pyham 2.0.0__py3-none-any.whl

pyham/genome.py

@@ -0,0 +1,148 @@
+import abc
+from ete4 import Tree
+
+
+class Genome(metaclass=abc.ABCMeta):
+    """  
+    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 (:obj:`ete3.TreeNode` of the :obj:`pyham.taxonomy`.tree): corresponding taxon.
+        | name (:obj:`str`): Name of the Genome. Get from the newick tree if specified otherwise build it by concatenating all children genome names.
+        | genes (:obj:`list`): list of :obj:`pyham.abstractgene.AbstractGene` related to this Genome.
+
+    """
+
+    def __init__(self):
+        self.genes = []
+        self.taxon = None
+        self.name = None
+
+    def add_gene(self, gene):
+
+        """  
+        This method adds an AbstractGene to the genes attributes and updates the AbstractGene.genome attribute.
+
+        Attributes:
+            | taxon (Taxonomy.tree node): corresponding taxon.
+            | name (:obj:`str`): Name of the Genome. Get from the newick tree if specified otherwise build it by concatenating all children genome names.
+            | genes (:obj:`list`): list of :obj:`AbstractGene` related to this Genome.
+        
+        Raises:
+            TypeError: if gene is not an AbstractGene.
+        """
+        from .abstractgene import AbstractGene
+        if not isinstance(gene, AbstractGene):
+            raise TypeError("expect subclass obj of '{}', got {}"
+                            .format(AbstractGene.__name__,
+                                    type(gene).__name__))
+
+        self.genes.append(gene)
+        gene.set_genome(self)
+
+    def set_taxon(self, 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.
+        """
+
+        if not isinstance(taxon, Tree):
+            raise TypeError("expect subclass obj of '{}', got {}"
+                            .format(Tree.__name__,
+                                    type(taxon).__name__))
+        if self.taxon is not None and taxon != self.taxon:
+            raise EvolutionaryConceptError("only one taxon can refer to one genome")
+        self.taxon = taxon
+
+    @abc.abstractmethod
+    def get_number_genes(self):
+        """ Return the number of genes"""
+        pass
+
+    def __str__(self):
+        return self.name
+
+
+class AncestralGenome(Genome):
+
+    """  
+    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.
+
+    """
+
+    def __init__(self):
+        super(AncestralGenome, self).__init__()
+        self.ancestral_clustering = None
+
+    def get_ancestral_clustering(self):
+
+        """ Lazy getter of the ancestral_clustering attribute.
+
+            Returns:
+                :obj:`dict`.
+
+        """
+
+        if self.ancestral_clustering is None:
+            self.ancestral_clustering = {}
+            for hog in self.genes:
+                self.ancestral_clustering[hog] = hog.get_all_descendant_genes()
+        return self.ancestral_clustering
+
+    def get_number_genes(self):
+        return len(self.genes)
+
+
+class ExtantGenome(Genome):
+
+    """  
+    ExtantGenome class representing extant genomes. An ExtantGenome is defined by a unique name and a NCBI taxId.
+
+    Attributes:
+        | name (:obj:`str`): unique genome name. This is the unique identifier of ExtantGenome.
+        | taxid (dict): NCBI taxId.
+
+    """
+
+    def __init__(self, name, NCBITaxId='-1', **kwargs):
+        super(ExtantGenome, self).__init__()
+        self.name = name
+        self.taxid = NCBITaxId
+        self.taxon_id = kwargs.get('taxon_id', None)
+
+    def get_number_genes(self, singleton=True): #  TODO: UT
+
+        """ Get the number of genes of this ExtantGenome.
+        
+            Args:
+                | singleton (:obj:`Bool`): boolean to take into account singleton or not.
+
+            Returns:
+                :obj:`int`.
+
+        """
+
+        if singleton:
+            return len(self.genes)
+        else:
+            nbr = 0
+            for g in self.genes:
+                if not g.is_singleton():
+                    nbr += 1
+            return nbr
+
+
+class EvolutionaryConceptError(Exception):
+    pass