def test_toExternalFiles(self):
bogusDS = DataSet("bam1.bam", "bam2.bam", strict=False)
self.assertEqual(['bam1.bam', 'bam2.bam'],
bogusDS.externalResources.resourceIds)
self.assertEquals(DataSet("bam1.bam", "bam2.bam",
strict=False).toExternalFiles(),
['bam1.bam', 'bam2.bam'])
realDS = DataSet(data.getXml(8))
files = realDS.toExternalFiles()
self.assertEqual(len(files), 1)
self.assertTrue(os.path.exists(files[0]))
self.assertTrue(os.path.isabs(files[0]))
def test_toExternalFiles(self):
bogusDS = DataSet("bam1.bam", "bam2.bam", strict=False)
self.assertEqual(['bam1.bam', 'bam2.bam'],
bogusDS.externalResources.resourceIds)
self.assertEquals(
DataSet("bam1.bam", "bam2.bam", strict=False).toExternalFiles(),
['bam1.bam', 'bam2.bam'])
realDS = DataSet(data.getXml(8))
files = realDS.toExternalFiles()
self.assertEqual(len(files), 1)
self.assertTrue(os.path.exists(files[0]))
self.assertTrue(os.path.isabs(files[0]))
def test_referenceInfoTableMerging(self):
log.info("Testing refIds, etc. after merging")
ds = DataSet(data.getXml(17))
also_lambda = ds.toExternalFiles()[0]
aln = AlignmentSet(data.getBam(0), data.getBam(0), also_lambda)
readers = aln.resourceReaders()
ids = sorted([i for _, i in aln.refInfo('ID')])
self.assertEqual(range(len(ids)), ids)
accNames = aln.refNames
expNames = reduce(np.append,
[reader.referenceInfoTable['Name']
for reader in readers])
expNames = np.unique(expNames)
self.assertEqual(sorted(expNames), sorted(accNames))
accNames = aln.fullRefNames
expNames = reduce(np.append,
[reader.referenceInfoTable['FullName']
for reader in readers])
expNames = np.unique(expNames)
self.assertEqual(sorted(expNames), sorted(accNames))
def test_referenceInfoTableMerging(self):
log.info("Testing refIds, etc. after merging")
ds = DataSet(data.getXml(17))
also_lambda = ds.toExternalFiles()[0]
aln = AlignmentSet(data.getBam(0), data.getBam(0), also_lambda)
readers = aln.resourceReaders()
ids = sorted([i for _, i in aln.refInfo('ID')])
self.assertEqual(range(len(ids)), ids)
accNames = aln.refNames
expNames = reduce(
np.append,
[reader.referenceInfoTable['Name'] for reader in readers])
expNames = np.unique(expNames)
self.assertEqual(sorted(expNames), sorted(accNames))
accNames = aln.fullRefNames
expNames = reduce(
np.append,
[reader.referenceInfoTable['FullName'] for reader in readers])
expNames = np.unique(expNames)
self.assertEqual(sorted(expNames), sorted(accNames))