API Reference#

This section contains a comprehensive reference of the public API of IGUA.

Pipeline#

`PipelineParameters`	The parameters of the IGUA pipeline.
`PipelineResult`	The results of the IGUA clustering pipeline.
`Pipeline`	The IGUA multi-stage clustering pipeline.

`ClusteringStrategy`	An abstract clustering strategy to cluster compositional data.
`HierarchicalClustering`	A clustering strategy implementing hierarchical clustering.
`LinearClustering`	A clustering strategy similar to MMseqs2 linear clustering.

A wrapper around an mmseqs binary and common parameters.

`Cluster`	A gene cluster.
`Protein`	A protein inside a gene cluster.
`BaseDataset`	An abstract dataset to provide clusters to a `ClusteringPipeline`.

A dataset consisting in a list of other datasets.

A dataset composed of gene clusters in a GenBank file.

`AntiSMASHGenBankDataset`	A dataset composed of antiSMASH regions in a GenBank file.
`AntiSMASHZipDataset`	A dataset composed of antiSMASH results in a Zip file.

Dataset for extracting sequences from FASTA/GFF files.

DefenseFinder-specific dataset class.