code: def generate_proteins(pepfn, proteins, pepheader, scorecol, minlog,
                        higherbetter=True, protcol=False):
      protein_peptides = {}
      if minlog:
          higherbetter = False
      if not protcol:
          protcol = peptabledata.HEADER_MASTERPROTEINS
      for psm in reader.generate_tsv_psms(pepfn, pepheader):
          p_acc = psm[protcol]
          if ';' in p_acc:
              continue
          protein_peptides = evaluate_peptide(protein_peptides, psm, p_acc,
                                              higherbetter, scorecol,
                                              fncol=False)
      if minlog:
          try:
              nextbestscore = min([pep['score'] for pep in
                                   protein_peptides.values()
                                   if pep['score'] > 0])
          except ValueError:
              import sys
              sys.stderr.write('Cannot find score of type {} which is above 0. '
                               'Only scores above zero can have a -log value. '
                               'Exiting.'.format(scorecol))
              sys.exit(1)
          nextbestscore = -log(nextbestscore, 10)
      for protein in proteins:
          try:
              peptide = protein_peptides[protein[prottabledata.HEADER_PROTEIN]]
          except KeyError:
              print('WARNING - protein {} not found in peptide '
                    'table'.format(protein[prottabledata.HEADER_PROTEIN]))
              peptide = {'score': 'NA'}
          if minlog and peptide['score'] != 'NA':
              peptide['score'] = log_score(peptide['score'], nextbestscore)
          protein[prottabledata.HEADER_QSCORE] = str(
              peptide['score'])
          yield protein