Sha256: 28957f4e2e1693cbc656edc20d3bdcc6826bc4b1452f9354cfbda793253d47b3
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Size: 1.98 KB
Versions: 51
Compression:
Stored size: 1.98 KB
Contents
require 'rbbt-util'
require 'rbbt/resource'
module PhosphoELM
extend Resource
self.subdir = 'share/databases/PhosphoELM'
def self.organism(org="Hsa")
require 'rbbt/sources/organism'
Organism.default_code(org)
end
#self.search_paths = {}
#self.search_paths[:default] = :lib
PhosphoELM.claim PhosphoELM[".source/dump.tgz"], :proc do |file|
raise "Place phosphoELM_all_latest.dump.tgz from http://phospho.elm.eu.org at #{file}. Please consult license."
end
PhosphoELM.claim PhosphoELM.data, :proc do
tgz = PhosphoELM[".source/dump.tgz"].produce.find
organism = PhosphoELM.organism
uni2ensp = Organism.identifiers(organism).tsv :key_field => "UniProt/SwissProt Accession", :fields => ["Ensembl Protein ID"], :type => :flat, :persist => true
ensp2seq = Organism.protein_sequence(organism).tsv :persist => true
dumper = TSV::Dumper.new(:key_field => "Phosphosite", :fields => ["Kinases", "Source", "PMID"], :type => :list)
dumper.init
TmpFile.with_file do |dir|
Misc.in_dir dir do
CMD.cmd("tar xvfz #{tgz}")
f = Dir.glob("*.dump").first
TSV.traverse Open.open(f), :type => :array, :into => dumper do |line|
next unless line =~ /Homo sapiens/
acc, sequence, position, code, pmids, kinases, source, species, entry_date = line.split("\t")
ensps = uni2ensp[acc]
Log.warn "No Ensembl Protein ID for #{acc}" if ensps.nil?
next if ensps.nil?
sequence << "*"
good = ensps.select{|ensp| sequence == ensp2seq[ensp]}
Log.warn "No sequence match for #{acc} - #{ensps*", "}" if good.empty?
next if good.empty?
res = []
good.each do |ensp|
phospho_site = [ensp,":", code, position] * ""
res << [phospho_site, [kinases, source, pmids]]
end
res.extend MultipleResult
res
end
end
end
dumper.stream
end
end
iif PhosphoELM.data.produce(true).find if __FILE__ == $0
Version data entries
51 entries across 51 versions & 1 rubygems