Class: Mascot::DAT::PSM

Inherits:
Object
  • Object
show all
Defined in:
lib/mascot/dat/psm.rb

Constant Summary collapse

ATTRS = 
[:query,:rank,:missed_cleavages,:mr, :delta,
:num_ions_matched,:pep,:ions1,:var_mods_str,:score,
:ion_series_str,:ions2,:ions3,:proteins,:dbs,:terms,:attrs]

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(*opts) ⇒ PSM

Returns a new instance of PSM.



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# File 'lib/mascot/dat/psm.rb', line 13

def initialize(*opts)
  @attrs = {}

  if opts.kind_of? Hash
    opts.keys.each do |k|
      if ATTRS.index(k.to_sym)
        eval "@#{k} = #{opts[k]}"
      end
    end
  end
end

Class Method Details

.parse(psm_arr) ⇒ Object 



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# File 'lib/mascot/dat/psm.rb', line 35

def self.parse psm_arr
  psm_result =  self.new()
  psm_arr.each do |l|
    next unless l =~ /^q/

    k,v = l.split "="
    case k
    when /^q(\d+)_p(\d+)$/
      psm_result.query = $1.to_i
      psm_result.rank = $2.to_i
      psm_vals, prots  = v.split(";")
      psm_vals = psm_vals.split(',')
      psm_result.missed_cleavages= psm_vals[0].to_i
      psm_result.mr              = psm_vals[1].to_f
      psm_result.delta           = psm_vals[2].to_f
      psm_result.num_ions_matched = psm_vals[3].to_i
      psm_result.pep             = psm_vals[4]
      psm_result.ions1           = psm_vals[5].to_i
      psm_result.var_mods_str    = psm_vals[6]
      psm_result.score           = psm_vals[7].to_f
      psm_result.ion_series_str  = psm_vals[8]
      psm_result.ions2           = psm_vals[9].to_i
      psm_result.ions3           = psm_vals[10].to_i

      # assign proteins
      psm_result.proteins = prots.split(",").map do |pe|
        acc,*other_vals =  pe.split(":")
        acc.gsub!(/\"/,'')
        [acc] + other_vals.map {|e| e.to_i }
      end
    when /db$/
      # split on 2 chars, call to_i
      psm_result.dbs = v.split(/(\d{2})/).grep(/^\d+$/) { |e| e.to_i }
    when /terms$/
      # for each protein, I have to add the term AA
      psm_result.terms = v.split(":").collect {|t| t.split(",") }
    else
      # returns the smaller key
      puts "****#{k}***"
      k_sym = k.slice(/q\d+_p\d+_?(.+)/,1).to_sym
      psm_result.attrs[k_sym] = v
    end
  end
  psm_result
end

Instance Method Details

#==(other) ⇒ Object 



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# File 'lib/mascot/dat/psm.rb', line 25

def ==(other)
  is_eql = true
  ATTRS.each do |a|
    if self.send(a) != other.send(a)
      is_eql = false
      break
    end
  end
  is_eql
end