Base dataset

class igua.dataset.base.Cluster(id, sequence, source=None)

A gene cluster.

id

The identifier of the gene cluster. Must be unique across all datasets, as the identifier will be used to refer to each cluster in the resulting gene cluster families.

Type:

str

sequence

The genomic sequence of the dataset.

Type:

str

source

The source of the gene cluster, usually the path to the file where this cluster record was extracted from.

Type:

str or None

property length

The length of the cluster sequence.

Type:

int

class igua.dataset.base.Protein(id, sequence, cluster_id)

A protein inside a gene cluster.

id

The identifier of the protein. Must be unique across all datasets, as the identifier will be used to refer to each protein while clustering.

Type:

str

sequence

The amino-acid sequence of the protein.

Type:

str

cluster_id

The identifier of the cluster this protein belongs to.

Type:

str

property length

The length of the protein sequence.

Type:

int

class igua.dataset.base.BaseDataset

An abstract dataset to provide clusters to a ClusteringPipeline.

IGUA needs the genomic sequences of the gene clusters to process, and the individual proteins of each gene cluster. To provide them to a clustering pipeline, the BaseDataset interface provides two functions: BaseDataset.extract_clusters and BaseDataset.extract_proteins which yield Cluster and Protein objects, respectively.

abstract extract_clusters(progress)

Extract the clusters from the dataset.

Parameters:

progress (rich.progress.Progress) – A Progress instance that can be used for tracking progress.

Yields:

Cluster – A cluster object for each gene cluster to be processed in the dataset.

abstract extract_proteins(progress, cluster_ids)

Extracts protein sequences from GenBank files.

Parameters:

• progress (rich.progress.Progress) – A Progress instance that can be used for tracking progress.

• cluster_ids (collections.abc.Collection of str) – A collection of cluster IDs from which to extract proteins.

Yields:

Protein – A protein object for each protein of the gene clusters to be processed in the dataset.