Module: COSMIC

Extended by:
Resource
Defined in:
lib/rbbt/sources/COSMIC.rb

Class Method Summary collapse

Class Method Details

.mutation_index(organism) ⇒ Object 



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# File 'lib/rbbt/sources/COSMIC.rb', line 131

def self.mutation_index(organism)
  build = Organism.hg_build(organism)
  file = COSMIC[build == "hg19" ? "mutations" : "mutations_hg18"]
  @mutation_index ||= {}
  @mutation_index[build] ||= file.tsv :persist => true, :fields => ["Genomic Mutation"], :type => :single, :persist => true
end

.rsid_index(organism, chromosome = nil) ⇒ Object 



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# File 'lib/rbbt/sources/COSMIC.rb', line 104

def self.rsid_index(organism, chromosome = nil)
  build = Organism.hg_build(organism)

  tag = [build, chromosome] * ":"
  fwt = nil
  Persist.persist("StaticPosIndex for COSMIC [#{ tag }]", :fwt, :persist => true) do
    value_size = 0
    file = COSMIC[build == "hg19" ? "mutations" : "mutations_hg18"]
    chr_positions = []
    begin
      Open.read(CMD.cmd("grep '\t#{chromosome}:'", :in => file.open, :pipe => true)) do |line|
        next if line[0] == "#"[0]
        rsid, mutation = line.split("\t").values_at 0, 25
        next if mutation.nil? or mutation.empty?
        chr, pos = mutation.split(":")
        next if chr != chromosome or pos.nil? or pos.empty?
        chr_positions << [rsid, pos.to_i]
        value_size = rsid.length if rsid.length > value_size
      end
    rescue
    end
    fwt = FixWidthTable.new :memory, value_size
    fwt.add_point(chr_positions)
    fwt
  end
end