Class: Ms::Quant::Qspec

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/quant/qspec.rb

Defined Under Namespace

Classes: Results

Constant Summary collapse

NBURNIN =

personal communication with Hyungwon Choi: “We typically use nburn=2000, niter=10000, which is quite sufficient to guarantee the reproducibility of results using the same data.”

2000
NITER = 
10000
INIT_HEADER = 
%w(protid protLen)
DELIMITER = 
"\t"
SUBMITTED_TO_QSPEC = 
'submitted_to_qspec.txt'

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(protname_length_pairs, condition_to_count_array) ⇒ Qspec

protname_length_pairs is an array of doublets: [protname, length] condition_to_count_array is an array doublets: [condition, array_of_counts]



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# File 'lib/ms/quant/qspec.rb', line 54

def initialize(protname_length_pairs, condition_to_count_array)
  @protname_length_pairs = protname_length_pairs
  @condition_to_count_array = condition_to_count_array
end

Class Method Details

.conditions_to_ints(conditions) ⇒ Object

takes an ordered list of conditions [‘cond1’, ‘cond1’, ‘cond2’, ‘cond2’] and returns an array of ints [0,0,0,1,1,1…]



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# File 'lib/ms/quant/qspec.rb', line 18

def self.conditions_to_ints(conditions)
  i = 0
  current_condition = conditions.first
  conditions.map do |cond| 
    if current_condition == cond ; i
    else
      i += 1
      current_condition = cond
      i
    end
  end
end

.executable(conditions) ⇒ Object

returns the right executable based on the array of conditions



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# File 'lib/ms/quant/qspec.rb', line 47

def self.executable(conditions)
  biggest_size = conditions.group_by {|v| v }.values.map(&:size).max
  (biggest_size >= 3) ? 'qspecgp' : 'qspec'
end

.results_array(resultsfile) ⇒ Object

returns an array of Results structs which is each row of the returned file works with V2 of QSpec



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# File 'lib/ms/quant/qspec.rb', line 33

def self.results_array(resultsfile)
  rows = IO.readlines(resultsfile).map {|line| line.chomp.split("\t") }
  headers = rows.shift
  start_bayes = headers.index {|v| v =~ /BayesFactor/i }
  rows.map do |row| 
    data = [row[0]]
    data.push( row[1...start_bayes].map(&:to_f) )
    data.push( *row[start_bayes,4].map(&:to_f) )
    data.push( row[start_bayes+4] )
    Results.new(*data)
  end
end

Instance Method Details

#conditions ⇒ Object 



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# File 'lib/ms/quant/qspec.rb', line 59

def conditions
  @condition_to_count_array.map(&:first)
end

#run(normalize = true, opts = {}) ⇒ Object

returns an array of Qspec::Results objects (each object can be considered a row of data)



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# File 'lib/ms/quant/qspec.rb', line 79

def run(normalize=true, opts={})
  puts "normalize: #{normalize}" if $VERBOSE
  tfile = Tempfile.new("qspec")
  write(tfile.path)
  if opts[:keep]
    local_file = File.join(Dir.pwd,File.basename(tfile.path))
    FileUtils.cp(tfile.path, local_file, :verbose => $VERBOSE)
    puts "(copy of) file submitted to qspec: #{local_file}" if $VERBOSE
  end
  qspec_exe = self.class.executable(conditions)
  cmd = [qspec_exe, tfile.path, NBURNIN, NITER, (normalize ? 1 : 0)].join(' ')
  if $VERBOSE
    puts "running #{cmd}" if $VERBOSE
  else
    cmd << " 2>&1"
  end
  reply = `#{cmd}`
  puts reply if $VERBOSE
  outfile = tfile.path + '_' + qspec_exe
  results = self.class.results_array(outfile)
  if opts[:keep]
    local_outfile = File.join(Dir.pwd, File.basename(outfile))
    FileUtils.cp(outfile, local_outfile, :verbose => $VERBOSE)
    puts "(copy of) file returned from qspec: #{outfile}"
  end
  tfile.unlink
  results
end

#write(filename) ⇒ Object

writes a qspec formatted file to filename



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# File 'lib/ms/quant/qspec.rb', line 64

def write(filename)
  ints = Ms::Quant::Qspec.conditions_to_ints(conditions)
  header_cats = INIT_HEADER + ints
  rows = @protname_length_pairs.map {|pair| pair.map.to_a }
  @condition_to_count_array.each do |cond,counts|
    rows.zip(counts) {|row,cnt| row << cnt }
  end
  File.open(filename,'w') do |out|
    out.puts header_cats.join(DELIMITER)
    rows.each {|row| out.puts row.join(DELIMITER) }
  end
end