Class: Ms::Mascot::Predict

Inherits:
Tap::FileTask
  • Object
show all
Defined in:
lib/ms/mascot/predict.rb

Overview

Ms::Mascot::Predict::manifest predicts the spectra for a protein sequence

Fragments a protein sequence and calculates the fragment spectra for each peptide. The peptide spectra are formatted as mgf and dumped to the target. 

% rap predict MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFS
  I[16:30:19]             digest MAEELVLERCD... to 15 peptides
  I[16:30:19]           fragment MAEELVLER
  I[16:30:19]           fragment MAEELVLERCDLELETNGR
  I[16:30:19]           fragment CDLELETNGR
  I[16:30:19]           fragment CDLELETNGRDHHTADLCR
  I[16:30:19]           fragment DHHTADLCR
  I[16:30:19]           fragment DHHTADLCREK
  I[16:30:19]           fragment EKLVVR
  I[16:30:19]           fragment LVVR
  I[16:30:19]           fragment LVVRR
  I[16:30:19]           fragment RGQPFWLTLHFEGR
  I[16:30:19]           fragment GQPFWLTLHFEGR
  I[16:30:19]           fragment GQPFWLTLHFEGRNYEASVDSLTFS
  I[16:30:19]           fragment NYEASVDSLTFS

Instance Method Summary collapse

Instance Method Details

#default_path(sequence) ⇒ Object

Infers a default path for the output mgf file from the sequence; the path is the sequence if the sequence is less than 10 characters, otherwise it’s like: “<first five>_<last five>.mgf”



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# File 'lib/ms/mascot/predict.rb', line 68

def default_path(sequence)
  sequence = "#{sequence[0,5]}_#{sequence[-5,5]}" if sequence.length > 10
  "#{sequence}.mgf"
end

#process(sequence, target = nil) ⇒ Object 



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# File 'lib/ms/mascot/predict.rb', line 73

def process(sequence, target=nil)
  sequence = sequence.gsub(/\s/, "")
  
  @entries = []
  digest.execute(sequence)
  
  # prepare and dump the predicted spectra
  # to the target path.
  target = default_path(sequence) if target == nil
  prepare(target)
  File.open(target, "wb") do |file|
    @entries.each do |entry|
      entry.dump(file, config)
      file.puts 
    end
  end
  
  target
end

#workflow ⇒ Object

Sequences digest and fragment. When fragment completes, it will add a new mgf entry to the internal entries collection.



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# File 'lib/ms/mascot/predict.rb', line 42

def workflow
  digest.on_complete do |_results|
    _results._iterate.each do |_result|
      next if min_length && _result._current.length < min_length
      fragment._execute(_result)
    end
  end
     
  fragment.on_complete do |_result|
    parent_ion_mass, data = _result._current
    next if data.empty?
    
    peptide = _result._values[-2]
    headers = {
      'TITLE' => "#{peptide} (#{fragment.series.join(', ')})",
      'CHARGE' => fragment.charge,
      'PEPMASS' => parent_ion_mass}
    
    @entries << Mgf::Entry.new(headers, data) 
  end
end