Class: Mspire::Mascot::Dat::Peptide

Inherits:
Struct
  • Object
show all
Includes:
Castable
Defined in:
lib/mspire/mascot/dat/peptide.rb,
lib/mspire/mascot/dat/peptide.rb

Overview

mr = relative molecular mass; data contains keys of relative

Constant Summary collapse

CAST = 
{
  missed_cleavages: :to_i, 
  mr: :to_f, 
  delta: :to_f, 
  num_ions_matched: :to_i,
  ions: :string, 
  ions_score: :to_f, 
  peaks_from_ions_2: :to_i,
  peaks_from_ions_3: :to_i,
}

Instance Attribute Summary collapse

Class Method Summary collapse

Methods included from Castable

#cast!

Instance Attribute Details

#data ⇒ Object

Returns the value of attribute data

Returns:

  • (Object) —

    the current value of data



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def data
  @data
end

#delta ⇒ Object

Returns the value of attribute delta

Returns:

  • (Object) —

    the current value of delta



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def delta
  @delta
end

#ion_series_found ⇒ Object

Returns the value of attribute ion_series_found

Returns:

  • (Object) —

    the current value of ion_series_found



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def ion_series_found
  @ion_series_found
end

#ions_score ⇒ Object

Returns the value of attribute ions_score

Returns:

  • (Object) —

    the current value of ions_score



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def ions_score
  @ions_score
end

#missed_cleavages ⇒ Object

Returns the value of attribute missed_cleavages

Returns:

  • (Object) —

    the current value of missed_cleavages



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def missed_cleavages
  @missed_cleavages
end

#mr ⇒ Object

Returns the value of attribute mr

Returns:

  • (Object) —

    the current value of mr



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def mr
  @mr
end

#num_ions_matched ⇒ Object

Returns the value of attribute num_ions_matched

Returns:

  • (Object) —

    the current value of num_ions_matched



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def num_ions_matched
  @num_ions_matched
end

#peaks_from_ions_1 ⇒ Object

Returns the value of attribute peaks_from_ions_1

Returns:

  • (Object) —

    the current value of peaks_from_ions_1



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def peaks_from_ions_1
  @peaks_from_ions_1
end

#peaks_from_ions_2 ⇒ Object

Returns the value of attribute peaks_from_ions_2

Returns:

  • (Object) —

    the current value of peaks_from_ions_2



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def peaks_from_ions_2
  @peaks_from_ions_2
end

#peaks_from_ions_3 ⇒ Object

Returns the value of attribute peaks_from_ions_3

Returns:

  • (Object) —

    the current value of peaks_from_ions_3



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def peaks_from_ions_3
  @peaks_from_ions_3
end

#peptide_num ⇒ Object

Returns the value of attribute peptide_num

Returns:

  • (Object) —

    the current value of peptide_num



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def peptide_num
  @peptide_num
end

#proteins ⇒ Object

Returns the value of attribute proteins

Returns:

  • (Object) —

    the current value of proteins



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def proteins
  @proteins
end

#query_num ⇒ Object

Returns the value of attribute query_num

Returns:

  • (Object) —

    the current value of query_num



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def query_num
  @query_num
end

#seq ⇒ Object

Returns the value of attribute seq

Returns:

  • (Object) —

    the current value of seq



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def seq
  @seq
end

#var_mods_string ⇒ Object

Returns the value of attribute var_mods_string

Returns:

  • (Object) —

    the current value of var_mods_string



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# File 'lib/mspire/mascot/dat/peptide.rb', line 7

def var_mods_string
  @var_mods_string
end

Class Method Details

.dissect_line(line) ⇒ Object

returns the query num and peptide num and info_tag and string. nil if they don’t exist.



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# File 'lib/mspire/mascot/dat/peptide.rb', line 40

def self.dissect_line(line)
  if md=/q(\d+)_p_?(\d+)(\w*)=(.*)/.match(line)
    [md[1].to_i, md[2].to_i, md[3], md[4]]
  end
end

.each(io, &block) ⇒ Object

returns each peptide hit. Some queries will not have any hits, and these are not yielded.



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# File 'lib/mspire/mascot/dat/peptide.rb', line 49

def self.each(io, &block)
  return to_enum(__method__, io) unless block
  before = io.pos
  peptide = nil
  while reply=dissect_line(io.readline("\n"))
    (qnum, pnum, info_tag, value) = reply
    if info_tag == ''
      track_pos = io.pos
      block.call(peptide) if peptide # yield the previous peptide
      io.pos = track_pos
      peptide = 
        (value == "-1") ? nil : self.from_value_string(value, qnum, pnum)
    else
      # implement reading in future
    end
    before = io.pos
  end
  # yield that last peptide

  track_pos = io.pos
  block.call(peptide) if peptide
  io.pos = track_pos
end

.from_value_string(value, qnum, pnum) ⇒ Object

given the value part of the initial peptide data (q1_p1=<value>), sets the object’s properties. returns the pephit



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# File 'lib/mspire/mascot/dat/peptide.rb', line 32

def self.from_value_string(value, qnum, pnum)
  (core, prots) = value.split(';', 2)
  pephit = self.new(*core.split(','), qnum, pnum)
  pephit.cast!
  pephit
end

.next_qp_data(io) ⇒ Object

reads the next line. If it contains valid query information returns an array [query_num, peptide_num, info_tag, value]. If it no valid query information, resets the io position to the beginning of the string and returns nil.



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# File 'lib/mspire/mascot/dat/peptide.rb', line 15

def self.next_qp_data(io)
  before = io.pos
  line = io.readline("\n")
  if line[0,2] == '--'
    io.pos = before
    nil
  else
    line.chomp!
    (qpstring, value) = line.split('=',2)
    (qns, pns, info_tag) = qpstring.split('_', 3)
    (qnum, pnum) = [qns, pns].map {|ns| ns[1..-1].to_i }
    [qnum, pnum, info_tag, value]
  end
end