Class: MzID::FilteredStreamingParser

Inherits:
StreamingParser show all
Defined in:
lib/mzid/filtered_streaming_parser.rb

Overview

class to parse an mzIdentML file in a streaming (i.e., mem-efficient) manner performs multi-pass filtering so that can maintain smallest datastruct in memory 1) first collect counts of elements 2) get list of peptide evidence from PSMs that pass filter 3)

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from BatchParser

#each_spectrum

Constructor Details

#initialize(file, sp_thresh = 10.0**-10,, use_pbar = nil) ⇒ FilteredStreamingParser

Returns a new instance of FilteredStreamingParser.



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# File 'lib/mzid/filtered_streaming_parser.rb', line 16

def initialize(file, sp_thresh = 10.0**-10, use_pbar = nil)
  @num_spec = 0
  #
  @pep_ev_h_protID = Hash.new
  @pep_ev_h_startPos = Hash.new
  @pep_ev_h_endPos = Hash.new
  @pep_ev_h_dbseqRef = Hash.new
  super(file, use_pbar)
end

Instance Attribute Details

#pep_ev_h_dbseqRef ⇒ Object

Returns the value of attribute pep_ev_h_dbseqRef.



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# File 'lib/mzid/filtered_streaming_parser.rb', line 38

def pep_ev_h_dbseqRef
  @pep_ev_h_dbseqRef
end

Instance Method Details

#cache_db_seq_entries(root) ⇒ Object

store database sequence entries (ids)



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# File 'lib/mzid/filtered_streaming_parser.rb', line 141

def cache_db_seq_entries(root)
  dbseq_lst = root.xpath('//DBSequence')
  dbseq_lst.each do |dnode|
    id = dnode["id"].to_sym
    acc_id = dnode["accession"]
    @db_seq_h[id] = acc_id.to_sym
  end
end

#cache_ids(use_pbar = @use_pbar) ⇒ Object

store peptide sequences in hash for lookup



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# File 'lib/mzid/filtered_streaming_parser.rb', line 43

def cache_ids(use_pbar = @use_pbar)
  num_pep, num_db_seq, num_pep_ev = get_num_elements(nil)
  puts "SPEC:\t#{@num_spec}"
  puts "PEP:\t#{num_pep}"
  puts "DB:\t#{num_db_seq}"
  puts "PEPEV:\t#{num_pep_ev}"

  #pbar1 = ProgressBar.new("Caching psm", num_pep) if use_pbar
  #reader = Nokogiri::XML::Reader(File.open(@mzid_file))
  #reader.each do |node|        
  #end

  @pep_h = Hash.new
  @mod_h = Hash.new
  #pbar = ProgressBar.new("Caching", num_pep+num_db_seq+num_pep_ev) if use_pbar
  pbar1 = ProgressBar.new("peptides", num_pep/2) if use_pbar
  reader = Nokogiri::XML::Reader(File.open(@mzid_file))
  reader.each do |node|
    #
    if node.name == "Peptide" then
      #pbar.inc if use_pbar
      # parse local peptide entry
      tmp_node = Nokogiri::XML.parse(node.outer_xml)
      tmp_node.remove_namespaces!
      root = tmp_node.root          
      pep_id = root["id"].to_sym
      # skip if already handled PepID
      next if @pep_h.has_key?(pep_id)
      # parse sequence/mods if haven't seen it yet
      pep_seq = get_peptide_sequence(root)
      mod_line = get_modifications(root)
      @pep_h[pep_id] = pep_seq
      @mod_h[pep_id] = mod_line
      pbar1.inc if use_pbar
    end
  end
  pbar1.finish if use_pbar
  #
  pbar2 = ProgressBar.new("db_seq", num_db_seq) if use_pbar
  IO.foreach(@mzid_file) do |line|
    next if !line.match(/^\s+<DBSequence\s/)
    
    prot_id = line.match(/accession=\"([\w|\|]+)/)[1]
    db_id = line.match(/id=\"(\w+)/)[1]
    
    @db_seq_h[db_id.to_sym] = prot_id.to_sym
    pbar2.inc if use_pbar
  end
  # reader2 = Nokogiri::XML::Reader(File.open(@mzid_file))
  # reader2.each do |node|
  #   #
  #   if node.name == "DBSequence" then
  #     # parse local DBSequence entry
  #     tmp_node = Nokogiri::XML.parse(node.outer_xml)
  #     tmp_node.remove_namespaces!
  #     root = tmp_node.root
  #     cache_db_seq_entries(root)
  #     pbar2.inc if use_pbar
  #   end
  # end
  pbar2.finish if use_pbar
  #
  pbar3 = ProgressBar.new("pep_ev", num_pep_ev) if use_pbar
  IO.foreach(@mzid_file) do |line|
    next if !line.match(/^\s+<PeptideEvidence\s/)
    
    db_id = line.match(/dBSequence_ref=\"(\w+)/)[1]
    pep_ev = line.match(/id=\"(\w+)/)[1]
    @pep_ev_h_dbseqRef[pep_ev.to_sym] = db_id.to_sym
    pbar3.inc if use_pbar
  end
  # reader3 = Nokogiri::XML::Reader(File.open(@mzid_file))
  # reader3.each do |node|
  #   if node.name == "PeptideEvidence" then
  #     # parse local DBSequence entry
  #     tmp_node = Nokogiri::XML.parse(node.outer_xml)
  #     tmp_node.remove_namespaces!
  #     root = tmp_node.root
  #     cache_pep_ev(root)
  #     pbar3.inc if use_pbar
  #   end 
  #   # if node.name == "PeptideEvidence" then
  #   #   tmp_node = Nokogiri::XML.parse(node.outer_xml)
  #   #   root = tmp_node.root
  #   #   pep_ref = root.to_s.match(/peptide_ref=\"(\w+)\"/)[1]
  #   #   id_ref = root.to_s.match(/id=\"(\w+)\"/)[1]
  #   #   db_ref = root.to_s.match(/dBSequence_ref=\"(\w+)\"/)[1]
  #   #   @pep_ev_h_dbseqRef[id_ref.to_sym] = db_ref.to_sym
  #   # end
  # end      
  pbar3.finish if use_pbar
  puts "PEP_H SIZE:\t#{@pep_h.size}"
  puts "DBSEQ_H SIZE:\t#{@db_seq_h.size}"
  puts "PEP_EV_H SIZE:\t#{@pep_ev_h_dbseqRef.size}"
end

#cache_ids2(use_pbar = @use_pbar) ⇒ Object 



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# File 'lib/mzid/filtered_streaming_parser.rb', line 27

def cache_ids2(use_pbar = @use_pbar)
end

#cache_pep_ev(root) ⇒ Object

store peptide evidence sequences in hash for lookup



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# File 'lib/mzid/filtered_streaming_parser.rb', line 152

def cache_pep_ev(root)
  pep_ev_lst = root.xpath('//PeptideEvidence')
  pep_ev_lst.each do |pnode|
    id = pnode["id"].to_sym
    # @pep_ev_h[id] = 
    #   PeptideEvidence.new(#:id => pnode["id"],
    #                       :db_seq_ref => pnode["dBSequence_ref"],
    #                       #:pep_id => pnode["peptide_ref"],
    #                       :start_pos => pnode["start"].to_i,
    #                       :end_pos => pnode["end"].to_i,
    #                       #:pre => pnode["pre"],
    #                       #:post => pnode["post"],
    #                       :prot_id => @db_seq_h[pnode["dBSequence_ref"]].to_sym)
    
    # @pep_ev_h_protID[id.to_sym] = @db_seq_h[pnode["dBSequence_ref"]].to_sym
    # @pep_ev_h_startPos[id.to_sym] = pnode["start"].to_i,
    # @pep_ev_h_endPos[id.to_sym] = pnode["end"].to_i
    @pep_ev_h_dbseqRef[id.to_sym] = pnode["dBSequence_ref"].to_sym
  end
end

#each_psm(use_pbar = @use_pbar) ⇒ Object

iterate through each psm



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# File 'lib/mzid/filtered_streaming_parser.rb', line 175

def each_psm(use_pbar=@use_pbar)
  hit_values = File.open(@mzid_file) do |io|
    doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS | Nokogiri::XML::ParseOptions::STRICT)
    doc.remove_namespaces!
    root = doc.root
    # get list of identifications
    spec_results = root.xpath('//SpectrumIdentificationResult')
    pbar = ProgressBar.new("PSMs", spec_results.size) if use_pbar
    spec_results.each do |sres|
      # 
      psms_of_spec = sres.xpath('.//SpectrumIdentificationItem')
      # go over each PSM from the spectra
      psms_of_spec.each do |psm_node|
        psm = get_psm(psm_node)
        # yield psm object
        yield psm
      end
      pbar.inc if use_pbar
    end
    pbar.finish if use_pbar
  end
end

#get_prot_id(pep_ev_id) ⇒ Object

def get_pep_ev_protID(pid) @pep_ev_h_protID end



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# File 'lib/mzid/filtered_streaming_parser.rb', line 32

def get_prot_id(pep_ev_id) 
  dbref = @pep_ev_h_dbseqRef[pep_ev_id]
  prot_id = @db_seq_h[dbref]
  prot_id
end

#get_psm(psm_node) ⇒ Object

given a xml node of a psm, return the PSM



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# File 'lib/mzid/filtered_streaming_parser.rb', line 200

def get_psm(psm_node)
  # get peptide evidence list
  pep_ev_raw_lst = psm_node.xpath('.//PeptideEvidenceRef')
  pep_ev_lst = pep_ev_raw_lst.map{|penode| pep_ev_ref_id = penode["peptideEvidence_ref"].to_sym}     
  # get cvparams
  cvlst = psm_node.xpath('.//cvParam')
  # find spectral prob
  tmp_lst = cvlst.select{|v| v['name'] == "MS-GF:SpecEValue"}
  spec_prob = tmp_lst[0]['value']
  # get peptide
  pep_seq = @pep_h[psm_node['peptide_ref'].to_sym]
  # get spectrum id/ref number
  spec_id = psm_node['id']
  spec_num = spec_id.split("_")[1].to_i
  spec_ref = spec_id.split("_")[-1].to_i
  #      
  # store in object
  psm = PSM.new(:spec_num => spec_num, 
                :spec_ref => spec_ref, 
                :pep => pep_seq, 
                :spec_prob => spec_prob.to_f,
                :mods => (@mod_h.has_key?(psm_node['peptide_ref']) ? @mod_h[psm_node['peptide_ref']] : nil),
                :pep_ev => pep_ev_lst)
end

#write_to_file(outfile, use_pbar = @use_pbar) ⇒ Object

load PSMs into memory, and go back to perform lookup for prot ids



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# File 'lib/mzid/filtered_streaming_parser.rb', line 227

def write_to_file(outfile, use_pbar=@use_pbar)
  
  pbar3 = ProgressBar.new("Caching pep_ev", num_db_seq) if use_pbar
  t1_db = Time.now
  reader3 = Nokogiri::XML::Reader(File.open(@mzid_file))
  reader3.each do |node|
    if node.name == "PeptideEvidence" then
      # parse local DBSequence entry
      tmp_node = Nokogiri::XML.parse(node.outer_xml)
      tmp_node.remove_namespaces!
      root = tmp_node.root
      #cache_pep_ev(root)
      pep_ev_lst = root.xpath('//PeptideEvidence')
      pep_ev_lst.each do |pnode|
        id = pnode["id"]
        start_pos = pnode["start"].to_i,
        end_pos = pnode["end"].to_i
        db_seq_ref = pnode["dBSequence_ref"].to_sym
      end 
      pbar3.inc if use_pbar
    end 
    
  end
  pbar3.finish if use_pbar

end