code: def kallisto_table(kallisto_dir, index):
      
      quant_dir = os.path.join(kallisto_dir, "quant")
      out_file = os.path.join(quant_dir, "matrix.csv")
      if file_exists(out_file):
          return out_file
      tsvfile = os.path.join(quant_dir, "matrix.tsv")
      ecfile = os.path.join(quant_dir, "matrix.ec")
      cellsfile = os.path.join(quant_dir, "matrix.cells")
      fastafile = os.path.splitext(index)[0] + ".fa"
      fasta_names = fasta.sequence_names(fastafile)
      ec_names = get_ec_names(ecfile, fasta_names)
      df = pd.read_table(tsvfile, header=None, names=["ec", "cell", "count"])
      df["ec"] = [ec_names[x] for x in df["ec"]]
      df = df.pivot(index='ec', columns='cell', values='count')
      cellnames = get_cell_names(cellsfile)
      colnames = [cellnames[x] for x in df.columns]
      df.columns = colnames
      df.to_csv(out_file)
      return out_file
docs: convert kallisto output to a count table where the rows are
      equivalence classes and the columns are cells