skills/bioskills/bio-epidemiological-genomics-transmission-inference/scripts/transmission_inference.py

• run_snp_dists · function · L45-L49 — def run_snp_dists(masked_alignment, out_csv)
• define_snp_clusters · function · L52-L65 — def define_snp_clusters(distance_df, threshold, population_caveat=None)
• warn_walker_threshold_outside_uk · function · L68-L74 — def warn_walker_threshold_outside_uk(setting_description)
• annotate_pairs_with_temporality · function · L77-L95 — def annotate_pairs_with_temporality(distance_df, sample_dates, snp_threshold)
• binomial_bottleneck_estimator · function · L98-L120 — def binomial_bottleneck_estimator(donor_freqs, recipient_freqs, depths_recipient, nb_max=200)
• compare_bottleneck_to_literature · function · L123-L129 — def compare_bottleneck_to_literature(nb_map, pathogen)
• run_hiv_trace · function · L132-L152 — def run_hiv_trace(fasta, out_dir, threshold=HIV_TRACE_DEFAULT_THRESHOLD, subtype=HIV_TRACE_SUBTYPE_DEFAULT)
• run_outbreaker2_via_r · function · L155-L171 — def run_outbreaker2_via_r(dates_csv, fasta, contact_matrix_csv, out_rds, n_iter=int(1e6), sample_every=200)
• run_transphylo_via_r · function · L174-L187 — def run_transphylo_via_r(dated_tree_nexus, date_last_sample, out_rds, w_shape=1.3, w_scale=10, ws_shape=1.1, ws_scale=7, start_neg=0.5, mcmc_iterations=int(1e5))