The GeneFamily class
- class ppanggolin.geneFamily.GeneFamily(ID, name)[source]
Bases:
objectThis represents a single gene family. It will be a node in the pangenome graph, and be aware of its genes and edges.
- addGene(gene)[source]
Add a gene to the gene family, and sets the gene’s :attr:family accordingly.
- Parameters
gene (
ppanggolin.genome.Gene) – the gene to add- Raises
TypeError – If the provided gene is of the wrong type
- addPartition(partition)[source]
Assigns a partition to the gene family. It should be the raw partition name provided by NEM.
- Parameters
partition (str) – The partition
- addSequence(seq)[source]
Assigns a protein sequence to the gene family.
- Parameters
seq (str) – the sequence to add to the gene family
- property edges
Returns all of the
ppanggolin.pangenome.Edgethat are linked to this gene family- Returns
Edges of the gene family
- Return type
- getGenesPerOrg(org)[source]
Returns the genes belonging to the gene family in the given Organism
- Parameters
org (
ppanggolin.genome.Organism) – Organism to look for- Returns
a set of gene(s)
- Return type
- getOrgDict()[source]
Returns the organisms and the genes belonging to the gene family
- Returns
a dictionnary of organism as key and set of genes as values
- Return type
dict[
ppanggolin.genome.Organism,set[ppanggolin.genome.Gene]
- mkBitarray(index)[source]
Produces a bitarray representing the presence / absence of the family in the pangenome using the provided index The bitarray is stored in the
bitarrayattribute and is agmpy2.xmpztype.- Parameters
index (dict[
ppanggolin.genome.Organism, int]) – The index computed byppanggolin.pangenome.Pangenome.getIndex()
- property namedPartition
Reads the :attr:partition attribute and returns a meaningful name
- Raises
Exception – If the gene family has no partition assigned
- Returns
the partition name of the gene family
- Return type
str
- property neighbors
Returns all of the
ppanggolin.geneFamily.GeneFamilythat are linked with an edge- Returns
Neighbors
- Return type
- property organisms
Returns all of the
ppanggolin.genome.Organismthat have this gene family- Returns
Organisms that have this gene family
- Return type