docs: def processTPED(uniqueSNPs, mapF, fileName, tfam, prefix):
      """Process the TPED file.
  
      :param uniqueSNPs: the unique markers.
      :param mapF: a representation of the ``map`` file.
      :param fileName: the name of the ``tped`` file.
      :param tfam: the name of the ``tfam`` file.
      :param prefix: the prefix of all the files.
  
      :type uniqueSNPs: dict
      :type mapF: list
      :type fileName: str
      :type tfam: str
      :type prefix: str
  
      :returns: a tuple with the representation of the ``tped`` file
                (:py:class:`numpy.array`) as first element, and the updated
                position of the duplicated markers in the ``tped``
                representation.
  
      Copies the ``tfam`` file into ``prefix.unique_snps.tfam``. While reading
      the ``tped`` file, creates a new one (``prefix.unique_snps.tped``)
      containing only unique markers.
  
      """
      # Copying the tfam file
      try:
          shutil.copy(tfam, prefix + ".unique_snps.tfam")
      except IOError:
          msg = "%s: can't write file" % prefix + ".unique_snps.tfam"
          raise ProgramError(msg)
  
      tped = []
      updatedSNPs = defaultdict(list)
      outputFile = None
      try:
          outputFile = open(prefix + ".unique_snps.tped", "w")
      except IOError:
          msg = "%s: can't write to file" % prefix + ".unique_snps.tped"
          raise ProgramError(msg)
      nbSNP = 0
      with open(fileName, 'r') as inputFile:
          for line in inputFile:
              nbSNP += 1
              row = line.rstrip("\r\n").split("\t")
              snpInfo = row[:4]
              genotype = [i.upper() for i in row[4:]]
  
              chromosome = snpInfo[0]
              position = snpInfo[3]
  
              if (chromosome, position) in uniqueSNPs:
                  # Printing the new TPED file (unique SNPs only)
                  print >>outputFile, "\t".join(snpInfo + genotype)
              else:
                  # Saving the TPED file (duplicated samples only)
                  currPos = len(tped)
                  tped.append(tuple(snpInfo + genotype))
                  updatedSNPs[(chromosome, position)].append(currPos)
      outputFile.close()
  
      if len(mapF) != nbSNP:
          msg = "%(fileName)s: no the same number of SNPs than MAP " \
                "file" % locals()
          raise ProgramError(msg)
  
      tped = np.array(tped)
  
      return tped, updatedSNPs