def test_hash(o_region):
""" a hash function returns an integer"""
# the same int if called twice on the same object
h = hash(o_region)
assert isinstance(h, int)
assert h == hash(o_region)
# different ints if called on objects representing the same entity
name = "charming"
assert hash(Region(name)) != hash(Region(name))
def extractRGP(contig, node, ID):
"""
Extract the region from the given starting node
"""
new_region = Region(contig.name + "_" + str(ID))
while node.state:
new_region.append(node.gene)
node.state = 0
node.score = 0
node = node.prev
if node is None: #it's the end of the contig and the end of the region.
break
return new_region
def test_cstr():
ID = 4
o_region = Region(ID)
assert isinstance(o_region, Region)
for attr in "genes", "name", "score":
assert hasattr(o_region, attr)
assert o_region.score == 0
assert o_region.name == ID
assert o_region.genes == []
def test_equality(o_region, l_genes):
"""2 regions are equals if they contains the same list of genes."""
for gene in l_genes:
o_region.append(gene)
# not the same list => False
o_other = Region("other")
assert o_region != o_other
# the exact same list => True
o_other = Region("other")
for gene in l_genes:
o_other.append(gene)
assert o_region == o_other
# the same list in reverse order => True
o_other = Region("other")
for gene in reversed(l_genes):
o_other.append(gene)
assert o_region == o_other
def getOrAddRegion(self, regionName):
"""Returns a region with the given `regionName`. Creates it if it does not exist.
:param regionName: The name of the region to return
:type regionName: str
:return: The region
:rtype: :class:`ppanggolin.region.Region`
"""
try:
return self._regionGetter[regionName]
except KeyError: #then the region is not stored in this pangenome.
newRegion = Region(regionName)
self._regionGetter[regionName] = newRegion
return newRegion
def extractRGP(contig, node, ID, naming):
"""
Extract the region from the given starting node
"""
if naming == "contig":
new_region = Region(contig.name + "_RGP_" + str(ID))
elif naming == "organism":
new_region = Region(node.gene.organism.name + "_" + contig.name + "_RGP_" + str(ID))
while node.state:
new_region.append(node.gene)
node.state = 0
node.score = 0
node = node.prev
if node is None:#it's the end of the contig and the end of the region.
break
return new_region
def o_region():
return Region(4)