def test_order_C002271_c19(self): # pylint: disable=invalid-name
cdss = {}
for i, name in enumerate([
"STAUR_3972", "STAUR_3982", "STAUR_3983", "STAUR_3984",
"STAUR_3985"
]):
cdss[name] = DummyCDS(start=i * 10, end=i * 10 + 1, locus_tag=name)
n_terms = {
'STAUR_3972': 'L-',
'STAUR_3982': 'ER',
'STAUR_3983': 'DK',
'STAUR_3984': 'SQ',
'STAUR_3985': 'SV'
}
c_terms = {
'STAUR_3972': 'ES',
'STAUR_3982': '--',
'STAUR_3983': 'DS',
'STAUR_3984': 'DS',
'STAUR_3985': 'DS'
}
start = None
end = cdss["STAUR_3982"]
# there are multiple orders of equal score, but sort for simple testing
possible_orders = orderfinder.find_possible_orders(
list(cdss.values()), start, end)
best = orderfinder.rank_biosynthetic_orders(n_terms, c_terms,
possible_orders)
best = [gene.get_name() for gene in best]
assert best == [
'STAUR_3983', 'STAUR_3972', 'STAUR_3984', 'STAUR_3985',
'STAUR_3982'
]
def run_ordering_simple(self, start, end, gene_list=None):
start_gene = self.gene_mapping.get(start)
end_gene = self.gene_mapping.get(end)
if gene_list is None:
gene_list = "abc"
genes = [self.gene_mapping[name] for name in gene_list]
orders = orderfinder.find_possible_orders(genes, start_gene, end_gene)
simple_orders = []
for order in orders:
simple_orders.append([g.locus_tag for g in order])
return simple_orders
def test_order_C002271_c19(self): # pylint: disable=invalid-name
n_terms = {'STAUR_3972': 'L-', 'STAUR_3982': 'ER',
'STAUR_3983': 'DK', 'STAUR_3984': 'SQ',
'STAUR_3985': 'SV'}
c_terms = {'STAUR_3972': 'ES', 'STAUR_3983': 'DS',
'STAUR_3984': 'DS', 'STAUR_3985': 'DS'}
start = ""
end = "STAUR_3982"
# there are multiple orders of equal score, but sort for simple testing
possible_orders = sorted(orderfinder.find_possible_orders(list(n_terms), start, end))
best = self.run_ranking_as_genes(n_terms, c_terms, possible_orders)
assert best == ['STAUR_3983', 'STAUR_3972', 'STAUR_3984', 'STAUR_3985', 'STAUR_3982']
def test_permutations_start_and_end(self):
perms = orderfinder.find_possible_orders(list("abc"), "a", "b")
assert perms == [["a", "c", "b"]]
perms = orderfinder.find_possible_orders(list("abce"), "a", "b")
assert perms == [["a", "c", "e", "b"], ["a", "e", "c", "b"]]
def test_permutations_start_only(self):
perms = orderfinder.find_possible_orders(list("abc"), "a", "")
assert perms == [["a", "b", "c"], ["a", "c", "b"]]
def test_order_finding_size(self):
cdss = [DummyCDS() for i in range(11)]
with self.assertRaisesRegex(AssertionError, "input too large"):
orderfinder.find_possible_orders(cdss, None, None)