How to calculate codon usage bias (RSCU) in biopython

Question

I'm looking to calculate the RSCU values for a given sequence using the module CodonUsage. In the source code for CodonUsage (here) RSCU values are calculated inside the function generate_index, which sits inside the class CodonAdaptionIndex (RSCU calculated at line 101). How do I access generate_index? Also, how do i get my script to access my sequences (so far they are in FASTA format on a .txt).

Thanks for reading

Answer 1

You can access the function by importing it like this and generating a CodonAdaptionIndex object:

from Bio.SeqUtils import CodonUsage as CU

myIndex = CU.CodonAdaptationIndex()
myIndex.generate_index("/path/to/myFastaFile")

From the documentation it looks like a FASTA formated file is perfectly fine to use.