Class: Bioworks::Pep

Inherits:
Object
  • Object
show all
Includes:
XML, SpecID::Pep, SpecIDXML
Defined in:
lib/spec_id/bioworks.rb

Overview

0=sequence 1=mass 2=deltamass 3=charge 4=xcorr 5=deltacn 6=sp 7=rsp 8=ions 9=count 10=tic 11=prots 12=base_name 13=first_scan 14=last_scan 15=peptide_probability 16=file 17=_num_prots 18=_first_prot 19=aaseq

Constant Summary collapse

@@file_split_first_re = 
/, /o
@@file_split_second_re = 
/ - /o
@@end_pep_re =

@@att_re = /<(.*)>(.*)</(.*)>/

/<\/peptide>/o
@@file_one_scan_re = 
/(.*), (\d+)/o
@@file_mult_scan_re = 
/(.*), (\d+) - (\d+)/o

Constants included from SpecIDXML

SpecIDXML::Special_chrs_hash

Constants included from SpecID::Pep

SpecID::Pep::Non_standard_amino_acid_char_re

Instance Attribute Summary

Attributes included from SpecID::Pep

#aaseq, #charge, #prots, #sequence

Class Method Summary collapse

Instance Method Summary collapse

Methods included from SpecIDXML

#attr_xml, #attrs_xml, #element_xml, #element_xml_and_att_string, #element_xml_no_atts, #escape_special_chars, #param_xml, #params_xml, #short_element_xml, #short_element_xml_and_att_string, #short_element_xml_from_instance_vars, #tabs

Methods included from SpecID::Pep

#<=>, #mass_accuracy, prepare_sequence, protein_groups_by_sequence, remove_non_amino_acids, sequence_to_aaseq, split_sequence

Class Method Details

.extract_file_info(arg) ⇒ Object

takes arguments in one of two forms:

1. file, first_scan[ - last_scan]
2. scan[ - last_scan]

returns base_name, first_scan, last_scan base_name will be set for #1, nil for #2



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# File 'lib/spec_id/bioworks.rb', line 425

def self.extract_file_info(arg)
  last_scan = nil
  (base_name, first_scan) = arg.split(@@file_split_first_re)
  unless first_scan
    first_scan = base_name
    base_name = nil
  end
  first_scan = first_scan.split(@@file_split_second_re)
  if first_scan.size > 1
    (first_scan, last_scan) = first_scan
  else
    first_scan = first_scan[0]
    last_scan = first_scan
  end
  [base_name, first_scan, last_scan]
end

Instance Method Details

#file=(arg) ⇒ Object 



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# File 'lib/spec_id/bioworks.rb', line 444

def file=(arg)
  ## Set these vals by index:
  #puts "AERRG: #{arg}"
  self[16] = arg
  self[12,3] = self.class.extract_file_info(arg)
end

#get(*args) ⇒ Object

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



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# File 'lib/spec_id/bioworks.rb', line 407

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

#inspect ⇒ Object 



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# File 'lib/spec_id/bioworks.rb', line 452

def inspect
  "<Bioworks::Pep sequence: #{sequence}, mass: #{mass}, deltamass: #{deltamass}, charge: #{charge}, xcorr: #{xcorr}, deltacn: #{deltacn}, prots(count):#{prots.size}, base_name: #{base_name}, first_scan: #{first_scan}, last_scan: #{last_scan}, file: #{file}, peptide_probability: #{peptide_probability}, aaseq:#{aaseq}>"


end

#mh ⇒ Object 



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# File 'lib/spec_id/bioworks.rb', line 397

def mh ; self[1] end

#ppm ⇒ Object

This is not a true ppm since it should be divided by the actual mh instead of the theoretical (but it is as close as we can get for this object)



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# File 'lib/spec_id/bioworks.rb', line 401

def ppm 
  1.0e6 * (self[2].abs/self[1])
  #1.0e6 * (self.deltamass.abs/self.mh)
end

#probability ⇒ Object

other accessors:



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# File 'lib/spec_id/bioworks.rb', line 396

def probability ; self[15] end

#set_from_hash(hash) ⇒ Object 



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# File 'lib/spec_id/bioworks.rb', line 458

def set_from_hash(hash)
  self[0,11] = [hash["sequence"], hash["mass"], hash["deltamass"], hash["charge"], hash["xcorr"], hash["deltacn"], hash["sp"], hash["rsp"], hash["ions"], hash["count"], hash["tic"]]
  self.file = hash["file"]
  self[15] = hash["peptide_probability"].to_f
  self[19] = SpecID::Pep.sequence_to_aaseq(self[0])  ## aaseq
end

#set_from_xml_stream(fh) ⇒ Object 



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# File 'lib/spec_id/bioworks.rb', line 465

def set_from_xml_stream(fh)
  hash = {}
  while line = fh.gets
    if line =~ @@att_re
      #hash[$1] = $2.dup
      hash[$1] = $2
      #puts "IN PEP: " + $1 + ": " + $2
    elsif line =~ @@end_pep_re
      set_from_hash(hash)
      #puts "SELF[12]: #{self[12]}"
      #puts "SELF[12]: #{self[12]}"
      break
    else
      puts "Bad parsing on: #{line}"
      puts "EXITING!"
      exit
    end
  end
  self
end