def addEdge(self, gene1, gene2):
"""Adds an edge between the two gene families that the two given genes belong to. Genes object are expected, and they are also expected to have a family assigned
:param gene1: The first gene
:type gene1: :class:`ppanggolin.genome.Gene`
:param gene2: The second gene
:type gene2: :class:`ppanggolin.genome.Gene`
:return: the created Edge
:rtype: :class:`ppanggolin.pangenome.Edge`
"""
key = frozenset([gene1.family, gene2.family])
edge = self._edgeGetter.get(key)
if edge is None:
edge = Edge(gene1, gene2)
self._edgeGetter[key] = edge
else:
edge.addGenes(gene1, gene2)
return edge
def test_cstr_error():
o_src = Gene('source')
o_tgt = Gene('target')
# genes should have a family
with pytest.raises(Exception):
_ = Edge(o_src, o_tgt)
o_family = GeneFamily(None, None)
o_family.addGene(o_src)
# both genes sould have a family
with pytest.raises(Exception):
_ = Edge(o_src, o_tgt)
# gene should belong to the same organism
o_family.addGene(o_tgt)
o_src.fill_parents("", None)
o_tgt.fill_parents(None, None)
with pytest.raises(Exception):
_ = Edge(o_src, o_tgt)
def test_cstr():
o_src = Gene('source')
o_tgt = Gene('target')
# set organism and contig to None.
o_src.fill_parents(None, None)
o_tgt.fill_parents(None, None)
# define the None GeneFamily, and add the 2 genes to it.
o_family = GeneFamily(None, None)
o_family.addGene(o_src)
o_family.addGene(o_tgt)
o_edge = Edge(o_src, o_tgt)
assert isinstance(o_edge, Edge)
assert o_edge.source == o_src.family
assert o_edge.target == o_tgt.family
assert dict(o_edge.organisms) == {None: [(o_src, o_tgt)]}
def filled_edge(make_gene_pair):
# Note that the same edge here links 4 families.
p1 = make_gene_pair("org1", "s1", "t1")
p2 = make_gene_pair("org1", "s2", "t1")
p3 = make_gene_pair("org2", "s1", "t2")
p4 = make_gene_pair("org2", "s1", "s2")
# org1: s1,s2 -- t1
# org2: s1 -- t2,s2
o_edge = Edge(*p1)
o_edge.addGenes(*p2)
o_edge.addGenes(*p3)
o_edge.addGenes(*p4)
return o_edge
def test_addGenes(make_gene_pair):
p1 = make_gene_pair("org1", "s1", "t1")
p2 = make_gene_pair("org1", "s2", "t1")
p3 = make_gene_pair("org2", "s1", "t2")
p4 = make_gene_pair("org2", "s1", "s2")
# org1: s1,s2 -- t1
# org2: s1 -- t2,s2
o_edge = Edge(*p1)
o_edge.addGenes(*p2)
o_edge.addGenes(*p3)
o_edge.addGenes(*p4)
assert set(o_edge.organisms.keys()) == set(["org1", "org2"])
assert o_edge.organisms["org1"] == [p1, p2]
assert o_edge.organisms["org2"] == [p3, p4]
def test_genePairs(make_gene_pair):
# cannot use filled_edge because i need access to pairs.
p1 = make_gene_pair("org1", "s1", "t1")
p2 = make_gene_pair("org1", "s2", "t1")
p3 = make_gene_pair("org2", "s1", "t2")
p4 = make_gene_pair("org2", "s1", "s2")
# org1: s1,s2 -- t1
# org2: s1 -- t2,s2
o_edge = Edge(*p1)
o_edge.addGenes(*p2)
o_edge.addGenes(*p3)
o_edge.addGenes(*p4)
# 'set' because the order is not guaranted due to '.values()'.
l_pairs = o_edge.genePairs
assert set(l_pairs) == set([p1, p2, p3, p4])
def o_edge(make_gene_pair):
p = make_gene_pair("org", "src", "tgt")
return Edge(*p)