CodonU.analyzer.cbi_comp

Module Contents

Functions

calculate_cbi(→ dict[str, tuple[float, ...)

Calculates cbi values for each amino acid based on Bennetzen and Hall (1982)
CodonU.analyzer.cbi_comp.calculate_cbi(handle: str, genetic_code_num: int, min_len_threshold: int = 66, gene_analysis: bool = False, save_file: bool = False, file_name: str = 'CBI_report', folder_path: str = 'Report') → dict[str, tuple[float, str] | dict[str, tuple[float, str]]]

Calculates cbi values for each amino acid based on Bennetzen and Hall (1982)

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_code_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene

  • gene_analysis – Option if gene analysis (True) or genome analysis (False) (optional)

  • save_file – Option for saving the values in xlsx format (Optional)

  • file_name – Intended file name (Optional)

  • folder_path – Folder path where image should be saved (optional)

Returns:

The dictionary containing amino acid and cbi value, optimal codon pairs if gene_analysis is false,

otherwise returns the dictionary containing gene name and dictionary containing amino acid and cbi value, optimal codon pairs