GC and AT contents do not sum to 1

[gavinmdouglas]

Hi there,

I read your preprint with great interest, and recently left a comment on bioRxiv, which would be easy to miss so I just wanted to point to it here: http://disq.us/p/2v7wa9j (I didn't realize until afterwards that the reviews were posted on eLife!).

I was recently trying to implement the CAIS approach and I noticed what I think is a bug where the total GC content is based on the GC contents specified in the Species_Total_GC_content dictionary, but the AT content is calculated as 1 - GC_genic_prob (although it is named notGC_total_prob, so I believe it should be 1 - GC_total_prob). The sum of these values (which are used when computing the expected codon probabilities based on GC content) != 1.

Note that I'm talking about line 518 in these two scripts:

Codon-Adaptation-Index-of-Species/CAIS_ENC_calculation/CAIS_total_GC_weighted_by_AA.py

Line 518 in 0ae74ed

notGC_total_prob = 1- GC_genic_prob

Codon-Adaptation-Index-of-Species/CAIS_ENC_calculation/CAIS_total_GC_AA_equal_weights.py

Line 518 in 0ae74ed

notGC_total_prob = 1- GC_genic_prob

Although I think this is a bug, I think it likely just added noise to the CAIS metrics analyzed in your paper (if they were based on this version of the scripts), so hopefully the overall results will actually just be cleaner with this resolved.

All the best,

Gavin