def test_subreadset_consolidate(self): log.debug("Test through API") aln = SubreadSet(data.getXml(10), data.getXml(13)) self.assertEqual(len(aln.toExternalFiles()), 2) outdir = tempfile.mkdtemp(suffix="dataset-unittest") outfn = os.path.join(outdir, 'merged.bam') aln.consolidate(outfn) self.assertTrue(os.path.exists(outfn)) self.assertEqual(len(aln.toExternalFiles()), 1) nonCons = SubreadSet(data.getXml(10), data.getXml(13)) self.assertEqual(len(nonCons.toExternalFiles()), 2) for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))): self.assertEqual(read1, read2) self.assertEqual(len(aln), len(nonCons))
def test_subreadset_consolidate(self): log.debug("Test through API") aln = SubreadSet(data.getXml(9), data.getXml(12)) assert len(aln.toExternalFiles()) == 2 outdir = tempfile.mkdtemp(suffix="dataset-unittest") outfn = os.path.join(outdir, 'merged.bam') aln.consolidate(outfn) assert os.path.exists(outfn) assert len(aln.toExternalFiles()) == 1 # lets make sure we're not getting extra entries: assert len(aln.externalResources) == 1 assert len(aln.externalResources[0].indices) == 2 nonCons = SubreadSet(data.getXml(9), data.getXml(12)) assert len(nonCons.toExternalFiles()) == 2 for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))): assert read1 == read2 assert len(aln) == len(nonCons)