Genome

class magna.gtdb.genome.Genome(accession, root)

A wrapper to a GTDB genome.

accession: str

The short accession of the genome.

cds_path: str

The path to the CDS file.

cds_seqio()

Read and return the CDS file as a SeqIO object.

Return type

Tuple[SeqRecord, …]

fna_path: str

The path to the FNA file.

fna_seqio()

Read and return the FNA file as a SeqIO object.

Return type

Tuple[SeqRecord, …]

root: str

The root directory where this genome is stored.

class magna.gtdb.genome.GenomeDirs(release)

An interface to the GtdbRelease accession to Genome mapping.

__init__(release)

Initialise the GenomeDirs class for a given release.

Parameters

release (GtdbRelease) – The release of GTDB to use.

get(accession)

Return the Genome for the given accession.

Parameters

accession (str) – The short accession of the genome (e.g. GCA_123456789.1).

Return type

Genome