There are five files here.

RDI_Calc.py uses a file with ribosome densities to calculate ribosome density index (RDI) values across the genome.

Process_Sim.py and Stall_Sim.py are two simulation files, where one simulates defects in ribosome processivity due to ribosome drop-off, and the other stimulates pausing or ribosome stalling.

Fraction_ORF_Compile.py and Fraction_ORF_Compile_Codons.py are used to calculate ribosome density aggregated over a large number of mRNAs and express the data in terms of density by codon or as a fraction of the open-reading frame. Outputs also contain confidence intervals and statistical analyses.