Module: Ms::ErrorRate::Qvalue::Mascot::Percolator

Defined in:
lib/ms/error_rate/qvalue/mascot/percolator.rb,
lib/ms/error_rate/qvalue/mascot/percolator.rb

Class Method Summary collapse

Class Method Details

.qvalues(datp_files, tab_txt_files, opts = {}) ⇒ Object

returns an array of Structs of PeptideHit(:filename, :query_title, :charge, :sequence, :mowse, :qvalue) opts = 

:min_peptide_length => Integer



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# File 'lib/ms/error_rate/qvalue/mascot/percolator.rb', line 49

def qvalues(datp_files, tab_txt_files, opts={})
  min_pep_len = opts[:min_peptide_length]

  # we only want the top hit per query title (which should ensure that we
  # get the top hit per scan)
  hits_by_query_title = Hash.new {|h,k| h[k] = [] }
  datp_files.zip(tab_txt_files) do |datp_file, tab_txt_file| 
    # build a hash based on the sequence
    structs = Ms::ErrorRate::Qvalue::Mascot::Percolator.tab_txt( tab_txt_file )
    qvalue_by_query_rank = {}
    structs.each do |struct|
      qvalue_by_query_rank[[struct.query_num, struct.rank]] = struct.q_value
    end

    base_no_ext = File.basename(datp_file, '.*')
    Ms::Mascot::Dat.open(datp_file) do |dat|
      dat.each_peptide_hit(:by => :groups, :yield_nil => false, :with_query => true) do |hits,query|
        hits.each do |hit|
          if qval = qvalue_by_query_rank[[hit.query_num, hit.hit_num]]
            hit_as_struct = Ms::ErrorRate::Qvalue::Mascot::MascotPeptideHit.new(base_no_ext, query.title, query.charge, hit.sequence, hit.score, qval)
            hits_by_query_title[hit_as_struct.query_title] << hit_as_struct
          end
        end
      end
    end
  end

  final_hits = []
  hits_by_query_title.each do |title, hits|
    best_hit = 
      if hits.size == 1
        hits.first
      else
        hits.sort_by(&:mowse).last
      end
    # FILTER HERE:
    # ONLY TAKE the BEST HIT IF it passes any filters
    if min_pep_len
      next unless best_hit.sequence.size >= min_pep_len
    end
    final_hits << best_hit
  end
  final_hits
end

.tab_txt(file) ⇒ Object

returns an array of Structs where the keys are the first line everything is cast properly three additional keys are available query_num, rank, sequence sequence is the amino acid sequence without the surrounding X’s and dots. (with ‘-’ substituted for ‘_’)



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# File 'lib/ms/error_rate/qvalue/mascot/percolator.rb', line 19

def tab_txt(file)
  hits = []
  File.open(file) do |io|
    # PSMId	score	q-value	posterior_error_prob	peptide	proteinIds
    atts = io.gets.chomp.split("\t").map {|v| v.gsub('-', '_').to_sym } 
    atts.push(:query_num, :rank, :sequence)
    struct_class = Struct.new("Hit", *atts)
    
    io.each do |line|
      (query_rank, score, qvalue, perrp, peptide, *prots ) = line.chomp.split("\t")
      (query, rank) = query_rank.split(';').map {|v| v.split(':').last.to_i }
      
      hits << struct_class.new(query_rank, score.to_f, qvalue.to_f, perrp.to_f, peptide, prots, query, rank, peptide.split('.')[1])
    end
  end
  hits
end