Module: TransFIC

Defined in:
lib/rbbt/mutation/transFIC.rb

Defined Under Namespace

Classes: NotDone

Constant Summary collapse

URL = 
"http://bg.upf.edu/transfic/taskService"
ASTERISK = 
"*"[0]

Class Method Summary collapse

Class Method Details

.chunked_predict(mutations, max = 1000) ⇒ Object 



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# File 'lib/rbbt/mutation/transFIC.rb', line 69

def self.chunked_predict(mutations, max = 1000)
  chunks = mutations.length.to_f / max
  chunks = chunks.ceil

  Log.debug("TransFIC ran with #{chunks} chunks of #{ max } mutations") if chunks > 1
  num = 1
  Misc.divide(mutations, chunks).inject(nil) do |acc, list|
    Log.debug("TransFIC ran with #{chunks} chunks: chunk #{num}") if chunks > 1
    begin
      result = predict(list)
    rescue
      if list.length > 2
        Log.debug("Error predicting in transFIC. Divinding list of size #{list.length}")
        result = chunked_predict(list, list.length / 2)
      else
        Log.debug("Error predicting in transFIC. Single error detected")
        next
      end
    end
    if acc.nil?
      acc = result
    else
      acc = TSV.setup(acc.merge(result))
    end
    num += 1
    acc
  end
end

.predict(mutations) ⇒ Object

mutations is a hash of genes in Uniprot protein accession pointing to lists of aminoacid substitutions



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# File 'lib/rbbt/mutation/transFIC.rb', line 18

def self.predict(mutations)
  options = {}
  ensp2uni = Organism.identifiers("Hsa").index :target => "UniProt/SwissProt ID", :fields => "Ensembl Protein ID", :persist => true
  searchText = mutations.collect{|mutation| protein, change = mutation.split(":"); next if ensp2uni[protein].nil?; [ensp2uni[protein], change] * "\t"}.compact.uniq * "\n"

  Log.debug "Querying TransFIC for: #{mutations.length} mutations"

  TmpFile.with_file(searchText) do |file|
    test_url = CMD.cmd("curl -X PUT -T '#{ file }' '#{ URL }'").read

    result = nil

    begin
      Misc.insist(5) do
        result = CMD.cmd("curl -X GET '#{ test_url }'").read

        raise result.split("\n").select{|line| line =~ /Error/}.first if result =~ /Error/

        while result =~ /executing/
          sleep 10
          result = CMD.cmd("curl -X GET '#{ test_url }'").read
        end

        raise result.split("\n").select{|line| line =~ /Error/}.first if result =~ /Error/
      end
    rescue
      if $!.message =~ /validating/
        Log.debug(Open.read(file))
      end
      raise $!
    end

    Log.medium("TransFIC DONE")
    
    tsv = TSV.setup({}, :key_field => "Protein Mutation", :fields => %w(siftTransfic siftTransficLabel pph2Transfic pph2TransficLabel maTransfic maTransficLabel), :type => :list)
    result.split("\n").each do |line|
      next if line[0] == "#"[0]

      id, hgnc, hgncdesc, transcript, ensp, sw, protein_position, amino_acids, sift, polyphen, mass, 
        siftTransfic, siftTransficLabel, pph2Transfic, pph2TransficLabel, maTransfic, maTransficLabel = line.split("\t")

      change = [amino_acids.split("/").first, protein_position, amino_acids.split("/").last] * ""
      mutation = [ensp,change] * ":"

      tsv[mutation] = [siftTransfic, siftTransficLabel, pph2Transfic, pph2TransficLabel, maTransfic, maTransficLabel]
    end

    tsv.select(mutations)
  end
end