autometa package

Subpackages

• autometa.binning package
  • Submodules
  • autometa.binning.large_data_mode module
    • checkpoint()
    • cluster_by_taxon_partitioning()
    • get_checkpoint_info()
    • get_kmer_embedding()
    • main()
  • autometa.binning.large_data_mode_loginfo module
    • add_clustering_runtime_summary_info()
    • add_embedding_runtime_summary_info()
    • format_total_times()
    • get_loginfo()
    • main()
  • autometa.binning.recursive_dbscan module
    • get_clusters()
    • main()
    • recursive_dbscan()
    • recursive_hdbscan()
    • run_dbscan()
    • run_hdbscan()
    • taxon_guided_binning()
  • autometa.binning.summary module
    • fragmentation_metric()
    • get_agg_stats()
    • get_metabin_stats()
    • get_metabin_taxonomies()
    • main()
    • write_cluster_records()
  • autometa.binning.unclustered_recruitment module
  • autometa.binning.utilities module
    • add_metrics()
    • apply_binning_metrics_filter()
    • filter_taxonomy()
    • read_annotations()
    • reindex_bin_names()
    • write_results()
    • zero_pad_bin_names()
  • Module contents
• autometa.common package
  • Subpackages
    • autometa.common.external package
      • Submodules
      • autometa.common.external.bedtools module
      • autometa.common.external.bowtie module
      • autometa.common.external.diamond module
      • autometa.common.external.hmmscan module
      • autometa.common.external.hmmsearch module
      • autometa.common.external.prodigal module
      • autometa.common.external.samtools module
      • Module contents
  • Submodules
  • autometa.common.coverage module
    • from_spades_names()
    • get()
    • main()
  • autometa.common.exceptions module
    • AutometaError
    • BinningError
    • ChecksumMismatchError
    • DatabaseOutOfSyncError
      • DatabaseOutOfSyncError.__str__()
    • ExternalToolError
    • TableFormatError
  • autometa.common.kmers module
    • autometa_clr()
    • count()
    • embed()
    • init_kmers()
    • load()
    • main()
    • mp_counter()
    • normalize()
    • record_counter()
    • seq_counter()
  • autometa.common.markers module
    • get()
    • load()
    • main()
  • autometa.common.metagenome module
    • Metagenome
      • Metagenome.sequences
      • Metagenome.seqrecords
      • Metagenome.nseqs
      • Metagenome.length_weighted_gc
      • Metagenome.size
      • Metagenome.largest_seq
      • Metagenome.describe()
      • Metagenome.fragmentation_metric()
      • Metagenome.gc_content()
      • Metagenome.largest_seq
      • Metagenome.length_filter()
      • Metagenome.length_weighted_gc
      • Metagenome.nseqs
      • Metagenome.seqrecords
      • Metagenome.sequences
      • Metagenome.size
    • main()
  • autometa.common.utilities module
    • calc_checksum()
    • file_length()
    • gunzip()
    • internet_is_connected()
    • is_gz_file()
    • make_pickle()
    • ncbi_is_connected()
    • read_checksum()
    • tarchive_results()
    • timeit()
    • unpickle()
    • untar()
    • write_checksum()
  • Module contents
• autometa.config package
  • Submodules
  • autometa.config.databases module
    • Databases
      • Databases.ncbi_dir
      • Databases.SECTIONS
      • Databases.compare_checksums()
      • Databases.configure()
      • Databases.download_gtdb_files()
      • Databases.download_markers()
      • Databases.download_missing()
      • Databases.download_ncbi_files()
      • Databases.extract_taxdump()
      • Databases.fix_invalid_checksums()
      • Databases.format_nr()
      • Databases.get_missing()
      • Databases.get_remote_checksum()
      • Databases.press_hmms()
      • Databases.satisfied()
    • main()
  • autometa.config.environ module
    • bedtools()
    • bowtie2()
    • configure()
    • diamond()
    • find_executables()
    • get_versions()
    • hmmpress()
    • hmmscan()
    • hmmsearch()
    • prodigal()
    • samtools()
  • autometa.config.utilities module
    • get_config()
    • main()
    • parse_args()
    • put_config()
    • set_home_dir()
    • update_config()
  • Module contents
• autometa.datasets package
  • Module contents
• autometa.taxonomy package
  • Submodules
  • autometa.taxonomy.database module
    • TaxonomyDatabase
      • TaxonomyDatabase.CANONICAL_RANKS
      • TaxonomyDatabase.UNCLASSIFIED
      • TaxonomyDatabase.convert_accessions_to_taxids()
      • TaxonomyDatabase.convert_taxid_dtype()
      • TaxonomyDatabase.get_lineage_dataframe()
      • TaxonomyDatabase.is_common_ancestor()
      • TaxonomyDatabase.lineage()
      • TaxonomyDatabase.name()
      • TaxonomyDatabase.parent()
      • TaxonomyDatabase.parse_delnodes()
      • TaxonomyDatabase.parse_merged()
      • TaxonomyDatabase.parse_names()
      • TaxonomyDatabase.parse_nodes()
      • TaxonomyDatabase.rank()
  • autometa.taxonomy.gtdb module
    • GTDB
      • GTDB.__repr__()
      • GTDB.__str__()
      • GTDB.convert_accessions_to_taxids()
      • GTDB.parse_delnodes()
      • GTDB.parse_merged()
      • GTDB.parse_names()
      • GTDB.parse_nodes()
      • GTDB.search_genome_accessions()
      • GTDB.verify_databases()
    • create_gtdb_db()
    • main()
  • autometa.taxonomy.lca module
    • LCA
      • LCA.disable
      • LCA.tour_fp
      • LCA.tour
      • LCA.level_fp
      • LCA.level
      • LCA.occurrence_fp
      • LCA.occurrence
      • LCA.sparse_fp
      • LCA.sparse
      • LCA.lca_prepared
      • LCA.blast2lca()
      • LCA.lca()
      • LCA.parse()
      • LCA.prepare_lca()
      • LCA.prepare_tree()
      • LCA.preprocess_minimums()
      • LCA.read_sseqid_to_taxid_table()
      • LCA.reduce_taxids_to_lcas()
      • LCA.write_lcas()
    • main()
  • autometa.taxonomy.majority_vote module
    • is_consistent_with_other_orfs()
    • lowest_majority()
    • main()
    • majority_vote()
    • rank_taxids()
    • write_votes()
  • autometa.taxonomy.ncbi module
    • NCBI
      • NCBI.__repr__()
      • NCBI.__str__()
      • NCBI.convert_accessions_to_taxids()
      • NCBI.convert_taxid_dtype()
      • NCBI.parse_delnodes()
      • NCBI.parse_merged()
      • NCBI.parse_names()
      • NCBI.parse_nodes()
      • NCBI.search_prot_accessions()
  • autometa.taxonomy.vote module
    • add_ranks()
    • assign()
    • get()
    • main()
    • write_ranks()
  • Module contents
• autometa.validation package
  • Submodules
  • autometa.validation.assess_metagenome_deconvolution module
  • autometa.validation.benchmark module
    • Labels
      • Labels.pred
      • Labels.true
    • Targets
      • Targets.pred
      • Targets.target_names
      • Targets.true
    • compute_classification_metrics()
    • compute_clustering_metrics()
    • evaluate_binning_classification()
    • evaluate_classification()
    • evaluate_clustering()
    • get_categorical_labels()
    • get_target_labels()
    • main()
    • write_reports()
  • autometa.validation.build_protein_marker_aln module
  • autometa.validation.calculate_f1_scores module
  • autometa.validation.cami module
    • format_genome_binning()
    • format_profiling()
    • format_taxon_binning()
    • get_biobox_format()
    • main()
  • autometa.validation.cluster_process module
    • assess_assembly()
    • main()
    • run_command()
  • autometa.validation.cluster_process_docker module
  • autometa.validation.cluster_taxonomy module
  • autometa.validation.compile_reference_training_table module
  • autometa.validation.confidence_vs_accuracy module
  • autometa.validation.datasets module
    • download()
    • main()
  • autometa.validation.download_random_bacterial_genomes module
  • autometa.validation.length_vs_accuracy module
  • autometa.validation.make_simulated_metagenome module
  • autometa.validation.make_simulated_metagenome_control_fasta module
  • autometa.validation.reference_genome_from_quast module
  • autometa.validation.show_clusters module
  • autometa.validation.summarize_f1_stats module
  • autometa.validation.tabulate_bins module
  • autometa.validation.tabulate_metaquast_alignments module
  • autometa.validation.vizualize_assembly_graph_by_bin module
  • Module contents

Module contents