Class: MS::Sequest::Sqt::Spectrum

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/sequest/sqt.rb

Overview

0=first_scan 1=last_scan 2=charge 3=time_to_process 4=node 5=mh 6=total_intensity 7=lowest_sp 8=num_matched_peptides 9=matches

Constant Summary collapse

Leader = 
'S'

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.set_deltacn(spectra) ⇒ Object 



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# File 'lib/ms/sequest/sqt.rb', line 276

def self.set_deltacn(spectra)
  spectra.each do |spec|
    matches = spec.matches
    if matches.size > 0

      (0...(matches.size-1)).each do |i|
        matches[i].deltacn = matches[i+1].deltacn_orig 
      end
      matches[-1].deltacn = 1.1
    end
  end
  spectra
end

.spectra_from_handle(fh, base_name, percolator_results = false) ⇒ Object

assumes the first line starts with an ‘S’



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# File 'lib/ms/sequest/sqt.rb', line 235

def self.spectra_from_handle(fh, base_name, percolator_results=false)
  peptides = []
  spectra = []
  
  while line = fh.gets
    case line[0,1]
    when MS::Sequest::Sqt::Spectrum::Leader
      spectrum = MS::Sequest::Sqt::Spectrum.new.from_line( line )
      spectra << spectrum
      matches = []
      spectrum.matches = matches
    when MS::Sequest::Sqt::Match::Leader
      match_klass = if percolator_results
                      MS::Sequest::Sqt::Match::Percolator
                    else
                      MS::Sequest::Sqt::Match
                    end
      match = match_klass.new.from_line( line )
      #match[10,3] = spectrum[0,3]
      # structs cannot set multiple values at a time :(
      match[10] = spectrum[0]
      match[11] = spectrum[1]
      match[12] = spectrum[2]
      match[15] = base_name
      matches << match
      peptides << match
      loci = []
      match.loci = loci
      matches << match
    when MS::Sequest::Sqt::Locus::Leader
      line.chomp!
      key = line.split(MS::Sequest::Sqt::Delimiter)[1]
      locus = MS::Sequest::Sqt::Locus.from_line( line )
      loci << locus
    end
  end
  # set the deltacn:
  set_deltacn(spectra)
  [spectra, peptides]
end

Instance Method Details

#from_line(line) ⇒ Object

returns an array -> [the next spectra line (or nil if eof), spectrum]



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# File 'lib/ms/sequest/sqt.rb', line 292

def from_line(line)
  line.chomp!
  ar = line.split(MS::Sequest::Sqt::Delimiter)
  self[0] = ar[1].to_i
  self[1] = ar[2].to_i
  self[2] = ar[3].to_i
  self[3] = ar[4].to_f
  self[4] = ar[5]
  self[5] = ar[6].to_f
  self[6] = ar[7].to_f
  self[7] = ar[8].to_f
  self[8] = ar[9].to_i
  self[9] = []
  self
end