MainHelperFunctions refactored from variable factory to MainHelpers with these variables as object instance variables
Encapsulated the ordered dictionaries and related variables as PlastidGenomeData
The logger log is in the scope of the script and not global
The causes of the "Partial codon, len(sequence) not a multiple of three" Biopython warning was already being handled, so the use of mult_err_flag removed
Addition of some class methods that execute common sequences of existing methods
MainHelperFunctionsrefactored from variable factory toMainHelperswith these variables as object instance variablesPlastidGenomeDatalogis in the scope of the script and notglobalmult_err_flagremoved