def test_existing(self):
ds = SubreadSet(data.getSubreadSet(), skipMissing=True)
# check that we aren't adding any additional biosamples elements:
self.assertEqual(
Counter(
ds.metadata.tags)['BioSamples'],
1)
self.assertEqual(ds.metadata.bioSamples[0].name, 'consectetur purus')
self.assertEqual(
ds.metadata.bioSamples[0].DNABarcodes[0].name,
'F1--R1')
self.assertTrue(ds.metadata.collections[0].getV('children',
'Automation'))
self.assertTrue(ds.metadata.collections[0].automation)
ds.metadata.collections[
0].automation.automationParameters.addParameter('foo', 'bar')
self.assertEqual(
ds.metadata.collections[
0].automation.automationParameters['foo'].value,
'bar')
self.assertEqual(
ds.metadata.collections[
0].automation.automationParameters.parameterNames,
[None, 'foo'])
def test_existing(self):
ds = SubreadSet(data.getSubreadSet(), skipMissing=True)
# check that we aren't adding any additional biosamples elements:
self.assertEqual(
Counter(ds.metadata.collections[0].wellSample.tags)['BioSamples'],
1)
self.assertEqual(
ds.metadata.collections[0].wellSample.bioSamples[0].name,
'consectetur purus')
self.assertEqual(
ds.metadata.collections[0].wellSample.bioSamples[0].DNABarcodes[0].
name, 'F1--R1')
self.assertTrue(ds.metadata.collections[0].getV(
'children', 'Automation'))
self.assertTrue(ds.metadata.collections[0].automation)
ds.metadata.collections[
0].automation.automationParameters.addParameter('foo', 'bar')
self.assertEqual(
ds.metadata.collections[0].automation.automationParameters['foo'].
value, 'bar')
self.assertEqual(
ds.metadata.collections[0].automation.automationParameters.
parameterNames, [None, 'foo'])
def test_existing(self):
ds = SubreadSet(data.getSubreadSet(), skipMissing=True)
self.assertEqual(ds.metadata.bioSamples[0].name,
'consectetur purus')
self.assertTrue(ds.metadata.collections[0].getV('children',
'Automation'))
self.assertTrue(ds.metadata.collections[0].automation)
def test_build(self):
# Progs like pbalign provide a .bam file:
# e.g. d = DataSet("aligned.bam")
# Something like the test files we have:
inBam = data.getBam()
self.assertTrue(inBam.endswith('.bam'))
d = DataSet(inBam)
# A UniqueId is generated, despite being a BAM input
self.assertTrue(d.uuid != '')
dOldUuid = d.uuid
# They can write this BAM to an XML:
# e.g. d.write("alignmentset.xml")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outXml = os.path.join(outdir, 'tempfile.xml')
d.write(outXml)
# And then recover the same XML (or a different one):
# e.g. d = DataSet("alignmentset.xml")
d = DataSet(outXml)
# The UniqueId will be the same
self.assertTrue(d.uuid == dOldUuid)
# Inputs can be many and varied
ds1 = DataSet(data.getXml(11), data.getBam())
self.assertEquals(ds1.numExternalResources, 2)
ds1 = DataSet(data.getFofn())
self.assertEquals(ds1.numExternalResources, 2)
# New! Use the correct constructor:
self.assertEquals(type(SubreadSet(data.getSubreadSet())).__name__,
'SubreadSet')
# Even with untyped inputs
self.assertTrue(str(SubreadSet(data.getBam())).startswith(
'<SubreadSet'))
self.assertEquals(type(SubreadSet(data.getBam())).__name__,
'SubreadSet')
self.assertEquals(type(DataSet(data.getBam())).__name__,
'DataSet')
# You can also cast up and down, but casting between siblings
# is limited (abuse at your own risk)
self.assertEquals(
type(DataSet(data.getBam()).copy(asType='SubreadSet')).__name__,
'SubreadSet')
self.assertEquals(
type(SubreadSet(data.getBam()).copy(asType='DataSet')).__name__,
'DataSet')
# Add external Resources:
ds = DataSet()
ds.externalResources.addResources(["IdontExist.bam"])
self.assertTrue(
ds.externalResources[-1].resourceId == "IdontExist.bam")
# Add an index file
ds.externalResources[-1].addIndices(["IdontExist.bam.pbi"])
self.assertTrue(
ds.externalResources[-1].indices[0].resourceId ==
"IdontExist.bam.pbi")
def test_build(self):
# Progs like pbalign provide a .bam file:
# e.g. d = DataSet("aligned.bam")
# Something like the test files we have:
inBam = data.getBam()
self.assertTrue(inBam.endswith('.bam'))
d = DataSet(inBam)
# A UniqueId is generated, despite being a BAM input
self.assertTrue(d.uuid != '')
dOldUuid = d.uuid
# They can write this BAM to an XML:
# e.g. d.write("alignmentset.xml")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outXml = os.path.join(outdir, 'tempfile.xml')
d.write(outXml)
# And then recover the same XML (or a different one):
# e.g. d = DataSet("alignmentset.xml")
d = DataSet(outXml)
# The UniqueId will be the same
self.assertTrue(d.uuid == dOldUuid)
# Inputs can be many and varied
ds1 = DataSet(data.getXml(11), data.getBam())
self.assertEquals(ds1.numExternalResources, 2)
ds1 = DataSet(data.getFofn())
self.assertEquals(ds1.numExternalResources, 2)
# New! Use the correct constructor:
self.assertEquals(
type(SubreadSet(data.getSubreadSet())).__name__, 'SubreadSet')
# Even with untyped inputs
self.assertTrue(
str(SubreadSet(data.getBam())).startswith('<SubreadSet'))
self.assertEquals(
type(SubreadSet(data.getBam())).__name__, 'SubreadSet')
self.assertEquals(type(DataSet(data.getBam())).__name__, 'DataSet')
# You can also cast up and down, but casting between siblings
# is limited (abuse at your own risk)
self.assertEquals(
type(DataSet(data.getBam()).copy(asType='SubreadSet')).__name__,
'SubreadSet')
self.assertEquals(
type(SubreadSet(data.getBam()).copy(asType='DataSet')).__name__,
'DataSet')
# Add external Resources:
ds = DataSet()
ds.externalResources.addResources(["IdontExist.bam"])
self.assertTrue(
ds.externalResources[-1].resourceId == "IdontExist.bam")
# Add an index file
ds.externalResources[-1].addIndices(["IdontExist.bam.pbi"])
self.assertTrue(ds.externalResources[-1].indices[0].resourceId ==
"IdontExist.bam.pbi")
def test_subread_build(self):
ds1 = SubreadSet(data.getXml(no=5), skipMissing=True)
ds2 = SubreadSet(data.getXml(no=5), skipMissing=True)
assert type(ds1).__name__ == 'SubreadSet'
assert ds1._metadata.__class__.__name__ == 'SubreadSetMetadata'
assert type(ds1._metadata).__name__ == 'SubreadSetMetadata'
assert type(ds1.metadata).__name__ == 'SubreadSetMetadata'
assert len(ds1.metadata.collections) == 1
assert len(ds2.metadata.collections) == 1
ds3 = ds1 + ds2
assert len(ds3.metadata.collections) == 2
ds4 = SubreadSet(data.getSubreadSet(), skipMissing=True)
assert type(ds4).__name__ == 'SubreadSet'
assert type(ds4._metadata).__name__ == 'SubreadSetMetadata'
assert len(ds4.metadata.collections) == 1
def test_subread_build(self):
ds1 = SubreadSet(data.getXml(no=5), skipMissing=True)
ds2 = SubreadSet(data.getXml(no=5), skipMissing=True)
self.assertEquals(type(ds1).__name__, 'SubreadSet')
self.assertEquals(ds1._metadata.__class__.__name__,
'SubreadSetMetadata')
self.assertEquals(type(ds1._metadata).__name__, 'SubreadSetMetadata')
self.assertEquals(type(ds1.metadata).__name__, 'SubreadSetMetadata')
self.assertEquals(len(ds1.metadata.collections), 1)
self.assertEquals(len(ds2.metadata.collections), 1)
ds3 = ds1 + ds2
self.assertEquals(len(ds3.metadata.collections), 2)
ds4 = SubreadSet(data.getSubreadSet(), skipMissing=True)
self.assertEquals(type(ds4).__name__, 'SubreadSet')
self.assertEquals(type(ds4._metadata).__name__, 'SubreadSetMetadata')
self.assertEquals(len(ds4.metadata.collections), 1)
def test_existing(self):
ds = SubreadSet(data.getSubreadSet(), skipMissing=True)
# check that we aren't adding any additional biosamples elements:
assert Counter(ds.metadata.tags)['BioSamples'] == 1
assert ds.metadata.bioSamples[0].name == 'consectetur purus'
assert ds.metadata.bioSamples[0].DNABarcodes[0].name == 'F1--R1'
assert ds.metadata.collections[0].getV('children', 'Automation')
assert ds.metadata.collections[0].automation
ds.metadata.collections[
0].automation.automationParameters.addParameter('foo', 'bar')
assert ds.metadata.collections[0].automation.automationParameters[
'foo'].value == 'bar'
assert ds.metadata.collections[
0].automation.automationParameters.parameterNames == [None, 'foo']
def test_subread_build(self):
ds1 = SubreadSet(data.getXml(no=5), skipMissing=True)
ds2 = SubreadSet(data.getXml(no=5), skipMissing=True)
self.assertEquals(type(ds1).__name__, 'SubreadSet')
self.assertEquals(ds1._metadata.__class__.__name__,
'SubreadSetMetadata')
self.assertEquals(type(ds1._metadata).__name__, 'SubreadSetMetadata')
self.assertEquals(type(ds1.metadata).__name__, 'SubreadSetMetadata')
self.assertEquals(len(ds1.metadata.collections), 1)
self.assertEquals(len(ds2.metadata.collections), 1)
ds3 = ds1 + ds2
self.assertEquals(len(ds3.metadata.collections), 2)
ds4 = SubreadSet(data.getSubreadSet(), skipMissing=True)
self.assertEquals(type(ds4).__name__, 'SubreadSet')
self.assertEquals(type(ds4._metadata).__name__, 'SubreadSetMetadata')
self.assertEquals(len(ds4.metadata.collections), 1)
def test_existing(self):
ds = SubreadSet(data.getSubreadSet(), skipMissing=True)
self.assertEqual(ds.metadata.bioSamples[0].name,
'consectetur purus')
self.assertTrue(ds.metadata.collections[0].getV('children',
'Automation'))
self.assertTrue(ds.metadata.collections[0].automation)
ds.metadata.collections[
0].automation.automationParameters.addParameter('foo', 'bar')
self.assertEqual(
ds.metadata.collections[
0].automation.automationParameters['foo'].value,
'bar')
self.assertEqual(
ds.metadata.collections[
0].automation.automationParameters.parameterNames,
[None, 'foo'])
