Sha256: ca29e90c77ac8bc04154cebe8f30dd6b88b813fbcc9800e29a47d41ca6280856
Contents?: true
Size: 1.59 KB
Versions: 18
Compression:
Stored size: 1.59 KB
Contents
require 'rbbt-util'
require 'rbbt/resource'
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/genre/proj/corum/allComplexes.csv"
tsv = TSV.open(url, :header_hash => "", :sep => ';', :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.slice("Complex name").to_single
end
CORUM.claim CORUM.complexes, :proc do
url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
tsv = TSV.open(url, :header_hash => "", :sep => ';', :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
18 entries across 18 versions & 1 rubygems