Class: SRF::OUT::Pep

Inherits:
Object
  • Object
show all
Includes:
SpecID::Pep
Defined in:
lib/spec_id/srf.rb

Overview

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

Constant Summary collapse

Unpack = 
'@64Ex8ex12eeIx18vvvx8Z*@240Z*'
Unpack_four_null_bytes = 
'a*'
Unpack_Zstar = 
'Z*'
FourNullBytes_as_string = 
"\0\0\0\0"
NewRecordStart =

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

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

Constants included from SpecID::Pep

SpecID::Pep::Non_standard_amino_acid_char_re

Instance Attribute Summary

Attributes included from SpecID::Pep

#aaseq, #charge, #probability, #sequence

Instance Method Summary collapse

Methods included from SpecID::Pep

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

Instance Method Details

#from_handle(fh, global_ref_hash) ⇒ Object 



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# File 'lib/spec_id/srf.rb', line 501

def from_handle(fh, global_ref_hash)
  ## get the first part of the info
  st = fh.read(320) ## read all the hit data
  self[0,10] = st.unpack(Unpack)
  # we are slicing the reference to 38 chars to be the same length as
  # duplicate references
  self[9] = [new_protein(self[9][0,38], self, global_ref_hash)]
  self[12] = SpecID::Pep.sequence_to_aaseq(self[8])
  read_extra_references(fh, global_ref_hash) 
  
  self
end

#inspect ⇒ Object 



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# File 'lib/spec_id/srf.rb', line 430

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

#new_protein(reference, peptide, global_ref_hash) ⇒ Object 



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# File 'lib/spec_id/srf.rb', line 492

def new_protein(reference, peptide, global_ref_hash)
  if global_ref_hash.key? reference
    global_ref_hash[reference].peps << peptide
  else
    global_ref_hash[reference] = SRF::OUT::Prot.new(reference, [peptide])
  end
  global_ref_hash[reference] 
end

#prots ⇒ Object 



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# File 'lib/spec_id/srf.rb', line 427

def prots() self[9] end

#read_extra_references(fh, global_ref_hash) ⇒ Object

There must be a better way to do this. We are checking that there are no additional protein references only so that we are in register for the next reading



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# File 'lib/spec_id/srf.rb', line 450

def read_extra_references(fh, global_ref_hash)
  $SRF_OUT_HIT_FH_POS = fh.pos
  st = fh.read(4)
  #puts "HHH: " + st.unpack("H*").first
  ## if we see 0000 0000 we are done
  if st.unpack(Unpack_four_null_bytes).first == FourNullBytes_as_string
    fh.pos = $SRF_OUT_HIT_FH_POS 
    return nil
  end
  # read in context of 4 bytes read above:

  ## NOTE: in context of 4 bytes read above!
  st = fh.read(36)
  if st[34,2] == NewRecordStart
    fh.pos = $SRF_OUT_HIT_FH_POS 
    return nil
  end

  # is this the end of the outfiles?
  ## BACK to beginning of this section
  fh.pos = $SRF_OUT_HIT_FH_POS
  if fh.read(9) == Sequest_record_start 
    fh.pos = $SRF_OUT_HIT_FH_POS
    return
  end

  ## we have extra references
  ## original read was fh.read(79)
  fh.seek(-1, IO::SEEK_CUR)
  self[9].push( new_protein(fh.read(80).unpack(Unpack_Zstar).first, self, global_ref_hash ) )
  
  #p self.prots
  #puts self.prots.size
  #$glob ||= 0
  #$glob += 1
  #if $glob == 20
  #  abort 
  #end

  read_extra_references(fh,global_ref_hash)
end