Index _ | A | B | C | D | E | F | G | H | I | L | M | N | P | R | S _ __init__() (igua.clustering.HierarchicalClustering method) (igua.clustering.LinearClustering method) (igua.dataset.defensefinder.DefenseFinderDataset method) (igua.dataset.fasta_gff.FastaGFFDataset method) (igua.dataset.genbank.GenBankDataset method) (igua.pipeline.Pipeline method) _create_genome_context() (igua.dataset.fasta_gff.FastaGFFDataset method) _extract_clusters_to_file() (igua.pipeline.Pipeline method) _extract_proteins_to_file() (igua.pipeline.Pipeline method) _extract_representatives() (igua.pipeline.Pipeline method) _hierarchical_clustering() (igua.pipeline.Pipeline method) _join_results() (igua.pipeline.Pipeline method) _load_and_filter_systems() (igua.dataset.defensefinder.DefenseFinderDataset method) (igua.dataset.fasta_gff.FastaGFFDataset method) _log_protein_summary() (igua.dataset.fasta_gff.FastaGFFDataset method) _make_compositions() (igua.pipeline.Pipeline method) _run_nucleotide_clustering() (igua.pipeline.Pipeline method) _run_nucleotide_deduplication() (igua.pipeline.Pipeline method) _run_protein_clustering() (igua.pipeline.Pipeline method) _wrap_progress() (igua.mmseqs.MMSeqs method) A AntiSMASHGenBankDataset (class in igua.dataset.antismash) AntiSMASHZipDataset (class in igua.dataset.antismash) B BaseDataset (class in igua.dataset.base) C Cluster (class in igua.dataset.base) cluster() (igua.clustering.ClusteringStrategy method) (igua.clustering.HierarchicalClustering method) (igua.clustering.LinearClustering method) cluster_id (igua.dataset.base.Protein attribute) ClusteringStrategy (class in igua.clustering) compositions (igua.pipeline.PipelineResult attribute) D DatasetList (class in igua.dataset.list) default() (igua.pipeline.PipelineParameters class method) DefenseFinderDataset (class in igua.dataset.defensefinder) E extract_clusters() (igua.dataset.antismash.AntiSMASHGenBankDataset method) (igua.dataset.antismash.AntiSMASHZipDataset method) (igua.dataset.base.BaseDataset method) (igua.dataset.fasta_gff.FastaGFFDataset method) (igua.dataset.genbank.GenBankDataset method) (igua.dataset.list.DatasetList method) extract_proteins() (igua.dataset.antismash.AntiSMASHGenBankDataset method) (igua.dataset.antismash.AntiSMASHZipDataset method) (igua.dataset.base.BaseDataset method) (igua.dataset.fasta_gff.FastaGFFDataset method) (igua.dataset.genbank.GenBankDataset method) (igua.dataset.list.DatasetList method) F FastaGFFDataset (class in igua.dataset.fasta_gff) G gcfs (igua.pipeline.PipelineResult attribute) GenBankDataset (class in igua.dataset.genbank) H HierarchicalClustering (class in igua.clustering) I id (igua.dataset.base.Cluster attribute) (igua.dataset.base.Protein attribute) L length (igua.dataset.base.Cluster property) (igua.dataset.base.Protein property) LinearClustering (class in igua.clustering) M MMSeqs (class in igua.mmseqs) N nuc1 (igua.pipeline.PipelineParameters attribute) nuc2 (igua.pipeline.PipelineParameters attribute) P Pipeline (class in igua.pipeline) PipelineParameters (class in igua.pipeline) PipelineResult (class in igua.pipeline) prot (igua.pipeline.PipelineParameters attribute) Protein (class in igua.dataset.base) R run() (igua.mmseqs.MMSeqs method) (igua.pipeline.Pipeline method) S sequence (igua.dataset.base.Cluster attribute) (igua.dataset.base.Protein attribute) source (igua.dataset.base.Cluster attribute)
