def test_valid(self):
# 0 Filename
# 1 Label
# 2 Strandedness (True/False)
# 3 Score (Float)
# 4 Reference
# 5 Exclude redundant
# 6 strip cds
# 7 skip split
with tempfile.NamedTemporaryFile(mode="wt") as out:
for _, item in self.files.items():
print(item["filename"],
item["label"],
item["stranded"],
item["score"],
item["reference"],
item["exclude_redundant"],
item["strip_cds"],
item["skip_split"],
sep="\t",
file=out)
out.flush()
configuration = parse_list_file(self.config, out.name)
for arr in (configuration.prepare.files.source_score,
configuration.prepare.files.reference,
configuration.prepare.files.exclude_redundant,
configuration.prepare.files.reference,
configuration.prepare.files.strip_cds,
configuration.pick.chimera_split.skip):
self.assertEqual(len(arr), 3)
for _, item in self.files.items():
label = item["label"]
self.assertIn(item["filename"], configuration.prepare.files.gff)
self.assertIn(item["label"], configuration.prepare.files.labels)
pos = configuration.prepare.files.gff.index(item["filename"])
self.assertEqual(
pos, configuration.prepare.files.labels.index(item["label"]))
if item["stranded"] is True:
self.assertIn(
item["filename"],
configuration.prepare.files.strand_specific_assemblies)
else:
self.assertNotIn(
item["filename"],
configuration.prepare.files.strand_specific_assemblies)
self.assertEqual(item["score"],
configuration.prepare.files.source_score[label])
self.assertEqual(
item["exclude_redundant"],
configuration.prepare.files.exclude_redundant[pos])
self.assertEqual(item["reference"],
configuration.prepare.files.reference[pos])
self.assertEqual(item["strip_cds"],
configuration.prepare.files.strip_cds[pos])
self.assertEqual(item["skip_split"],
configuration.pick.chimera_split.skip[pos])
def test_default(self):
with tempfile.NamedTemporaryFile(mode="wt") as out:
# Test that header lines are skipped
print("# Filename label stranded", file=out)
print("", file=out)
for _, item in self.files.items():
print(item["filename"],
item["label"],
item["stranded"],
sep="\t",
file=out)
out.flush()
configuration = parse_list_file(self.config, out.name)
for name, arr in zip(("source_score", "reference", "exclude_redundant",
"strip_cds", "skip_split"),
(configuration.prepare.files.source_score,
configuration.prepare.files.reference,
configuration.prepare.files.exclude_redundant,
configuration.prepare.files.strip_cds,
configuration.pick.chimera_split.skip)):
self.assertEqual(len(arr), 3, name)
for _, item in self.files.items():
label = item["label"]
self.assertIn(item["filename"], configuration.prepare.files.gff)
self.assertIn(item["label"], configuration.prepare.files.labels)
pos = configuration.prepare.files.gff.index(item["filename"])
self.assertEqual(
pos, configuration.prepare.files.labels.index(item["label"]))
if item["stranded"] is True:
self.assertIn(
item["filename"],
configuration.prepare.files.strand_specific_assemblies)
else:
self.assertNotIn(
item["filename"],
configuration.prepare.files.strand_specific_assemblies)
# for arr, pos, default in [("reference", 4, False), ("exclude_redundant", 5, False),
# ("strip_cds", 6, False), ("skip_split", 7, False)]:
self.assertEqual(
configuration.prepare.files.source_score,
dict((label, 0) for label in configuration.prepare.files.labels))
self.assertEqual(configuration.prepare.files.reference, [False] * 3)
self.assertEqual(configuration.prepare.files.exclude_redundant,
[False] * 3)
self.assertEqual(configuration.prepare.files.strip_cds, [False] * 3)
self.assertEqual(configuration.pick.chimera_split.skip, [False] * 3)
def test_parse_failing_basic_list_file(self):
# 0 Filename
# 1 Label
# 2 Strandedness (True/False)
# 3 Score (Float)
# 4 Reference
# 5 Exclude redundant
# 6 strip cds
# 7 skip split
with tempfile.NamedTemporaryFile(mode="wt") as fail:
print(*[self.files[_]["filename"] for _ in self.files], sep="\n", file=fail)
fail.flush()
with self.assertRaises(IndexError):
parse_list_file(self.config, fail.name)
with tempfile.NamedTemporaryFile("wt") as fail:
for key, item in self.files.items():
print(item["filename"], item["label"], file=fail, sep="\t")
fail.flush()
with self.assertRaises(IndexError):
parse_list_file(self.config, fail.name)
with tempfile.NamedTemporaryFile("wt") as fail:
for key, item in self.files.items():
print(item["filename"], item["label"], "foo", file=fail, sep="\t")
fail.flush()
with self.assertRaises(ValueError):
parse_list_file(self.config, fail.name)
with tempfile.NamedTemporaryFile("wt") as fail:
for key, item in self.files.items():
# Double labels
print(item["filename"], self.files["pacbio"]["label"], item["stranded"], file=fail, sep="\t")
fail.flush()
with self.assertRaises(ValueError):
parse_list_file(self.config, fail.name)
with tempfile.NamedTemporaryFile("wt") as fail, tempfile.TemporaryDirectory() as tmp:
for key, item in self.files.items():
fname = os.path.join(tmp, os.path.basename(item["filename"]))
self.assertFalse(os.path.exists(fname))
print(fname, item["label"], item["stranded"], file=fail, sep="\t")
fail.flush()
with self.assertRaises(ValueError):
parse_list_file(self.config, fail.name)
with tempfile.NamedTemporaryFile("wt") as fail:
for key, item in self.files.items():
print(item["filename"], item["label"], item["stranded"], "wrong", file=fail, sep="\t")
fail.flush()
with self.assertRaises(ValueError) as exc:
parse_list_file(self.config, fail.name)
self.assertIsNotNone(re.search(r"Invalid score specified for", str(exc.exception)))