def test_loadMetadata(self):
aln = AlignmentSet(data.getXml(7))
assert not aln.metadata.collections
aln.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
assert aln.metadata.collections
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
assert not sset.metadata.collections
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
sset.write(fn)
validateFile(fn)
validateFile(sset_fn)
assert sset.metadata == orig_metadata
# load the wrong thing...
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
assert not sset.metadata.collections
with pytest.raises(InvalidDataSetIOError):
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.sts.xml')
def test_loadMetadata(self):
aln = AlignmentSet(data.getXml(no=8))
self.assertFalse(aln.metadata.collections)
aln.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
self.assertTrue(aln.metadata.collections)
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
self.assertFalse(sset.metadata.collections)
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
sset.write(fn)
validateFile(fn)
validateFile(sset_fn)
self.assertEqual(sset.metadata, orig_metadata)
# load the wrong thing...
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
self.assertFalse(sset.metadata.collections)
with self.assertRaises(InvalidDataSetIOError):
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.sts.xml')
def test_loadMetadata(self):
aln = AlignmentSet(data.getXml(no=8))
self.assertFalse(aln.metadata.collections)
aln.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
self.assertTrue(aln.metadata.collections)
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
self.assertFalse(sset.metadata.collections)
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.run.metadata.xml')
stack = zip(sset.metadata, orig_metadata)
fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
sset.write(fn)
validateFile(fn)
validateFile(sset_fn)
self.assertEqual(sset.metadata, orig_metadata)
# load the wrong thing...
sset_fn = ('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.subreadset.xml')
sset = SubreadSet(sset_fn)
orig_metadata = copy.deepcopy(sset.metadata)
sset.metadata.collections = None
self.assertFalse(sset.metadata.collections)
with self.assertRaises(InvalidDataSetIOError):
sset.loadMetadata('/pbi/dept/secondary/siv/testdata/'
'SA3-Sequel/lambda/roche_SAT/'
'm54013_151205_032353.sts.xml')
