Calculate Gene B Recovery

Bvalcalc --gene --pop_params Params.py

--gene: Calculate B values for a range of neutral sites flanking a single selected element.

Core Arguments

--pop_params [path/to/YourParams.py]: Path to a Python file defining population genetic parameters, see here for accessing pre-built templates, Generate Parameters, and here for adjusting parameters to new species/populations, Tailoring Parameters.
--gene_size [int]: Total length of the selected region, e.g. gene or exon, (default: 10000).
--flank_len [int]: Length of the flanking neutral region to calculate B (default: 40000)

--plot_output [path]: Generate a B recovery slope output with a specified path (default: ./Bplot.png if no path is given)
--out [path]: Write B-values to a CSV file with the specified path (must also provide --out_binsize)
--out_binsize [int]: Bin size to average B-values in the CSV output, required if --out is used.
--pop_change: If included, compute current B (Bcur) under a step population size change, as described in Johri et al 2021 (MBE). Note that Bcur and time_of_change should be set in the parameters file when active.
--gamma_dfe: If included, use a gamma distribution to define the DFE (instead of fixed f0, f1, f2, f3). Note that mean, shape and proportion_synonymous should be set in the parameters file when active.
--quiet: Suppress console output

Bvalcalc --gene \
    --pop_params HumanParams.py \
    --gene_size 10000 \
    --flank_len 40000 \
    --plot_output ./Bplot.png

Calculates B for a 40 kb neutral region flanking a single gene under selection of length 10 kb using example human parameters, and plot the output.