Refactoring peptide aligner

peptide_mapper4.rb

#command-line usage: 
#% ruby /Users/timrand/Dropbox/NAT1/peptide_mapper3.rb peptide_file target_file
#      1 M  0 
#      2 S  0 
#      3 P  8 [][][][][][][][]
#      4 A  8 [][][][][][][][]
#      5 G  8 [][][][][][][][]
#      6 S  8 [][][][][][][][]
#      7 C  8 [][][][][][][][]
#      8 D  8 [][][][][][][][]
#      9 L  5 [][][][][]
#     10 A  5 [][][][][]
#     11 E  1 []
#     12 D  1 []
#     13 A  1 []
#     14 A  1 []
#     15 C  1 []
#     16 Q  2 [][]
#     17 L  2 [][]
#     18 Q  2 [][]
#     19 C  2 [][]
#     20 V  2 [][]
#======================================
#Define the target and the peptide list
#======================================
require "English"

def peptide_list
  [  "PAGSXXAGS", "AGSCDLXAEDAACQLQ"]
  #File.readlines(ARGV[0]).collect{|line| line.chomp}
end

def target  
  "MSPAGSCDLAEDAACQLQCVIDCAAELLAEDCLLAEDPAGSCD"
  #File.readlines(ARGV[1]).collect{|line| line.chomp}
end

#======================================
#======================================
class String  
  def digitize_as(dig)
    gsub(/./,dig.to_s)
  end
  def each_with_index(&blk)
    split('').each_with_index(&blk)
  end
  alias :dig_as :digitize_as
end

class Array
  #   returns an array of column sums from an Array with rows of arrays with digits
  #       [[0,0,1,1,0,0],
  #        [0,0,0,1,1,0]].summed_by_site
  # =>     [0,0,1,2,1,0]
  def summed_by_site
    unless self.empty? #edge case: could be no peptides sites in target, so self is an empty array, then we skip to end
      collection = Array.new(self.first.length){0}
      for r in self do
        for i in (0..first.length-1) do
          collection[i] =  collection[i] + r[i]
        end
      end
    end
    collection || []  #but if you skipped to get here, there is no collection, so we have to return []
  end
end

#===============================================================
#functions for mapping and printing peptides onto an AA sequence
#===============================================================
#returns a digital mapping of peptide alignments
def map_peptides(tar, pep_list)
  digit_hits = []
  for pep in pep_list do 
    #the block is only entered if the scan finds a match
    tar.scan(pep){ digit_hits << ($PREMATCH.dig_as(0)+$MATCH.dig_as(1)+$POSTMATCH.dig_as(0)).split('').collect(&:to_i) }
  end
  case digit_hits #return either digit_hits or an array with all zeros
    when [] then digit_hits << Array.new(tar.length){0}
    else digit_hits 
    end
end

def printer arr
  printf("%5s %s %2s %s\n" % arr)
end

def graph_bar(i)
  scalar = 1   
  '[]' * i * scalar
end

aligned_map = map_peptides(target, peptide_list)
target.each_with_index{ |aa,i| printer [i+1, aa, aligned_map.summed_by_site[i], graph_bar(aligned_map.summed_by_site[i])] }