Module: CHASM

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

Defined Under Namespace

Classes: NotDone

Constant Summary collapse

URL = 
"http://www.cravat.us/ClassifierSelect1"
ASTERISK = 
"*"[0]

Class Method Summary collapse

Class Method Details

.chunked_predict(mutations, max = 1000) ⇒ Object 



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# File 'lib/rbbt/mutation/chasm.rb', line 49

def self.chunked_predict(mutations, max = 1000)
  flattened_mutations = mutations.collect{|g,list| list = [list] unless Array === list; list.collect{|m| [g,m] } }.flatten(1)
  chunks = flattened_mutations.length.to_f / max
  chunks = chunks.ceil

  Log.debug("Mutation Assessor ran with #{chunks} chunks of #{ max } mutations") if chunks > 1
  num = 1
  Misc.divide(flattened_mutations, chunks).inject(nil) do |acc, list|
    Log.debug("Mutation Assessor ran with #{chunks} chunks: chunk #{num}") if chunks > 1
    unflattened_mutations = {}
    list.each{|g,m| next if g.nil?; unflattened_mutations[g] ||= []; unflattened_mutations[g] << m}
    if acc.nil?
      acc = predict(unflattened_mutations)
    else
      acc = TSV.setup(acc.merge(predict(unflattened_mutations)))
    end
    num += 1
    acc
  end
end

.predict(mutations_by_sample, options = {}) ⇒ Object

Hash of samples pointing to mutations specified in Ensembl Transcript ID



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# File 'lib/rbbt/mutation/chasm.rb', line 15

def self.predict(mutations_by_sample, options = {})
  options = Misc.add_defaults options, :chosendb => "CHASM", :emailbox => '[email protected]', :analysistype => 'driver', :inputfile => nil
  mutationbox = []
  i = 1
  mutations_by_sample.each do |sample,mutations|
    mutations.each do |mutation|
      mutationbox << [i, sample].concat(mutation.split(":"))
    end
    i += 1
  end

  options[:mutationbox] = mutationbox.collect{|line| line * "\t"} * "\n"
  post_data = options.collect{|k,v| [k,v] * "="} * "&"

  Log.debug "Querying CHASM for: #{mutationbox.length} mutations in #{mutations_by_sample.length} samples"

  tries = 0
  nocache = false
  begin
    doc = nil
    TmpFile.with_file(post_data) do |post_file|
      Log.medium "Updating cache:" if nocache == :update

      url = URI.parse(URL)
      req = Net::HTTP::Post::Multipart.new url.path, options
      res = Net::HTTP.start(url.host, url.port) do |http|
        http.request(req)
      end
      job_id = JSON.parse(res.body)["jobId"]
      puts job_id
    end
  end
end