def test_insertion_inside_insertion():
testCase = ({
1267: ["A", "ACGTGCTAAC", [(0, 1267)] + [(70, x) for x in range(0, 9)]],
1276: ["A", "AGCACTTTCTGT", [(0, 1276)] + [(54, x) for x in range(0, 11)]]
},
{54: 1276, 70: 1267},
[mutation(mType=mType.INS, genomePos=5, insertionPos=70, source="", target="GCGGGCGC", index=1)])
apply_general_test(testCase)
def test_deletion_overlapping_starting_from_indel():
testCase = ({
1267: ["A", "ACGTGCTAAC", [(0, 1267)] + [(70, x) for x in range(0, 9)]],
1276: ["A", "AGCACTTTCTGT", [(0, 1276)] + [(54, x) for x in range(0, 11)]]
},
{54: 1276, 70: 1267},
[mutation(mType=mType.DEL, genomePos=5, insertionPos=70, source="TAACAAAAAAAAAGC", target="")])
apply_general_test(testCase)
def test_substitution_on_genome():
testCase = ({
1267: ["A", "ACGTGCTAAC", [(0, 1267)] + [(70, x) for x in range(0, 9)]],
1276: ["A", "AGCACTTTCTGT", [(0, 1276)] + [(54, x) for x in range(0, 11)]]
},
{54: 1276, 70: 1267},
[mutation(mType=mType.SUB, genomePos=1, insertionPos=0, source="A", target="G")])
apply_general_test(testCase)
def test_multiple_deletions_together_slightly_different():
testCase = ({
1406: ['A', '-CTG', [(0, 1406), (23, 0), (23, 1), (23, 2)]],
1401: ['AAAA', '----', [(0, 1401), (0, 1402), (0, 1403), (0, 1404)]],
1408: ['AAA', '---', [(0, 1408), (0, 1409), (0, 1410)]]
},
{23: 1406},
[mutation(mType=mType.DEL, genomePos=1399, insertionPos=0, source="AAACTGAAAAAAAA", target="")])
apply_general_test(testCase)
def test_printing_functions():
genome_tree = setup_genome_tree()
class MockFile:
"""
A class which has 1 method called write,
so that I can use it as a mock file object in this test.
"""
def __init__(self):
self.written_data = ""
def write(self, string):
self.written_data += string
def parameterised_test(mutDict, insertionDict, mutations, expected_output):
f = MockFile()
node = TreeNode(name="test_node")
node.mutations = mutations
original_mD = mutDict.copy()
original_iD = insertionDict.copy()
genome_tree.writeGenomeShortIndels(node=node,
file=f,
mutDict=mutDict,
insertionDict=insertionDict)
# the whole point of this function is that the genome tree updates and then de-updates
# any mutations. So we need the mutDict and insertionDict to remain the same before and after printing.
assert mutDict == original_mD
assert insertionDict == original_iD
assert f.written_data == expected_output #
parameterised_test(mutDict={},
insertionDict={},
mutations=[
phastSim.mutation(mType=phastSim.mType.DEL,
genomePos=4,
insertionPos=0,
source="GAAT",
target="")
],
expected_output=">test_node\nGAAT5----\n")