Calculate Gene B Recovery

Bvalcalc --gene --params Params.py
--gene

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

Core Arguments

--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.

--element_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)

Optional Arguments

--plot [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). 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 using a grid of selection coefficients from 1 to 1e-8 in 10-fold steps (instead of the basic DFE parameters set by f0, f1, f2, f3). Adding this flag overrides the basic DFE parameters set by f0, f1, f2, f3). Note that mean, shape and proportion_synonymous should be set in the parameters file when active.

--constant_dfe

If included, use a constant fixed s value as the DFE of selected sites (instead of the basic DFE parameters set by f0, f1, f2, f3). Adding this flag overrides the basic DFE parameters set by f0, f1, f2, f3). Note that s and proportion_synonymous should be set in the parameters file when active.

--custom_dfe

If included, set the discrete breakpoints for homozygous selection coefficients s_breaks within which uniform distributions are modelled with proportions set by bin_proportions. Setting this overrides the basic DFE parameters set by f0, f1, f2, f3). Note that s_breaks and bin_proportions should be set in the parameters file when active.

--quiet

Suppress console output

Example

Bvalcalc --gene \
    --params HomSap_Cds_Params.py \
    --element_size 10000 \
    --flank_len 40000 \
    --plot ./Bplot.png

# B for adjacent site: 0.9617168921951618
# Mean B for flanking region: 0.979953881508711

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

B region example