Class: Ms::Sequest::Srf::Out::Pep

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

Overview

0=mh 1=deltacn_orig 2=sp 3=xcorr 4=id 5=num_other_loci 6=rsp 7=ions_matched 8=ions_total 9=sequence 10=prots 11=deltamass 12=ppm 13=aaseq 14=base_name 15=first_scan 16=last_scan 17=charge 18=srf 19=deltacn 20=deltacn_orig_updated

Constant Summary collapse

Unpack_35 = 
'@64Ex8ex8eeeIx18Ivx2vvx8Z*@246Z*'
Unpack_32 =

translation: @64=(64 bytes in to the record), E=mH, x8=8unknown bytes, e=deltacn, x8=8unknown bytes, e=sf, e=sp, e=xcorr, I=ID#, x18=18 unknown bytes, v=rsp, v=ions_matched, v=ions_total, x8=8unknown bytes, Z*=sequence, 240Z*=at byte 240 grab the string (which is proteins). Unpack_32 = ‘@64Ex8ex12eeIx18vvvx8Z*@240Z*’

'@64Ex8ex8eeeIx14Ivvvx8Z*@240Z*'
Unpack_four_null_bytes = 
'a*'
Unpack_Zstar = 
'Z*'
Read_35 = 
426
Read_32 = 
320
FourNullBytes_as_string = 
"\0\0\0\0"
NewRecordStart =

NewRecordStart = “00” + 0x3a.chr + 0x1a.chr + “00”

0x01.chr + 0x00.chr
Sequest_record_start = 
"[SEQUEST]"

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.read_extra_references(fh, num_extra_references, pep_hits) ⇒ Object 



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# File 'lib/ms/sequest/srf.rb', line 634

def self.read_extra_references(fh, num_extra_references, pep_hits)
  num_extra_references.times do
    # 80 bytes total (with index number)
    pep = pep_hits[fh.read(8).unpack('x4I').first - 1]

    ref = fh.read(80).unpack('A*').first
    pep[11] << Ms::Sequest::Srf::Out::Prot.new(ref[0,38])
  end
  #  fh.read(6) if unpack_35
end

.set_deltacn_from_deltacn_orig(ar) ⇒ Object

creates the deltacn that is meaningful for the top hit (the deltacn_orig or the second best hit and so on). assumes sorted



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# File 'lib/ms/sequest/srf.rb', line 612

def self.set_deltacn_from_deltacn_orig(ar)
  (1...ar.size).each {|i| ar[i-1].deltacn = ar[i].deltacn_orig }
  ar[-1].deltacn = 1.1
end

.update_deltacns_from_xcorr(ar) ⇒ Object

(assumes sorted) recalculates deltacn from xcorrs and sets deltacn_orig_updated and deltacn



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# File 'lib/ms/sequest/srf.rb', line 619

def self.update_deltacns_from_xcorr(ar)
  if ar.size > 0
    top_score = ar.first[4]
    other_scores = (1...(ar.size)).to_a.map do |i|
      1.0 - (ar[i][4]/top_score)
    end
    ar.first[21] = 0.0
    (0...(ar.size-1)).each do |i|
      ar[i][20] = other_scores[i]    # deltacn
      ar[i+1][21] = other_scores[i]  # deltacn_orig_updated
    end
    ar.last[20] = 1.1
  end
end

Instance Method Details

#from_io(fh, unpack_35) ⇒ Object

extra_references_array is an array that grows with peptides as extra references are discovered.



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# File 'lib/ms/sequest/srf.rb', line 683

def from_io(fh, unpack_35)
  unpack = 
    if unpack_35 ; Unpack_35
    else ; Unpack_32
    end

  ## get the first part of the info
  st = fh.read(( unpack_35 ? Read_35 : Read_32) ) ## read all the hit data

  self[0,11] = st.unpack(unpack)


  # set deltacn_orig_updated 
  self[21] = self[1]

  # we are slicing the reference to 38 chars to be the same length as
  # duplicate references
  self[11] = [Ms::Sequest::Srf::Out::Prot.new(self[11][0,38])]

  self[14] = Ms::Id::Peptide.sequence_to_aaseq(self[10])

  fh.read(6) if unpack_35

  self
end

#inspect ⇒ Object 



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# File 'lib/ms/sequest/srf.rb', line 663

def inspect
  st = %w(aaseq sequence mh deltacn_orig sf sp xcorr id rsp ions_matched ions_total prots deltamass ppm base_name first_scan last_scan charge deltacn).map do |v| 
    if v == 'prots'
      "#{v}(#)=#{send(v.to_sym).size}"
    elsif v.is_a? Array
      "##{v}=#{send(v.to_sym).size}"
    else
      "#{v}=#{send(v.to_sym).inspect}"
    end
  end
  st.unshift("<#{self.class}")
  if srf
    st.push("srf(base_name)=#{srf.base_name.inspect}")
  end
  st.push('>')
  st.join(' ')
  #"<Ms::Sequest::Srf::Out::Pep @mh=#{mh}, @deltacn=#{deltacn}, @sp=#{sp}, @xcorr=#{xcorr}, @id=#{id}, @rsp=#{rsp}, @ions_matched=#{ions_matched}, @ions_total=#{ions_total}, @sequence=#{sequence}, @prots(count)=#{prots.size}, @deltamass=#{deltamass}, @ppm=#{ppm} @aaseq=#{aaseq}, @base_name=#{base_name}, @first_scan=#{first_scan}, @last_scan=#{last_scan}, @charge=#{charge}, @srf(base_name)=#{srf.base_name}>"
end