Class: SampleEnzyme

Inherits:
Object
  • Object
show all
Includes:
SpecIDXML
Defined in:
lib/spec_id.rb,
lib/sample_enzyme.rb

Constant Summary

Constants included from SpecIDXML

SpecIDXML::Special_chrs_hash

Instance Attribute Summary collapse

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

Constructor Details

#initialize(name = nil) ⇒ SampleEnzyme

Currently, recognize: 

trypsin

For other enzymes, you must set :cut, :no_cut, :name, and :sense



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# File 'lib/sample_enzyme.rb', line 21

def initialize(name=nil)
  @sense = nil
  @cut = nil
  @no_cut = nil
  @name = name
  if @name
    # set the values if we recognize this name
    send(@name.to_sym)
  end
end

Instance Attribute Details

#cut ⇒ Object

amino acids after which to cleave



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# File 'lib/sample_enzyme.rb', line 12

def cut
  @cut
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/sample_enzyme.rb', line 10

def name
  @name
end

#no_cut ⇒ Object

cleave at ‘cut’ amino acids UNLESS it is followed by ‘no_cut’



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# File 'lib/sample_enzyme.rb', line 14

def no_cut
  @no_cut
end

#sense ⇒ Object

‘C’ or ‘N’



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# File 'lib/sample_enzyme.rb', line 16

def sense
  @sense
end

Class Method Details

.tryptic(string, missed_cleavages = 0) ⇒ Object 



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# File 'lib/sample_enzyme.rb', line 94

def self.tryptic(string, missed_cleavages=0)
  self.new("trypsin").digest(string, missed_cleavages)
end

Instance Method Details

#digest(string, missed_cleavages = 0) ⇒ Object

returns all peptides of missed cleavages <= ‘missed_cleavages’ so 2 missed cleavages will return all no missed cleavage peptides all 1 missed cleavages and all 2 missed cleavages.



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# File 'lib/sample_enzyme.rb', line 47

def digest(string, missed_cleavages=0)
  s = StringScanner.new(string)
  no_cut_regex = Regexp.new("[#{@no_cut}]")
  regex = Regexp.new("[#{@cut}]")
  peps = []
  last_pos = 0
  current_pep = ''
  loop do
    if s.eos?
      break
    end
    m = s.scan_until(regex)
    if m  ## found a cut point
      last_pos = s.pos
      # is the next amino acid a no_cut?
      if string[s.pos,1] =~ no_cut_regex 
        current_pep << m
      else
        # cut it 
        current_pep << m
        peps << current_pep
        current_pep = ''
      end
    else  ## didn't find a cut point
      current_pep << string[last_pos..-1]
      peps << current_pep 
      break
    end
  end
  ## LOOP through and grab each set of missed cleavages from num down to 0
  all_sets_of_peps = []
  (0..missed_cleavages).to_a.reverse.map do |num_mc|
    all_sets_of_peps.push( *(get_missed_cleavages(peps, num_mc)) )
  end
  all_sets_of_peps 
end

#get_missed_cleavages(tryptic_peps, num) ⇒ Object

takes an array of peptides and returns an array containing ‘num’ missed cleavages DOES NOT contain peptides that contain < num of missed cleavages (i.e., will not return missed cleaveages of 1 or 2 if num == 3



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# File 'lib/sample_enzyme.rb', line 88

def get_missed_cleavages(tryptic_peps, num)
  (0...(tryptic_peps.size - num)).to_a.map do |i|
    tryptic_peps[i,num+1].join
  end
end

#to_pepxml ⇒ Object 



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# File 'lib/sample_enzyme.rb', line 38

def to_pepxml
  element_xml(:sample_enzyme, [:name]) do
    short_element_xml(:specificity, [:cut, :no_cut, :sense])
  end
end

#trypsin ⇒ Object 



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# File 'lib/sample_enzyme.rb', line 32

def trypsin
  @sense = 'C'
  @cut = 'KR'
  @no_cut = 'P'
end