def _make_gene_pair(org, gene_id1, gene_id2):
"""create a pair of genes that belong to the same organism."""
lo_genes = []
for k in gene_id1, gene_id2:
o_gene = Gene(k)
o_gene.fill_parents(org, None)
lo_genes.append(o_gene)
o_family = GeneFamily(k, k)
o_family.addGene(o_gene)
return tuple(lo_genes)
def _make_gene_pair(org, gene_id1, gene_id2):
"""create 2 genes from org.
each gene belong to its own family."""
lo_genes = []
for k in gene_id1, gene_id2:
o_gene = Gene(k)
o_gene.fill_parents(org, None)
lo_genes.append(o_gene)
o_family = GeneFamily(k, k)
o_family.addGene(o_gene)
return tuple(lo_genes)
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_families():
"""
return a list of families and genes.
there will be between 3 and 10 genes/families.
Each family has only one gene.
"""
lo_genes = []
lo_fam = []
n_families = randint(3, 10)
for fam in range(n_families):
o_gene = Gene(fam)
o_gene.fill_parents(None, None)
o_family = GeneFamily(fam,fam)
o_family.addGene(o_gene)
lo_genes.append(o_gene)
lo_fam.append(o_family)
return lo_fam, lo_genes
def test_cstr():
ID = 33
name = "33"
o_family = GeneFamily(ID, name)
assert isinstance(o_family, GeneFamily)
for attr in "ID", "name", "genes", \
"removed", "sequence", "partition":
assert hasattr(o_family, attr)
assert o_family.ID == ID
assert o_family.name == name
assert o_family.genes == set()
assert o_family.removed == False
assert o_family.sequence == ""
assert o_family.partition == ""
def test_cstr_error():
o_src = Gene('source')
o_tgt = Gene('target')
# genes should have a family
with pytest.raises(Exception):
o_edge = 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):
o_edge = 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):
o_edge = Edge(o_src, o_tgt)
def o_family():
return GeneFamily(33, "trente-trois")