Class: Bioworks::Prot

Inherits:
Object
  • Object
show all
Includes:
XML, ProteinReferenceable, SpecID::Prot
Defined in:
lib/ms/sequest/bioworks.rb

Constant Summary collapse

@@end_prot_re = 
/<\/protein>/o
@@pep_re = 
/<peptide>/o
@@atts = 
%w(reference protein_probability consensus_score sf unified_score coverage pi weight accession peps)

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Prot

Returns a new instance of Prot.



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# File 'lib/ms/sequest/bioworks.rb', line 307

def initialize
  @peps = []
  @peptide_hit_counts = [0,0,0,0,0,0]
end

Instance Attribute Details

#accession ⇒ Object

Returns the value of attribute accession.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def accession
  @accession
end

#bioworks ⇒ Object

Returns the value of attribute bioworks.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def bioworks
  @bioworks
end

#consensus_score ⇒ Object

Returns the value of attribute consensus_score.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def consensus_score
  @consensus_score
end

#coverage ⇒ Object

Returns the value of attribute coverage.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def coverage
  @coverage
end

#peps ⇒ Object

Returns the value of attribute peps.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def peps
  @peps
end

#peptide_hit_counts ⇒ Object

Returns the value of attribute peptide_hit_counts.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def peptide_hit_counts
  @peptide_hit_counts
end

#pi ⇒ Object

Returns the value of attribute pi.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def pi
  @pi
end

#protein_probability ⇒ Object

Returns the value of attribute protein_probability.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def protein_probability
  @protein_probability
end

#reference ⇒ Object

Returns the value of attribute reference.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def reference
  @reference
end

#sf ⇒ Object

Returns the value of attribute sf.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def sf
  @sf
end

#unified_score ⇒ Object

Returns the value of attribute unified_score.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def unified_score
  @unified_score
end

#weight ⇒ Object

Returns the value of attribute weight.



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# File 'lib/ms/sequest/bioworks.rb', line 305

def weight
  @weight
end

Instance Method Details

#get(*args) ⇒ Object

returns array of values of the attributes given (as symbols)



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# File 'lib/ms/sequest/bioworks.rb', line 314

def get(*args)
  args.collect do |arg|
    send(arg)
  end
end

#set_from_xml_hash(hash) ⇒ Object

changes the sf to Sf and pI to pi



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# File 'lib/ms/sequest/bioworks.rb', line 367

def set_from_xml_hash(hash)
  @reference = hash["reference"]
  @protein_probability = hash["protein_probability"].to_f
  #@probability = @protein_probability.to_f
  @consensus_score = hash["consensus_score"].to_f
  @sf = hash["Sf"].to_f
  @unified_score = hash["unified_score"].to_f
  @coverage = hash["coverage"].to_f
  @pi = hash["pI"].to_f
  @weight = hash["weight"].to_f
  @accession = hash["accession"]
end

#set_from_xml_hash_xmlparser(hash) ⇒ Object 



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# File 'lib/ms/sequest/bioworks.rb', line 358

def set_from_xml_hash_xmlparser(hash)
  hash.delete("sequestresults")
  hash.delete("bioworksinfo")
  hash["sf"] = hash.delete("Sf")
  hash["pi"] = hash.delete("pI")
  set_from_xml_hash(hash)
end

#set_from_xml_stream(fh, uniq_pephit_hash) ⇒ Object 



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# File 'lib/ms/sequest/bioworks.rb', line 320

def set_from_xml_stream(fh, uniq_pephit_hash)
  hash = {}
  @peps = []
  while line = fh.gets
    if line =~ @@att_re
      hash[$1] = $2
    elsif line =~ @@pep_re
      ## Could do a look ahead to grab the file and sequence to check
      ## uniqueness to increase speed here.
      pep = Bioworks::Pep.new.set_from_xml_stream(fh)
      # normal search results files have a global filename
      # while multi-consensus do not
      pep[12] ||= bioworks.global_filename

      ## figure out uniqueness 
      ky = [pep.base_name, pep.first_scan, pep.charge, pep.sequence]
      if uniq_pephit_hash.key? ky
        pep = uniq_pephit_hash[ky]
      else
        ## insert the new protein
        pep.prots = []
        uniq_pephit_hash[ky] = pep
      end
      pep.prots << self
      @peps << pep
      
    elsif line =~ @@end_prot_re
      set_from_xml_hash(hash)
      break
    else
      puts "Bad parsing on: #{line}"
      puts "EXITING!"
      exit
    end
  end
  self
end