Class: Mspire::Quant::Qspec

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

Defined Under Namespace

Classes: Results

Constant Summary collapse

EXE =

qspec: discrete spectral count data qprot: continuous protein abundance data (could be non-discrete spectral counts or quantitation data) paired: one sample against another sample param: one sample against another sample but with one or more replicates

{
  qspec: {
    paired: 'qspec-paired',  # <- the old qspec (use qspec here if you have old software)
    param: 'qspec-param',    # <  the old qspecgp (use qspecgp if you have old software)
  },
  qprot: {
    paired: 'qprot-paired',
    param: 'qprot-param',
  },
  getfdr: 'getfdr',
}
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"

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(protnames, condition_to_count_array) ⇒ Qspec

protname is a list of protein names. by default, qprot will be run. If you really want qspec to be run, then supply a [protname, length] doublet in place of each protname. condition_to_count_array is an array doublets: [condition, array_of_counts]



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# File 'lib/mspire/quant/qspec.rb', line 73

def initialize(protnames, condition_to_count_array)
  @protnames = protnames
  if @protnames.first.is_a?(Array)
    @protname_length_pairs = @protnames
    @protnames = nil
  end
  @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/mspire/quant/qspec.rb', line 36

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

.results_array(resultsfile) ⇒ Object

returns an array of Results structs which is each row of the returned file works with version 1.2.2 of Qprot



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# File 'lib/mspire/quant/qspec.rb', line 51

def self.results_array(resultsfile)
  rows = IO.readlines(resultsfile).map {|line| line.chomp.split("\t") }
  headers = rows.shift
  start_log_fold = headers.index {|v| v =~ /LogFoldChange/i }
  rows.map do |row| 
    data = [row[0]]
    data.push( row[1...start_log_fold].map(&:to_f) )
    data.push( *row[start_log_fold,5].map(&:to_f) )
    Results.new(*data)
  end
end

Instance Method Details

#conditions ⇒ Object 



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# File 'lib/mspire/quant/qspec.rb', line 82

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

#executable ⇒ Object

returns the right executable based on the array of conditions



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

def executable
  biggest_size = conditions.group_by {|v| v }.values.map(&:size).max
  EXE[@protnames ? :qprot : :qspec][(biggest_size >= 3) ? :param : :paired]
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/mspire/quant/qspec.rb', line 104

def run(normalize=true, opts={})
  exe = executable
  puts "using #{exe}" if $VERBOSE
  executable_base = exe.split('-')[0]

  puts "normalize: #{normalize}" if $VERBOSE
  tfile = Tempfile.new(executable_base)
  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 #{exe}: #{local_file}" if $VERBOSE
  end
  cmd = [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 + '_' + executable_base
  system EXE[:getfdr], outfile
  fdr_file = outfile + "_fdr"
  puts "FDR_FILE: #{fdr_file} exists? #{fdr_file}" if $VERBOSE
  results = self.class.results_array(fdr_file)
  if opts[:keep]
    local_outfile = File.join(Dir.pwd, File.basename(outfile))
    local_fdrfile = File.join(Dir.pwd, File.basename(fdr_file))
    FileUtils.cp(outfile, local_outfile, :verbose => $VERBOSE)
    FileUtils.cp(fdr_file, local_fdrfile, :verbose => $VERBOSE)
    if $VERBOSE
      puts "(copy of) file returned from qspec: #{outfile}"
      puts "(copy of) file returned from qspec: #{fdr_file}"
    end
  end
  tfile.unlink
  results
end

#write(filename) ⇒ Object

writes a qspec formatted file to filename



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# File 'lib/mspire/quant/qspec.rb', line 87

def write(filename)
  header_cats = %w(protid)
  header_cats << 'protLen' if @protname_length_pairs
  header_cats.push(*Mspire::Quant::Qspec.conditions_to_ints(conditions))
  ar = @protnames || @protname_length_pairs
  rows = ar.map {|obj| Array(obj) }
  @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