Genome

AbstractGene is an abstract class representing extant or ancestral genes. An AbstractGene is defined by an unique id, the genome it belongs to and its parent AbstractGene.

class pyham.genome.Genome

Genome is an abstract class representing extant or ancestral genomes. An Genome is defined by a unique taxon (node) in the Taxonomy.tree.

Attributes:

taxon (ete3.TreeNode of the pyham.taxonomy.tree): corresponding taxon.

name (str): Name of the Genome. Get from the newick tree if specified otherwise build it by concatenating all children genome names.

genes (list): list of pyham.abstractgene.AbstractGene related to this Genome.

add_gene(gene)

This method adds an AbstractGene to the genes attributes and updates the AbstractGene.genome attribute.

Attributes:

taxon (Taxonomy.tree node): corresponding taxon.

name (str): Name of the Genome. Get from the newick tree if specified otherwise build it by concatenating all children genome names.

genes (list): list of AbstractGene related to this Genome.

Raises:

TypeError: if gene is not an AbstractGene.

abstractmethod get_number_genes()

Return the number of genes

set_taxon(taxon)

This method sets the taxon of the Genome.

Attributes:

taxon (Taxonomy.tree node): corresponding taxon.

Raises:

TypeError: if taxon is not an ete4.Tree. EvolutionaryConceptError: if the genome already has a taxon set.

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class pyham.genome.ExtantGenome(name, NCBITaxId='-1', **kwargs)

ExtantGenome class representing extant genomes. An ExtantGenome is defined by a unique name and a NCBI taxId.

Attributes:

name (str): unique genome name. This is the unique identifier of ExtantGenome.

taxid (dict): NCBI taxId.

get_number_genes(singleton=True)

Get the number of genes of this ExtantGenome.

Args:

singleton (Bool): boolean to take into account singleton or not.

Returns:

int.

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class pyham.genome.AncestralGenome

AncestralGenome class representing ancestral genomes.

Attributes:

ancestral_clustering (dict): a dictionary that map each of this ancestral genome HOGs to its list of descendant extant genes.

get_ancestral_clustering()

Lazy getter of the ancestral_clustering attribute.

Returns:

dict.

get_number_genes()

Return the number of genes