skills/bioskills/bio-epidemiological-genomics-amr-surveillance/scripts/amr_surveillance.py

• species_uses_tbprofiler · function · L23-L24 — def species_uses_tbprofiler(species)
• run_amrfinder · function · L27-L32 — def run_amrfinder(assembly, species, out_tsv, threads=8)
• run_tbprofiler · function · L35-L43 — def run_tbprofiler(reads_r1, reads_r2, prefix, out_dir)
• parse_tbprofiler_drugs · function · L46-L58 — def parse_tbprofiler_drugs(tbp_json)
• hamronize_amrfinder · function · L61-L69 — def hamronize_amrfinder(amrf_tsv, sample_id, out_tsv)
• hamronize_resfinder · function · L72-L80 — def hamronize_resfinder(resfinder_json, sample_id, out_tsv)
• summarize_hamronized · function · L83-L87 — def summarize_hamronized(hamr_dir, out_tsv)
• run_mob_recon · function · L90-L96 — def run_mob_recon(assembly, out_dir)
• join_amr_with_plasmid · function · L99-L108 — def join_amr_with_plasmid(amrf_df, mob_df)
• flag_partial_contig_hits · function · L111-L121 — def flag_partial_contig_hits(amrf_df, critical_gene_patterns=None)
• flag_oxa48_subfamily_resolution · function · L124-L132 — def flag_oxa48_subfamily_resolution(amrf_df)
• per_isolate_pipeline · function · L135-L153 — def per_isolate_pipeline(sample_id, assembly, species, hamr_dir, mob_dir)
• cohort_pipeline · function · L156-L163 — def cohort_pipeline(samples, hamr_dir, mob_dir, cohort_table)