phensim 1.0.0__py3-none-any.whl

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Files changed (17) hide show
  1. phensim/__init__.py +109 -0
  2. phensim/_coalescent.py +649 -0
  3. phensim/_common.py +76 -0
  4. phensim/_numba.py +19 -0
  5. phensim/ancestry.py +596 -0
  6. phensim/genotypes.py +551 -0
  7. phensim/hapnest.py +197 -0
  8. phensim/io.py +198 -0
  9. phensim/kinship.py +222 -0
  10. phensim/pedigree.py +444 -0
  11. phensim/phenotypes.py +629 -0
  12. phensim/sumstats.py +749 -0
  13. phensim-1.0.0.dist-info/METADATA +331 -0
  14. phensim-1.0.0.dist-info/RECORD +17 -0
  15. phensim-1.0.0.dist-info/WHEEL +5 -0
  16. phensim-1.0.0.dist-info/licenses/LICENSE +19 -0
  17. phensim-1.0.0.dist-info/top_level.txt +1 -0
phensim/__init__.py ADDED
@@ -0,0 +1,109 @@
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+ """phensim: genotype and phenotype simulators for genetic studies."""
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+
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+ __version__ = "1.0.0"
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+
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+ __all__ = [
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+ "simulate_independent",
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+ "simulate_population_structure",
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+ "simulate_haplotype_blocks",
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+ "simulate_ar1_blocks",
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+ "realistic_block_sizes",
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+ "simulate_coalescent",
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+ "simulate_by_mutation_rate",
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+ "simulate_hapnest",
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+ "iter_hapnest",
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+ "drift_frequencies",
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+ "simulate_populations",
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+ "simulate_admixed",
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+ "simulate_split_coalescent",
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+ "simulate_genome",
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+ "simulate_meta_sumstats",
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+ "simulate_trait",
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+ "simulate_binary_trait",
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+ "simulate_confounded_trait",
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+ "simulate_gxe_trait",
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+ "simulate_correlated_traits",
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+ "ascertain_case_control",
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+ "n_eff_case_control",
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+ "h2_liability",
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+ "simulate_effects",
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+ "simulate_effects_pair",
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+ "genetic_correlation",
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+ "simulate_sumstats",
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+ "simulate_sumstats_pair",
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+ "prepare_blocks",
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+ "simulate_gaussian_individuals",
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+ "gwas_scan",
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+ "shake_ld",
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+ "simulate_pedigree",
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+ "pedigree_birth_times",
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+ "kinship_from_pedigree",
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+ "mendelian_draw",
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+ "grm",
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+ "ibs_kinship",
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+ "iter_loco_kinships",
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+ "loco_kinships",
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+ "windowed_kinships",
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+ "write_plink",
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+ "HAVE_NUMBA",
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+ "__version__",
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+ ]
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+
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+ _MAP = {
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+ "simulate_hapnest": ("phensim.hapnest", "simulate_hapnest"),
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+ "iter_hapnest": ("phensim.hapnest", "iter_hapnest"),
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+ "drift_frequencies": ("phensim.ancestry", "drift_frequencies"),
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+ "simulate_populations": ("phensim.ancestry", "simulate_populations"),
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+ "simulate_admixed": ("phensim.ancestry", "simulate_admixed"),
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+ "simulate_split_coalescent": ("phensim.ancestry", "simulate_split_coalescent"),
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+ "simulate_genome": ("phensim.ancestry", "simulate_genome"),
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+ "simulate_meta_sumstats": ("phensim.ancestry", "simulate_meta_sumstats"),
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+ "simulate_independent": ("phensim.genotypes", "simulate_independent"),
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+ "simulate_population_structure": ("phensim.genotypes", "simulate_population_structure"),
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+ "simulate_haplotype_blocks": ("phensim.genotypes", "simulate_haplotype_blocks"),
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+ "simulate_ar1_blocks": ("phensim.genotypes", "simulate_ar1_blocks"),
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+ "realistic_block_sizes": ("phensim.genotypes", "realistic_block_sizes"),
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+ "simulate_coalescent": ("phensim.genotypes", "simulate_coalescent"),
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+ "simulate_by_mutation_rate": ("phensim.genotypes", "simulate_by_mutation_rate"),
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+ "simulate_trait": ("phensim.phenotypes", "simulate_trait"),
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+ "simulate_binary_trait": ("phensim.phenotypes", "simulate_binary_trait"),
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+ "simulate_confounded_trait": ("phensim.phenotypes", "simulate_confounded_trait"),
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+ "simulate_gxe_trait": ("phensim.phenotypes", "simulate_gxe_trait"),
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+ "simulate_correlated_traits": ("phensim.phenotypes", "simulate_correlated_traits"),
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+ "ascertain_case_control": ("phensim.phenotypes", "ascertain_case_control"),
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+ "n_eff_case_control": ("phensim.phenotypes", "n_eff_case_control"),
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+ "h2_liability": ("phensim.phenotypes", "h2_liability"),
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+ "simulate_effects": ("phensim.sumstats", "simulate_effects"),
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+ "simulate_effects_pair": ("phensim.sumstats", "simulate_effects_pair"),
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+ "genetic_correlation": ("phensim.sumstats", "genetic_correlation"),
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+ "simulate_sumstats": ("phensim.sumstats", "simulate_sumstats"),
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+ "simulate_sumstats_pair": ("phensim.sumstats", "simulate_sumstats_pair"),
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+ "prepare_blocks": ("phensim.sumstats", "prepare_blocks"),
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+ "simulate_gaussian_individuals": ("phensim.sumstats", "simulate_gaussian_individuals"),
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+ "gwas_scan": ("phensim.sumstats", "gwas_scan"),
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+ "shake_ld": ("phensim.sumstats", "shake_ld"),
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+ "simulate_pedigree": ("phensim.pedigree", "simulate_pedigree"),
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+ "pedigree_birth_times": ("phensim.pedigree", "pedigree_birth_times"),
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+ "kinship_from_pedigree": ("phensim.pedigree", "kinship_from_pedigree"),
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+ "mendelian_draw": ("phensim.pedigree", "mendelian_draw"),
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+ "grm": ("phensim.kinship", "grm"),
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+ "ibs_kinship": ("phensim.kinship", "ibs_kinship"),
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+ "iter_loco_kinships": ("phensim.kinship", "iter_loco_kinships"),
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+ "loco_kinships": ("phensim.kinship", "loco_kinships"),
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+ "windowed_kinships": ("phensim.kinship", "windowed_kinships"),
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+ "write_plink": ("phensim.io", "write_plink"),
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+ "HAVE_NUMBA": ("phensim._numba", "HAVE_NUMBA"),
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+ }
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+
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+
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+ def __getattr__(name):
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+ if name in _MAP:
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+ import importlib
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+
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+ module_name, attr = _MAP[name]
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+ return getattr(importlib.import_module(module_name), attr)
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+ raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
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+
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+
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+ def __dir__():
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+ return sorted(__all__)