Sha256: f65a8619b12c4e4ff4ab16b679b035a4ae03805d32e69d894b7fbb964d8e814a
Contents?: true
Size: 1.36 KB
Versions: 37
Compression:
Stored size: 1.36 KB
Contents
require 'rbbt-util'
require 'rbbt/resource'
module PRO
extend Resource
self.subdir = 'share/databases/PRO'
def self.organism(org="Hsa")
require 'rbbt/sources/organism'
Organism.default_code(org)
end
#self.search_paths = {}
#self.search_paths[:default] = :lib
PRO.claim PRO.identifiers, :proc do
url = "ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/PRO_mappings/uniprotmapping.txt"
dumper = TSV::Dumper.new :key_field => "PRO ID", :fields => ["UniProt/SwissProt Accession"], :type => :double, :namespace => PRO.organism
dumper.init
TSV.traverse Open.open(url), :type => :array, :into => dumper, :bar => true do |line|
pro, uni = line.split("\t")
[pro, [uni.split(":").last]]
end
TSV.collapse_stream dumper
end
PRO.claim PRO.uniprot_equivalences, :proc do
dumper = TSV::Dumper.new :key_field => "UniProt/SwissProt Accession", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :namespace => PRO.organism
dumper.init
TSV.traverse PRO.identifiers, :into => dumper, :bar => true do |pro,values|
res = []
res.extend MultipleResult
unis = values.flatten
unis.flatten.each do |uni|
res << [uni,unis]
end
res
end
end
end
iif PRO.identifiers.produce(true).find if __FILE__ == $0
iif PRO.uniprot_equivalences.produce(true).find if __FILE__ == $0
Version data entries
37 entries across 37 versions & 1 rubygems