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Contents
require 'rbbt-util'
require 'rbbt/resource'
require 'rbbt/sources/organism'
module CORUM
extend Resource
self.subdir = 'share/databases/CORUM'
def self.organism(org="Hsa")
Organism.default_code(org)
end
CORUM.claim CORUM.complex_names, :proc do
url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip"
tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
tsv.namespace = organism
tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
tsv.key_field = "CORUM Complex ID"
tsv = tsv.slice("ComplexName").to_single
tsv.fields = ["Complex name"]
tsv
end
CORUM.claim CORUM.complexes, :proc do
url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip"
tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
tsv.namespace = organism
tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}.collect{|f|
case f
when "subunits (UniProt IDs)"
"UniProt/SwissProt Accession"
when "subunits (Entrez IDs)"
"Entrez Gene ID"
else
f
end
}
tsv.key_field = "CORUM Complex ID"
tsv.identifiers = CORUM.complex_names.produce.find
tsv
end
end
if defined? Entity
module CORUMComplex
extend Entity
self.annotation :format
self.annotation :organism
self.add_identifiers CORUM.complex_names, "CORUM Complex ID", "Complex name"
property :genes => :array2single do
@genes ||= CORUM.complexes.tsv(:persist => true, :fields => ["UniProt/SwissProt Accession"], :type => :flat).values_at *self
end
end
end
Version data entries
49 entries across 49 versions & 1 rubygems