add wrapper v02 with more simulations

Analysis/simulations/binomial_growth/parameters/simple_v02.yaml

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+# One set of parameters for simulating cells and their lineages
+#local_outdir: 'simulation'
+prefix: 'sweep_v02'
+
+num_iterations: 1000
+num_cells: 10000
+num_mt_positions: 10
+
+cpus: 36
+
+initialize:
+  coverage:
+    type: 'constant' # {'poisson', 'constant', 'growth'}
+    cov_constant: 50
+    poisson_mu_per_cell: 50
+
+  clone_sizes: #distribution of clone sizes. The first one is the non-clone population. Length should be len(het)+1, and it should sum to 1
+    [0.5, 0.4, 0.1]
+
+  mt_clone_map:
+    # [(10), (16500)]
+    # [(10), (16500), (16500, 7)]
+
+het: # Heterozygous values
+  [0.2, 0.2]
+het_err_rate: 0.05
+
+
+sequence_subsample: #10000
+
+growth:
+  type: binomial
+  binomial:
+    rates: [0.1, 0.8, 0.01]
+    time_steps: 10
+  #type: poisson
+  poisson:
+    rates: [0.05, 1, 0.9]
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: False
+
+

Analysis/simulations/binomial_growth/parameters/sweep_v02.yaml

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+# One set of parameters for simulating cells and their lineages
+outdir: 'results'
+prefix: 'sweep_v02'
+data_outdir: 'data/out'
+#num_iterations: 100
+#num_cells: 10000
+#num_mt_positions: 10
+cpus: 36
+
+save_sim: false
+
+grid:
+  cov_constant: [5, 10, 50, 100]
+  dominant_clone_sizes: [0.02,0.1,0.2, 0.4]
+  dominant_het: [0.02, 0.2, 0.5, 0.8]
+  dominant_growth: [0.1, 0.5, 0.8]
+  het_err_rate: [0.05, 0.15]

Analysis/simulations/binomial_growth/results/sweep_v02/0.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.1
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.02
+- 0.2
+het_err_rate: 0.05
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 5.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '0'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/1.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.1
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.02
+- 0.2
+het_err_rate: 0.15
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 5.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '1'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/10.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.5
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.2
+- 0.2
+het_err_rate: 0.05
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 5.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '10'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/100.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.1
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.5
+- 0.2
+het_err_rate: 0.05
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 10.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '100'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/101.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.1
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.5
+- 0.2
+het_err_rate: 0.15
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 10.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '101'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/102.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.1
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.8
+- 0.2
+het_err_rate: 0.05
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 10.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '102'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/103.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.1
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.8
+- 0.2
+het_err_rate: 0.15
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 10.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '103'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null

Analysis/simulations/binomial_growth/results/sweep_v02/104.yaml

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+cpus: 36
+data_outdir: data/out/sweep_v02
+growth:
+  binomial:
+    rates:
+    - 0.1
+    - 0.5
+    - 0.01
+    time_steps: 10
+  mutant_af_sigma_noise: 0.05
+  non_mutants:
+    to_mutate: false
+  poisson:
+    rates:
+    - 0.05
+    - 1
+    - 0.9
+  type: binomial
+het:
+- 0.02
+- 0.2
+het_err_rate: 0.05
+initialize:
+  clone_sizes:
+  - 0.88
+  - 0.02
+  - 0.1
+  coverage:
+    cov_constant: 10.0
+    poisson_mu_per_cell: 50
+    type: constant
+  mt_clone_map: null
+local_outdir: results/sweep_v02
+name: '104'
+num_cells: 10000
+num_iterations: 1000
+num_mt_positions: 10
+prefix: sweep_v02
+sequence_subsample: null