def test_for_good_measure(self):
tree = dendropy.Tree.get(
path="%s/EPI_ISL_418192.aln.fasta.nexus.tree" % data_dir,
schema="nexus",
preserve_underscores=True)
collapse_nodes(tree, lambda x: x.edge.length == 0)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(subtyper.get_subtype("EPI_ISL_418192||"), "B.1")
def test_polytomy_no_tip_Siblings(self):
tree = dendropy.Tree.get(
path="%s/EPI_ISL_416626.aln.fasta.nexus.tree" % data_dir,
schema="nexus",
preserve_underscores=True)
collapse_nodes(tree, lambda x: x.edge.length == 0)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(subtyper.get_subtype("EPI_ISL_416626||"), "B")
def test_doesnt_find_tip(self):
tree = dendropy.Tree.get(path="%s/EPI_ISL_667.aln.fasta.tree" %
data_dir,
schema="newick",
preserve_underscores=True)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(
subtyper.get_subtype(
"Testland___TLD32___2020|EPI_ISL_667||Testland|||2020-03-11"),
"B")
def test_between_clades_fall_back(self):
tree = dendropy.Tree.get(
path="%s/representative_sequences.aln.fasta.nexus.tree" % data_dir,
schema="nexus",
preserve_underscores=True)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(
subtyper.get_subtype(
"USA/CZB-RR057-013/2020|EPI_ISL_417937|B.1.3|USA|||2020-03-18"
), "B.1")
def test_nested_no_sibling(self):
tree = dendropy.Tree.get(
path="%s/representative_sequences.aln.fasta.nexus.tree" % data_dir,
schema="nexus",
preserve_underscores=True)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(
subtyper.get_subtype(
"France/IDF2256/2020|EPI_ISL_416498|B.1.4|France|||2020-03-11"
), "B.1.4")
def test_sibling(self):
tree = dendropy.Tree.get(
path="%s/representative_sequences.aln.fasta.nexus.tree" % data_dir,
schema="nexus",
preserve_underscores=True)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(
subtyper.get_subtype(
"Iceland/222/2020|EPI_ISL_417837|B.1.8|Iceland|||2020-03-16"),
"B.1.8")
def test_empty_subtype(self):
tree = dendropy.Tree.get(
path="%s/EPI_ISL_413581X.aln.fasta.nexus.tree" % data_dir,
schema="nexus",
preserve_underscores=True)
collapse_nodes(tree, lambda x: x.edge.length == 0)
subtyper = Subtyper(tree, 2, "|")
self.assertEqual(
subtyper.get_subtype(
"Netherlands___Oss_1363500___2020|EPI_ISL_413581X|2020-02-29"),
"B")
def run(options):
tree = prepare_tree(options, options.input)
subtyper = Subtyper(tree, options.trait)
write_tree(subtyper.tree, options)