[Python] How do I properly use codonbias.scores.FrequencyOfOptimalCodons?

I am trying to write a script analyzing codon usage in sequence utilizing the codon-bias package.

I am trying to use the class codonbias.scores.FrequencyOfOptimalCodons, but when I do so in my code:

FOC = cb.scores.FrequencyOfOptimalCodons (ref_seq=sequence_list, genetic_code=11)

where sequence_list is a list of str objects containing ORFs, and the genetic_code is set for Bacterial, archaeal and plant plastid code,

I get the following from my Shell:

Traceback (most recent call last):
File "I:\R&D\Product Research Group\Metabolic&Regulatory modeling\Codon usage\Python scripts\CodonBias CAI analyzer.py", line 117, in <module>
codon_df, total_orfs, analyzed_orfs = analyze_codon_usage(orfs_file, trna_file)
File "I:\R&D\Product Research Group\Metabolic&Regulatory modeling\Codon usage\Python scripts\CodonBias CAI analyzer.py", line 71, in analyze_codon_usage
FOC = cb.scores.FrequencyOfOptimalCodons (ref_seq=sequence_list, genetic_code=11)
File "C:\Users\shlomog\AppData\Local\Programs\Python\Python312\Lib\site-packages\codonbias\scores.py", line 199, in __init__
self.weights = self.weights.droplevel('aa')
File "C:\Users\shlomog\AppData\Local\Programs\Python\Python312\Lib\site-packages\pandas\core\generic.py", line 943, in droplevel
new_labels = labels.droplevel(level)
File "C:\Users\shlomog\AppData\Local\Programs\Python\Python312\Lib\site-packages\pandas\core\indexes\base.py", line 2155, in droplevel
levnums = sorted(self._get_level_number(lev) for lev in level)[::-1]
File "C:\Users\shlomog\AppData\Local\Programs\Python\Python312\Lib\site-packages\pandas\core\indexes\base.py", line 2155, in <genexpr>
levnums = sorted(self._get_level_number(lev) for lev in level)[::-1]
File "C:\Users\shlomog\AppData\Local\Programs\Python\Python312\Lib\site-packages\pandas\core\indexes\multi.py", line 1660, in _get_level_number
raise ValueError(
ValueError: The name aa occurs multiple times, use a level number


Any idea what I'm doing wrong? I had the program print out the sequences in sequence_list before the call, and they appear in order.

Here the offending code in init of FrequencyOfOptimalCodons.

Continue reading...