FASTA/GFF dataset

class igua.dataset.fasta_gff.FastaGFFDataset(inputs, column_mapping=None)

Dataset for extracting sequences from FASTA/GFF files.

__init__(inputs, column_mapping=None)

Initialize the FastaGFFDataset class.

Parameters:

• inputs – List of input paths (metadata TSV or individual files).

• column_mapping – Custom column mapping. If None, uses default generic mapping.

_create_genome_context(row, genome_id)

Create GenomeContext from metadata row.

Parameters:

• row – Dictionary with file paths from metadata TSV.

• genome_id – Genome identifier.

Returns:

GenomeContext instance.

_load_and_filter_systems(tsv_path, console)

Load systems TSV file.

Parameters:

• tsv_path – Path to systems TSV.

• console – Rich console for logging.

Returns:

Polars DataFrame with system data.

_log_protein_summary(progress, results, representatives)

Log summary of protein extraction results.

Parameters:

• progress – Rich progress bar instance.

• results – Dictionary of extracted proteins.

• representatives – Container of representative cluster IDs.

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.

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.