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Contents
require 'rbbt'
require 'rbbt/resource'
module Pina
extend Resource
self.subdir = "share/databases/pina"
Pina.claim Pina.root, :rake, Rbbt.share.install.Pina.Rakefile.find(:lib)
end
if defined? Entity and defined? Gene and Entity === Gene
require 'rbbt/entity/interactor'
require 'rbbt/sources/PSI_MI'
module Gene
property :pina_interactors => :array2single do
ens2uniprot = Organism.identifiers(organism).tsv :key_field => "Ensembl Gene ID", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :persist => true, :unnamed => true
pina = Pina.protein_protein.tsv(:persist => true, :fields => ["Interactor UniProt/SwissProt Accession", "Method", "PMID"], :type => :double, :merge => true, :unnamed => true)
int = self.ensembl.collect do |ens|
uniprot = ens2uniprot[ens]
list = pina.values_at(*uniprot).compact.collect do |v|
Misc.zip_fields(v).collect do |o, method, articles|
Interactor.setup(o, PSI_MITerm.setup(method.split(";;")), PMID.setup(articles.split(";;")))
end
end.flatten.uniq
Gene.setup(list, "UniProt/SwissProt Accession", organism).extend(AnnotatedArray)
end
Gene.setup(int, "UniProt/SwissProt Accession", organism).extend(AnnotatedArray)
end
end
end
Version data entries
7 entries across 7 versions & 1 rubygems