Sha256: b1027e64113bf904357647675d283d5a585e2439fd967df3ffcfc386de52a000
Contents?: true
Size: 904 Bytes
Versions: 92
Compression:
Stored size: 904 Bytes
Contents
require 'rbbt'
require 'rbbt/resource'
module STRING
extend Resource
self.subdir = "share/databases/string"
STRING.claim STRING.root, :rake, Rbbt.share.install.STRING.Rakefile.find(:lib)
end
if defined? Entity and defined? Gene and Entity === Gene
module Gene
property :string_interactors => :array2single do |*args|
threshold = args.first || 800
string = STRING.protein_protein.tsv(:unnamed => true, :persist => true, :type => :double)
all = self.ensembl.collect do |gene|
interactors = gene.proteins.collect{|protein| Misc.zip_fields((string[protein] || [[],[]])).select{|i, score| score.to_i > threshold}.collect{|ints,s| ints}}.compact.flatten.uniq
Protein.setup(interactors, "Ensembl Protein ID", organism).transcript.gene.compact.uniq
end
all.compact.first.annotate all if Annotated === all.compact.first
all
end
end
end
Version data entries
92 entries across 92 versions & 1 rubygems