Simulation

Haplotype-based simulation of admixed mosaics from phased founder panels. Requires PyTorch (pip install "snputils[torch]"). OnlineSimulator draws crossover breakpoints from an optional genetic map and returns batched haplotype labels with SNP matrices on CPU or GPU.

OnlineSimulator

class snputils.simulation.simulator.simulator.OnlineSimulator(snp_data, meta, genetic_map=None, make_haploid=True, window_size=None, store_latlon_as_nvec=False, cp_tolerance=0)

Bases: object

A refactored ‘OnlineSimulator’ for haplotype simulation with window-based SNP data.

Core Functionality:

• Simulates admixed haplotypes.

• Supports:

  1. discrete labels (e.g., population codes), or

  2. lat/lon (converted to n-vectors) stored per window of SNPs.

Example usage:

sim = OnlineSimulator(

snp_data=my_snpobj, meta=metadata_df, genetic_map=genetic_map_df, # optional …

) # Then to simulate: snps, labels_discrete, labels_continuous, changepoints = sim.simulate(batch_size=32)

simulate(batch_size=256, num_generation_max=10, balanced=False, single_ancestry=False, device='cpu', pool_method='mode')

Returns a tuple of:

( batch_snps, final_discrete_labels_window, final_continuous_labels_window )

where:

• batch_snps.shape == (B, D)

• final_discrete_labels_window == (B, n_windows) if discrete was present, else None

• final_continuous_labels_window == (B, n_windows, cdim) if continuous was present, else None

See Analysis for a Python example and the Command-Line Interface simulate subcommand for file-backed batch generation.