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))