d0c42bcb30d1aa759f309b30bffc
Contents?: true
Size: 1.07 KB
Versions: 47
Compression:
Stored size: 1.07 KB
Contents
require 'rbbt-util'
require 'rbbt/resource'
module Oreganno
extend Resource
self.subdir = 'share/databases/Oreganno'
def self.organism(org="Hsa")
require 'rbbt/sources/organism'
Organism.default_code(org)
end
#self.search_paths = {}
#self.search_paths[:default] = :lib
Oreganno.claim Oreganno.data, :proc do
url = "http://www.oreganno.org/dump/ORegAnno_Combined_2016.01.19.tsv"
TSV.open(url, :header_hash => '', :type => :list).to_s
end
Oreganno.claim Oreganno.tf_tg, :proc do
dumper = TSV::Dumper.new :key_field => "Transcription Factor (Associated Gene Name)", :fields => ["Target Gene (Associated Gene Name)"], :type => :flat, :namespace => Oreganno.organism
dumper.init
TSV.traverse Oreganno.data, :type => :array, :into => dumper, :bar => true do |line|
parts = line.split("\t")
next unless parts[1] == "Homo sapiens"
tf = parts[4]
tg = parts[7]
next if tf == "N/A" or tg == "N/A"
[tf, [tg]]
end
TSV.collapse_stream dumper
end
end
iif Oreganno.tf_tg.produce(true).find if __FILE__ == $0
Version data entries
47 entries across 47 versions & 1 rubygems