Calculate Single Site B

Bvalcalc --site --params Params.py

--site

Calculate B for a single site at a specified distance from 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 CDS, (default: 10000)

--distance [int]

Distance from the focal neutral site to the edge of the selected element in bp (default: 1). Note that this assumes recombinant distance increases linearly with physical distance.

Optional Arguments

--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.

If set, the s_breaks and bin_proportions parameters in the params file will be used to define discretized DFE break points with defined proportions to replace f0-f3”) --quiet

Suppress console output

Example

Bvalcalc --site --params HomSap_Cds_Params.py --distance 1500 --element_size 10000

# B for site 1500bp away from 10000bp region: 0.964573141826118

Calculates B for a single site 1500bp away from a gene under selection of length 10kb using the template human CDS parameters.