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config.json
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config.json
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{
"active_builds": "simulated_sample_3 simulated_sample_3_test_tree natural_sample_1_with_90_vpm_sliding natural_sample_1_with_90_vpm_sliding_test_tree natural_sample_20191001 natural_sample_20191001_with_fra",
"datasets": {
"simulated_sample_1": {
"description": "Require a minimum fitness for randomly select amino acids in non-stationary positive selection",
"seed": 1,
"lineage": "simulated",
"segment": "ha",
"viruses_per_month": 10
},
"simulated_sample_3": {
"description": "Highest density sampling of simulated populations with same settings as simulated_sample_1",
"seed": 3,
"lineage": "simulated",
"segment": "ha",
"viruses_per_month": 90
},
"natural_sample_1_with_90_vpm": {
"lineage": "h3n2",
"segment": "ha",
"fauna_fields": "strain virus accession collection_date region country division location passage_category submitting_lab age gender",
"fasta_fields": "strain virus accession date region country division location passage submitting_lab age gender",
"titer_databases": "tdb cdc_tdb crick_tdb vidrl_tdb niid_tdb",
"titer_assay": "hi",
"titer_passage": "cell",
"viruses_per_month": 90,
"min_sequence_length": 900,
"outliers": "config/outliers_h3n2.txt",
"required_strains": "config/references_h3n2.txt",
"frozen_strains": "data/natural/natural_sample_1_with_90_vpm/frozen_strains.txt",
"start_date": "1990-10-01",
"end_date": "2015-10-01"
},
"natural_sample_1_with_90_vpm_test_tree": {
"lineage": "h3n2",
"segment": "ha",
"fauna_fields": "strain virus accession collection_date region country division location passage_category submitting_lab age gender",
"fasta_fields": "strain virus accession date region country division location passage submitting_lab age gender",
"titer_databases": "tdb cdc_tdb crick_tdb vidrl_tdb niid_tdb",
"titer_assay": "hi",
"titer_passage": "cell",
"viruses_per_month": 90,
"min_sequence_length": 900,
"outliers": "config/outliers_h3n2.txt",
"required_strains": "config/references_h3n2.txt",
"frozen_strains": "data/natural/natural_sample_1_with_90_vpm_test_tree/frozen_strains.txt",
"start_date": "1990-10-01",
"end_date": "2019-10-01"
},
"natural_sample_1_with_90_vpm_test_tree_with_fra_titers": {
"lineage": "h3n2",
"segment": "ha",
"fauna_fields": "strain virus accession collection_date region country division location passage_category submitting_lab age gender",
"fasta_fields": "strain virus accession date region country division location passage submitting_lab age gender",
"titer_databases": "tdb cdc_tdb crick_tdb vidrl_tdb niid_tdb",
"titer_assay": "hi",
"titer_passage": "cell",
"titers_for_strain_selection": "fra",
"viruses_per_month": 90,
"min_sequence_length": 900,
"outliers": "config/outliers_h3n2.txt",
"required_strains": "config/references_h3n2.txt",
"start_date": "1990-10-01",
"end_date": "2019-10-01"
}
},
"builds": {
"simulated": {
"simulated_sample_1": {
"description": "Analysis of simulated A/H3N2-like populations",
"sequences": "data/simulated/simulated_sample_1/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_1/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_1/strains.txt",
"start_date": "2010-10-01",
"end_date": "2040-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"normalized_fitness",
"ep_x",
"ne_star",
"lbi",
"delta_frequency",
"lbi-ne_star"
],
"best_predictor": "results/builds/simulated/simulated_sample_1/minimal_models_by_distances/normalized_fitness.json"
},
"simulated_sample_1_full_tree": {
"dataset_sample": "simulated_sample_1",
"description": "Full tree for analysis of sparse simulated A/H3N2-like populations",
"sequences": "data/simulated/simulated_sample_1/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_1/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_1/strains.txt",
"start_date": "2010-10-01",
"end_date": "2040-10-01",
"pivot_interval": 6,
"min_years_per_build": 30,
"years_back_to_build_trees": 30,
"reference": "config/reference_h3n2_ha.gb",
"best_predictor": "results/builds/simulated/simulated_sample_1/minimal_models_by_distances/normalized_fitness.json"
},
"simulated_sample_1_test_tree": {
"dataset_sample": "simulated_sample_1",
"description": "Test data for analysis of sparse simulated A/H3N2-like populations",
"sequences": "data/simulated/simulated_sample_1/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_1/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_1/strains.txt",
"start_date": "2034-10-01",
"end_date": "2050-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"best_predictor": "results/builds/simulated/simulated_sample_1/minimal_models_by_distances/normalized_fitness.json"
},
"simulated_sample_3": {
"description": "Analysis of simulated A/H3N2-like populations (current best)",
"full_tree_build": "simulated_sample_3_full_tree",
"sequences": "data/simulated/simulated_sample_3/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_3/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_3/strains.txt",
"start_date": "2010-10-01",
"end_date": "2040-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"normalized_fitness",
"ep_star",
"ep_x",
"ne_star",
"lbi",
"delta_frequency",
"distance_from_consensus",
"ep_star-ne_star",
"ep_x-ne_star",
"lbi-ne_star"
],
"best_predictor": "results/builds/simulated/simulated_sample_3/minimal_models_by_distances/normalized_fitness.json",
"validation_predictors": [
"naive",
"lbi-ne_star",
"normalized_fitness"
]
},
"simulated_sample_3_full_tree": {
"dataset_sample": "simulated_sample_3",
"description": "Full tree for analysis of dense simulated A/H3N2-like populations",
"sequences": "data/simulated/simulated_sample_3/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_3/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_3/strains.txt",
"start_date": "2030-10-01",
"end_date": "2040-10-01",
"pivot_interval": 6,
"min_years_per_build": 10,
"years_back_to_build_trees": 10,
"reference": "config/reference_h3n2_ha.gb",
"best_predictor": "results/builds/simulated/simulated_sample_3/minimal_models_by_distances/normalized_fitness.json"
},
"simulated_sample_3_test_tree": {
"dataset_sample": "simulated_sample_3",
"validation_build": "simulated_sample_3",
"full_tree_build": "simulated_sample_3_full_test_tree",
"description": "Test data for analysis of dense simulated A/H3N2-like populations",
"sequences": "data/simulated/simulated_sample_3/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_3/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_3/strains.txt",
"start_date": "2034-04-01",
"end_date": "2049-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"normalized_fitness",
"ep_star",
"ep_x",
"ne_star",
"lbi",
"delta_frequency",
"distance_from_consensus",
"ep_star-ne_star",
"ep_x-ne_star",
"lbi-ne_star"
],
"best_predictor": "results/builds/simulated/simulated_sample_3/minimal_models_by_distances/normalized_fitness.json",
"validation_predictors": [
"naive",
"lbi-ne_star",
"normalized_fitness"
]
},
"simulated_sample_3_full_test_tree": {
"dataset_sample": "simulated_sample_3",
"description": "Full tree for test data for analysis of dense simulated A/H3N2-like populations",
"sequences": "data/simulated/simulated_sample_3/filtered_sequences.fasta",
"metadata": "data/simulated/simulated_sample_3/filtered_metadata.tsv",
"strains": "data/simulated/simulated_sample_3/strains.txt",
"start_date": "2039-10-01",
"end_date": "2049-10-01",
"pivot_interval": 6,
"min_years_per_build": 10,
"years_back_to_build_trees": 10,
"reference": "config/reference_h3n2_ha.gb",
"best_predictor": "results/builds/simulated/simulated_sample_3/minimal_models_by_distances/normalized_fitness.json"
}
},
"natural": {
"natural_sample_1_with_90_vpm_sliding": {
"description": "Very dense sampling of viruses over 25 years of H3N2 evolution after filtering outliers that don't match clock rate (current best)",
"dataset_sample": "natural_sample_1_with_90_vpm",
"full_tree_build": "natural_sample_1_with_90_vpm_sliding_full_tree",
"sequences": "data/natural/natural_sample_1_with_90_vpm/filtered_sequences.fasta",
"metadata": "data/natural/natural_sample_1_with_90_vpm/strains_metadata.tsv",
"titers": "data/natural/natural_sample_1_with_90_vpm/titers.tsv",
"start_date": "1990-10-01",
"end_date": "2015-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"ep_star",
"ep_x_koel",
"ep_x_wolf",
"ep_x",
"oracle_x",
"cTiter",
"cTiter_x",
"cTiterSub_x",
"ne_star",
"dms_star",
"dms_nonepitope",
"dms_entropy",
"lbi",
"delta_frequency",
"distance_from_consensus",
"ep_star-ne_star",
"ep_x-ne_star",
"ne_star-lbi",
"cTiter_x-ne_star",
"cTiter_x-distance_from_consensus",
"cTiterSub_x-ne_star",
"cTiter_x-ne_star-lbi"
],
"best_predictor": "results/builds/natural/natural_sample_1_with_90_vpm_sliding/minimal_models_by_distances/ne_star-lbi.json",
"validation_predictors": [
"naive",
"ne_star-lbi",
"cTiter_x-ne_star"
]
},
"natural_sample_1_with_90_vpm_sliding_full_tree": {
"description": "Full tree for very dense sampling of viruses over 25 years of H3N2 evolution after filtering outliers that don't match clock rate",
"dataset_sample": "natural_sample_1_with_90_vpm",
"sequences": "data/natural/natural_sample_1_with_90_vpm/filtered_sequences.fasta",
"metadata": "data/natural/natural_sample_1_with_90_vpm/strains_metadata.tsv",
"titers": "data/natural/natural_sample_1_with_90_vpm/titers.tsv",
"start_date": "1990-10-01",
"end_date": "2015-10-01",
"pivot_interval": 6,
"min_years_per_build": 25,
"years_back_to_build_trees": 30,
"reference": "config/reference_h3n2_ha.gb",
"predictors": ["ne_star-lbi"],
"best_predictor": "results/builds/natural/natural_sample_1_with_90_vpm_sliding/minimal_models_by_distances/ne_star-lbi.json"
},
"natural_sample_1_with_90_vpm_sliding_test_tree": {
"description": "Test data for very dense sampling of viruses over 25 years of H3N2 evolution after filtering outliers that don't match clock rate",
"dataset_sample": "natural_sample_1_with_90_vpm_test_tree",
"validation_build": "natural_sample_1_with_90_vpm_sliding",
"full_tree_build": "natural_sample_1_with_90_vpm_sliding_full_test_tree",
"sequences": "data/natural/natural_sample_1_with_90_vpm_test_tree/filtered_sequences.fasta",
"metadata": "data/natural/natural_sample_1_with_90_vpm_test_tree/strains_metadata.tsv",
"titers": "data/natural/natural_sample_1_with_90_vpm_test_tree/titers.tsv",
"start_date": "2009-04-01",
"end_date": "2019-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"ep_star",
"ep_x_koel",
"ep_x_wolf",
"ep_x",
"oracle_x",
"cTiter",
"cTiter_x",
"cTiterSub_x",
"ne_star",
"dms_star",
"dms_nonepitope",
"dms_entropy",
"lbi",
"delta_frequency",
"distance_from_consensus",
"ep_star-ne_star",
"ep_x-ne_star",
"ne_star-lbi",
"cTiter_x-ne_star",
"cTiter_x-distance_from_consensus",
"cTiterSub_x-ne_star",
"cTiter_x-ne_star-lbi"
],
"best_predictor": "results/builds/natural/natural_sample_1_with_90_vpm_sliding/minimal_models_by_distances/cTiter_x-ne_star.json",
"validation_predictors": [
"naive",
"ne_star-lbi",
"cTiter_x-ne_star"
]
},
"natural_sample_1_with_90_vpm_sliding_full_test_tree": {
"description": "Full tree for test data for very dense sampling of viruses over 25 years of H3N2 evolution after filtering outliers that don't match clock rate",
"dataset_sample": "natural_sample_1_with_90_vpm_test_tree",
"sequences": "data/natural/natural_sample_1_with_90_vpm_test_tree/filtered_sequences.fasta",
"metadata": "data/natural/natural_sample_1_with_90_vpm_test_tree/strains_metadata.tsv",
"titers": "data/natural/natural_sample_1_with_90_vpm_test_tree/titers.tsv",
"start_date": "2009-10-01",
"end_date": "2019-10-01",
"pivot_interval": 6,
"min_years_per_build": 10,
"years_back_to_build_trees": 10,
"reference": "config/reference_h3n2_ha.gb",
"predictors": ["ne_star-lbi"],
"best_predictor": "results/builds/natural/natural_sample_1_with_90_vpm_sliding/minimal_models_by_distances/cTiter_x-ne_star.json"
},
"natural_sample_20191001": {
"description": "Most recent build with very dense sampling of viruses to evaluate change in model coefficients during timepoints in the test period",
"dataset_sample": "natural_sample_1_with_90_vpm_test_tree",
"sequences": "data/natural/natural_sample_1_with_90_vpm_test_tree/filtered_sequences.fasta",
"metadata": "data/natural/natural_sample_1_with_90_vpm_test_tree/strains_metadata.tsv",
"titers": "data/natural/natural_sample_1_with_90_vpm_test_tree/titers.tsv",
"fra_titers": "data/natural/natural_sample_1_with_90_vpm_test_tree/fra_titers.tsv",
"start_date": "2002-04-01",
"end_date": "2019-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"fra_cTiter_x-ne_star",
"ne_star-lbi",
"cTiter_x-ne_star",
"cTiter_x-ne_star-lbi"
],
"best_predictor": "results/builds/natural/natural_sample_1_with_90_vpm_sliding/minimal_models_by_distances/cTiter_x-ne_star.json"
},
"natural_sample_20191001_with_fra": {
"description": "Most recent build with very dense sampling of viruses to evaluate change in model coefficients during timepoints in the test period (preference given to samples with FRA titer data)",
"dataset_sample": "natural_sample_1_with_90_vpm_test_tree_with_fra_titers",
"sequences": "data/natural/natural_sample_1_with_90_vpm_test_tree_with_fra_titers/filtered_sequences.fasta",
"metadata": "data/natural/natural_sample_1_with_90_vpm_test_tree_with_fra_titers/strains_metadata.tsv",
"titers": "data/natural/natural_sample_1_with_90_vpm_test_tree_with_fra_titers/titers.tsv",
"fra_titers": "data/natural/natural_sample_1_with_90_vpm_test_tree_with_fra_titers/fra_titers.tsv",
"start_date": "2002-04-01",
"end_date": "2019-10-01",
"pivot_interval": 6,
"min_years_per_build": 6,
"years_back_to_build_trees": 6,
"reference": "config/reference_h3n2_ha.gb",
"predictors": [
"naive",
"cTiter_x",
"fra_cTiter_x",
"fra_cTiter_x-ne_star",
"ne_star-lbi",
"cTiter_x-ne_star",
"cTiter_x-ne_star-lbi"
],
"best_predictor": "results/builds/natural/natural_sample_1_with_90_vpm_sliding/minimal_models_by_distances/fra_cTiter_x-ne_star.json"
}
}
},
"path_to_fauna": "../fauna",
"years_for_titer_alignments": 10,
"min_tips_per_clade": 1,
"min_frequency_per_clade": 0.0,
"delta_pivots": 1,
"months_for_distance_season": 12,
"months_back_for_current_samples": 6,
"max_years_for_distances": 5,
"years_back_for_target_distance": 3,
"target_distance_attribute": "hamming",
"titers": {
"passages": ["cell"],
"assays": ["hi"]
},
"predictors": [
"naive",
"lbi",
"ep",
"ep_star",
"ep_x",
"cTiter",
"cTiterSub",
"cTiterSub_star",
"cTiterSub_x",
"delta_frequency",
"dms_star",
"ne_star",
"lbi-delta_frequency",
"lbi-ne_star",
"lbi-cTiter-ne_star",
"lbi-ep_x-ne_star"
],
"predictors_simulated": [
"naive",
"fitness",
"lbi",
"ep_x",
"delta_frequency",
"ne_star",
"ep_x-ne_star",
"lbi-ne_star",
"lbi-ep_x-ne_star"
],
"frequencies": {
"narrow_bandwidth": 0.1667,
"wide_bandwidth": 0.25,
"proportion_wide": 0.0,
"pivot_frequency": 6,
"bandwidths": [0.02, 0.04, 0.08, 0.16, 0.25, 0.33, 0.5],
"min_mutation_frequency": 0.0,
"stiffness": 20,
"inertia": 0.2,
"min_freq": 0.01,
"preferred_method": "kde",
"max_years_for_diffusion": 2
},
"lbi": {
"tau": 0.3,
"window": 0.5
},
"excluded_node_data_fields": [
"aa_muts",
"aa_sequences",
"country_confidence",
"ep_pairwise",
"cTiterSub_pairwise",
"ep_luksza_pairwise",
"ep_kratsch_pairwise",
"muts",
"num_date_confidence",
"region_confidence",
"sequence"
],
"cross_immunity": {
"h3n2": {
"ha": {
"simulated": {
"distance_attributes": "ep_pairwise",
"immunity_attributes": "ep_x",
"decay_factors": "14.0"
},
"natural": {
"distance_attributes": "ep_pairwise ep_pairwise_wolf ep_pairwise_koel oracle_pairwise",
"immunity_attributes": "ep_x ep_x_wolf ep_x_koel oracle_x",
"decay_factors": "14.0 14.0 14.0 14.0"
}
}
}
},
"fitness_model": {
"min_freq": 0.01,
"max_freq": 0.99,
"training_window": 6,
"delta_months_to_fit": 12,
"delta_months": [6, 12],
"primary_segment": "ha",
"clade_cost_function": "information_gain",
"distance_cost_function": "diffsum",
"l1_lambda": 0.1,
"pseudocount": 0.001
}
}