code: def pWMRead(fileHandle, alphabetSize=4):
      
      lines = fileHandle.readlines()
      assert len(lines) == alphabetSize
      l = [ [ float(i) ] for i in lines[0].split() ]
      for line in lines[1:]:
          l2 = [ float(i) for i in line.split() ]
          assert len(l) == len(l2)
          for i in xrange(0, len(l)):
              l[i].append(l2[i])
      for i in xrange(0, len(l)):
          j = sum(l[i]) + 0.0
          l[i] = [ k/j for k in l[i] ]
      return l
docs: reads in standard position weight matrix format,
      rows are different types of base, columns are individual residues